Starting phenix.real_space_refine on Sat Jan 18 08:09:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rbq_19034/01_2025/8rbq_19034.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rbq_19034/01_2025/8rbq_19034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rbq_19034/01_2025/8rbq_19034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rbq_19034/01_2025/8rbq_19034.map" model { file = "/net/cci-nas-00/data/ceres_data/8rbq_19034/01_2025/8rbq_19034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rbq_19034/01_2025/8rbq_19034.cif" } resolution = 3.32 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= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 18 7.16 5 P 4 5.49 5 S 96 5.16 5 C 7820 2.51 5 N 2012 2.21 5 O 2190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 12140 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1394 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 179} Chain: "C" Number of atoms: 3523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3523 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 37, 'TRANS': 439} Chain: "E" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1601 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 203} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1478 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 187} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 548 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 4, 'TRANS': 66} Chain: "B" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 807 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain breaks: 2 Chain: "D" Number of atoms: 2320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2320 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 282} Chain breaks: 1 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FES': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 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 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 302 Unusual residues: {'LMT': 5, 'PTY': 2, 'RBF': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 184 SG CYS A 25 37.283 73.370 59.357 1.00 45.39 S ATOM 5726 SG CYS E 122 39.028 70.965 57.132 1.00 75.02 S ATOM 844 SG CYS A 113 41.347 74.017 54.715 1.00 51.48 S ATOM 5117 SG CYS E 39 40.026 77.348 56.316 1.00 71.75 S ATOM 4136 SG CYS C 376 42.148 90.594 96.617 1.00 33.81 S ATOM 4451 SG CYS C 419 37.986 92.158 96.996 1.00 10.84 S ATOM 4094 SG CYS C 370 38.758 90.272 90.582 1.00 10.19 S ATOM 4119 SG CYS C 373 41.448 95.623 93.319 1.00 21.56 S ATOM 4382 SG CYS C 409 44.294 81.309 102.702 1.00 8.31 S ATOM 4404 SG CYS C 412 45.896 86.890 105.913 1.00 13.57 S ATOM 4420 SG CYS C 415 43.140 87.210 100.674 1.00 27.24 S ATOM 4162 SG CYS C 380 48.681 86.177 100.503 1.00 26.58 S ATOM 8944 SG CYS B 119 30.378 43.473 108.328 1.00 82.60 S ATOM 9117 SG CYS B 145 24.857 44.427 108.411 1.00 80.07 S ATOM 9098 SG CYS B 142 28.973 45.573 103.259 1.00 66.64 S ATOM 9081 SG CYS B 139 27.627 49.973 107.492 1.00 27.27 S ATOM 8868 SG CYS B 109 22.343 40.394 118.183 1.00 84.64 S ATOM 8886 SG CYS B 112 22.377 35.360 113.998 1.00 89.96 S ATOM 8910 SG CYS B 115 26.384 40.027 113.855 1.00 72.60 S ATOM 9147 SG CYS B 149 19.627 39.516 112.504 1.00101.78 S Time building chain proxies: 7.56, per 1000 atoms: 0.62 Number of scatterers: 12140 At special positions: 0 Unit cell: (82.82, 143.5, 157.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 18 26.01 S 96 16.00 P 4 15.00 O 2190 8.00 N 2012 7.00 C 7820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.53 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 200 " pdb="FE1 FES A 200 " - pdb=" SG CYS A 25 " pdb="FE1 FES A 200 " - pdb=" SG CYS E 122 " pdb="FE2 FES A 200 " - pdb=" SG CYS E 39 " pdb="FE2 FES A 200 " - pdb=" SG CYS A 113 " pdb=" SF4 B 201 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 145 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 142 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 119 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 139 " pdb=" SF4 B 202 " pdb="FE3 SF4 B 202 " - pdb=" SG CYS B 115 " pdb="FE4 SF4 B 202 " - pdb=" SG CYS B 149 " pdb="FE2 SF4 B 202 " - pdb=" SG CYS B 112 " pdb="FE1 SF4 B 202 " - pdb=" SG CYS B 109 " pdb=" SF4 C 501 " pdb="FE2 SF4 C 501 " - pdb=" SG CYS C 419 " pdb="FE1 SF4 C 501 " - pdb=" SG CYS C 376 " pdb="FE3 SF4 C 501 " - pdb=" SG CYS C 370 " pdb="FE4 SF4 C 501 " - pdb=" SG CYS C 373 " pdb=" SF4 C 502 " pdb="FE3 SF4 C 502 " - pdb=" SG CYS C 415 " pdb="FE1 SF4 C 502 " - pdb=" SG CYS C 409 " pdb="FE2 SF4 C 502 " - pdb=" SG CYS C 412 " pdb="FE4 SF4 C 502 " - pdb=" SG CYS C 380 " Number of angles added : 54 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2826 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 9 sheets defined 54.1% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 removed outlier: 3.648A pdb=" N PHE A 6 " --> pdb=" O GLU A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 31 removed outlier: 4.012A pdb=" N SER A 31 " --> pdb=" O PHE A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 62 removed outlier: 3.695A pdb=" N SER A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 67 Processing helix chain 'A' and resid 71 through 94 removed outlier: 4.062A pdb=" N ALA A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE A 77 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU A 86 " --> pdb=" O GLY A 82 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS A 93 " --> pdb=" O MET A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 112 removed outlier: 4.080A pdb=" N ILE A 109 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR A 111 " --> pdb=" O PRO A 107 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 105 through 112' Processing helix chain 'A' and resid 113 through 125 Proline residue: A 119 - end of helix removed outlier: 3.527A pdb=" N GLU A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 159 removed outlier: 4.045A pdb=" N LEU A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'C' and resid 124 through 134 removed outlier: 3.609A pdb=" N LEU C 128 " --> pdb=" O ASP C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 157 removed outlier: 3.615A pdb=" N ARG C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS C 157 " --> pdb=" O GLN C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 183 removed outlier: 3.508A pdb=" N ARG C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 198 Processing helix chain 'C' and resid 211 through 222 Processing helix chain 'C' and resid 236 through 240 removed outlier: 3.623A pdb=" N MET C 239 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY C 240 " --> pdb=" O TYR C 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 236 through 240' Processing helix chain 'C' and resid 241 through 250 removed outlier: 3.576A pdb=" N GLN C 247 " --> pdb=" O LYS C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 removed outlier: 3.500A pdb=" N ASP C 262 " --> pdb=" O ARG C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 282 Processing helix chain 'C' and resid 311 through 319 removed outlier: 3.509A pdb=" N LEU C 315 " --> pdb=" O PRO C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 395 Processing helix chain 'C' and resid 397 through 404 removed outlier: 3.699A pdb=" N GLU C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.563A pdb=" N TYR C 417 " --> pdb=" O GLY C 413 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C 418 " --> pdb=" O CYS C 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 413 through 418' Processing helix chain 'C' and resid 424 through 478 Processing helix chain 'E' and resid 17 through 26 removed outlier: 4.147A pdb=" N PHE E 21 " --> pdb=" O PRO E 17 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU E 25 " --> pdb=" O PHE E 21 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TRP E 26 " --> pdb=" O THR E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 44 removed outlier: 3.542A pdb=" N THR E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 72 Processing helix chain 'E' and resid 73 through 76 removed outlier: 3.877A pdb=" N ILE E 76 " --> pdb=" O ARG E 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 73 through 76' Processing helix chain 'E' and resid 80 through 101 removed outlier: 3.778A pdb=" N VAL E 84 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET E 85 " --> pdb=" O ARG E 81 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL E 92 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 removed outlier: 3.642A pdb=" N VAL E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 117 removed outlier: 4.404A pdb=" N ALA E 116 " --> pdb=" O GLY E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'E' and resid 136 through 168 Processing helix chain 'E' and resid 173 through 179 Processing helix chain 'E' and resid 180 through 186 removed outlier: 4.442A pdb=" N TRP E 184 " --> pdb=" O HIS E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 228 removed outlier: 4.038A pdb=" N PHE E 206 " --> pdb=" O PRO E 202 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE E 207 " --> pdb=" O PRO E 203 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL E 208 " --> pdb=" O GLY E 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 81 removed outlier: 3.886A pdb=" N LEU G 43 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU G 55 " --> pdb=" O ALA G 51 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY G 57 " --> pdb=" O LEU G 53 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASN G 58 " --> pdb=" O LEU G 54 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLY G 63 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR G 64 " --> pdb=" O MET G 60 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN G 68 " --> pdb=" O THR G 64 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL G 80 " --> pdb=" O THR G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 93 removed outlier: 3.582A pdb=" N ALA G 92 " --> pdb=" O ASN G 89 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP G 93 " --> pdb=" O PRO G 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 89 through 93' Processing helix chain 'G' and resid 159 through 163 removed outlier: 4.232A pdb=" N ILE G 162 " --> pdb=" O ALA G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 173 removed outlier: 4.001A pdb=" N PHE G 173 " --> pdb=" O ILE G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 222 Processing helix chain 'H' and resid 25 through 34 Processing helix chain 'H' and resid 34 through 39 removed outlier: 3.772A pdb=" N CYS H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 23 removed outlier: 3.688A pdb=" N ALA B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 removed outlier: 3.510A pdb=" N LYS B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 Processing helix chain 'D' and resid 17 through 41 Proline residue: D 31 - end of helix removed outlier: 3.513A pdb=" N PHE D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 67 Processing helix chain 'D' and resid 69 through 75 removed outlier: 4.065A pdb=" N ASP D 75 " --> pdb=" O ARG D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.530A pdb=" N THR D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 106 removed outlier: 3.815A pdb=" N GLY D 98 " --> pdb=" O PRO D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 135 Processing helix chain 'D' and resid 156 through 164 Processing helix chain 'D' and resid 215 through 232 removed outlier: 3.558A pdb=" N GLU D 219 " --> pdb=" O GLY D 215 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 258 Processing helix chain 'D' and resid 262 through 266 removed outlier: 3.672A pdb=" N GLY D 265 " --> pdb=" O TYR D 262 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU D 266 " --> pdb=" O ALA D 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 262 through 266' Processing helix chain 'D' and resid 273 through 280 Processing helix chain 'D' and resid 292 through 312 Processing helix chain 'D' and resid 317 through 337 removed outlier: 4.626A pdb=" N PHE D 321 " --> pdb=" O GLU D 317 " (cutoff:3.500A) Proline residue: D 331 - end of helix Processing sheet with id=AA1, first strand: chain 'C' and resid 34 through 38 removed outlier: 6.526A pdb=" N VAL C 102 " --> pdb=" O VAL C 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 38 Processing sheet with id=AA3, first strand: chain 'C' and resid 48 through 49 Processing sheet with id=AA4, first strand: chain 'C' and resid 228 through 233 removed outlier: 4.536A pdb=" N VAL C 164 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 288 through 293 Processing sheet with id=AA6, first strand: chain 'C' and resid 328 through 329 Processing sheet with id=AA7, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.489A pdb=" N GLU G 133 " --> pdb=" O LEU G 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 14 through 18 Processing sheet with id=AA9, first strand: chain 'B' and resid 100 through 101 612 hydrogen bonds defined for protein. 1773 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.31 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 4859 1.42 - 1.64: 7372 1.64 - 1.86: 120 1.86 - 2.07: 0 2.07 - 2.29: 52 Bond restraints: 12403 Sorted by residual: bond pdb=" O5' FMN C 500 " pdb=" P FMN C 500 " ideal model delta sigma weight residual 1.610 1.823 -0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C8 PTY D 403 " pdb=" O7 PTY D 403 " ideal model delta sigma weight residual 1.331 1.451 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" C30 PTY D 403 " pdb=" O4 PTY D 403 " ideal model delta sigma weight residual 1.331 1.446 -0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" N CYS E 39 " pdb=" CA CYS E 39 " ideal model delta sigma weight residual 1.463 1.424 0.039 6.90e-03 2.10e+04 3.17e+01 bond pdb=" C CYS A 113 " pdb=" N ALA A 114 " ideal model delta sigma weight residual 1.333 1.263 0.069 1.38e-02 5.25e+03 2.52e+01 ... (remaining 12398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.59: 16445 3.59 - 7.17: 348 7.17 - 10.76: 71 10.76 - 14.35: 14 14.35 - 17.93: 3 Bond angle restraints: 16881 Sorted by residual: angle pdb=" N CYS A 25 " pdb=" CA CYS A 25 " pdb=" CB CYS A 25 " ideal model delta sigma weight residual 110.39 122.79 -12.40 9.50e-01 1.11e+00 1.71e+02 angle pdb=" CA PRO B 158 " pdb=" N PRO B 158 " pdb=" CD PRO B 158 " ideal model delta sigma weight residual 112.00 96.10 15.90 1.40e+00 5.10e-01 1.29e+02 angle pdb=" C CYS A 25 " pdb=" N PRO A 26 " pdb=" CA PRO A 26 " ideal model delta sigma weight residual 119.28 107.39 11.89 1.10e+00 8.26e-01 1.17e+02 angle pdb=" CA PRO H 61 " pdb=" N PRO H 61 " pdb=" CD PRO H 61 " ideal model delta sigma weight residual 112.00 98.55 13.45 1.40e+00 5.10e-01 9.23e+01 angle pdb=" N CYS B 149 " pdb=" CA CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sigma weight residual 110.32 96.92 13.40 1.48e+00 4.57e-01 8.20e+01 ... (remaining 16876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.95: 6960 24.95 - 49.90: 565 49.90 - 74.85: 89 74.85 - 99.79: 32 99.79 - 124.74: 18 Dihedral angle restraints: 7664 sinusoidal: 3253 harmonic: 4411 Sorted by residual: dihedral pdb=" CA PHE C 3 " pdb=" C PHE C 3 " pdb=" N ASN C 4 " pdb=" CA ASN C 4 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ILE E 89 " pdb=" C ILE E 89 " pdb=" N ALA E 90 " pdb=" CA ALA E 90 " ideal model delta harmonic sigma weight residual -180.00 -152.41 -27.59 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" N CYS B 149 " pdb=" C CYS B 149 " pdb=" CA CYS B 149 " pdb=" CB CYS B 149 " ideal model delta harmonic sigma weight residual 122.80 109.20 13.60 0 2.50e+00 1.60e-01 2.96e+01 ... (remaining 7661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.008: 2020 1.008 - 2.016: 0 2.016 - 3.024: 0 3.024 - 4.032: 0 4.032 - 5.040: 3 Chirality restraints: 2023 Sorted by residual: chirality pdb=" C2' FMN G 301 " pdb=" C1' FMN G 301 " pdb=" C3' FMN G 301 " pdb=" O2' FMN G 301 " both_signs ideal model delta sigma weight residual False -2.47 2.57 -5.04 2.00e-01 2.50e+01 6.35e+02 chirality pdb=" CB THR G 202 " pdb=" CA THR G 202 " pdb=" OG1 THR G 202 " pdb=" CG2 THR G 202 " both_signs ideal model delta sigma weight residual False 2.55 -2.47 5.02 2.00e-01 2.50e+01 6.30e+02 chirality pdb=" C4' FMN G 301 " pdb=" C3' FMN G 301 " pdb=" C5' FMN G 301 " pdb=" O4' FMN G 301 " both_signs ideal model delta sigma weight residual False -2.47 2.45 -4.92 2.00e-01 2.50e+01 6.05e+02 ... (remaining 2020 not shown) Planarity restraints: 2066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN G 301 " 0.148 2.00e-02 2.50e+03 4.11e-02 8.03e+01 pdb=" C10 FMN G 301 " -0.016 2.00e-02 2.50e+03 pdb=" C2 FMN G 301 " -0.022 2.00e-02 2.50e+03 pdb=" C4 FMN G 301 " 0.014 2.00e-02 2.50e+03 pdb=" C4A FMN G 301 " 0.000 2.00e-02 2.50e+03 pdb=" C5A FMN G 301 " 0.004 2.00e-02 2.50e+03 pdb=" C6 FMN G 301 " 0.008 2.00e-02 2.50e+03 pdb=" C7 FMN G 301 " -0.004 2.00e-02 2.50e+03 pdb=" C7M FMN G 301 " 0.005 2.00e-02 2.50e+03 pdb=" C8 FMN G 301 " -0.020 2.00e-02 2.50e+03 pdb=" C8M FMN G 301 " -0.038 2.00e-02 2.50e+03 pdb=" C9 FMN G 301 " -0.023 2.00e-02 2.50e+03 pdb=" C9A FMN G 301 " -0.010 2.00e-02 2.50e+03 pdb=" N1 FMN G 301 " -0.027 2.00e-02 2.50e+03 pdb=" N10 FMN G 301 " -0.005 2.00e-02 2.50e+03 pdb=" N3 FMN G 301 " -0.001 2.00e-02 2.50e+03 pdb=" N5 FMN G 301 " 0.004 2.00e-02 2.50e+03 pdb=" O2 FMN G 301 " -0.062 2.00e-02 2.50e+03 pdb=" O4 FMN G 301 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER H 60 " 0.117 5.00e-02 4.00e+02 1.65e-01 4.37e+01 pdb=" N PRO H 61 " -0.285 5.00e-02 4.00e+02 pdb=" CA PRO H 61 " 0.087 5.00e-02 4.00e+02 pdb=" CD PRO H 61 " 0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 86 " 0.100 5.00e-02 4.00e+02 1.50e-01 3.62e+01 pdb=" N PRO C 87 " -0.260 5.00e-02 4.00e+02 pdb=" CA PRO C 87 " 0.083 5.00e-02 4.00e+02 pdb=" CD PRO C 87 " 0.077 5.00e-02 4.00e+02 ... (remaining 2063 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2147 2.77 - 3.31: 10984 3.31 - 3.84: 19985 3.84 - 4.37: 22185 4.37 - 4.90: 39444 Nonbonded interactions: 94745 Sorted by model distance: nonbonded pdb=" OD1 ASP D 284 " pdb=" O2' RBF D 404 " model vdw 2.242 3.040 nonbonded pdb=" O THR E 41 " pdb=" OG1 THR E 45 " model vdw 2.258 3.040 nonbonded pdb=" O ILE G 203 " pdb=" N ARG G 206 " model vdw 2.285 3.120 nonbonded pdb=" OG SER C 21 " pdb=" OG1 THR C 174 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR C 237 " pdb=" O CYS C 412 " model vdw 2.300 3.040 ... (remaining 94740 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: 2.610 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: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.190 Process input model: 32.620 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 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 : 0.008 0.213 12403 Z= 0.540 Angle : 1.298 17.933 16881 Z= 0.669 Chirality : 0.203 5.040 2023 Planarity : 0.011 0.165 2066 Dihedral : 19.502 124.742 4838 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.39 % Favored : 94.09 % Rotamer: Outliers : 0.65 % Allowed : 24.55 % Favored : 74.80 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.20), residues: 1541 helix: -0.57 (0.17), residues: 775 sheet: -0.82 (0.55), residues: 105 loop : -1.47 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 96 HIS 0.007 0.001 HIS E 105 PHE 0.035 0.002 PHE A 70 TYR 0.044 0.002 TYR H 7 ARG 0.019 0.001 ARG D 347 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 193 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 81 ARG cc_start: 0.8485 (ptt-90) cc_final: 0.8202 (ptt90) REVERT: E 110 VAL cc_start: 0.9025 (t) cc_final: 0.8754 (p) REVERT: G 88 ASN cc_start: 0.4531 (p0) cc_final: 0.4247 (p0) outliers start: 8 outliers final: 3 residues processed: 200 average time/residue: 0.2943 time to fit residues: 80.4355 Evaluate side-chains 144 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 141 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain G residue 39 GLN Chi-restraints excluded: chain G residue 202 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.9990 chunk 115 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 0.1980 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN G 39 GLN G 125 ASN G 152 HIS G 217 GLN H 31 GLN D 327 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.097066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.064247 restraints weight = 33414.447| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.04 r_work: 0.2967 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12403 Z= 0.243 Angle : 0.703 10.199 16881 Z= 0.334 Chirality : 0.046 0.349 2023 Planarity : 0.006 0.087 2066 Dihedral : 12.935 103.259 2217 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.52 % Favored : 94.22 % Rotamer: Outliers : 3.43 % Allowed : 22.19 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.22), residues: 1541 helix: 1.03 (0.19), residues: 780 sheet: -0.98 (0.55), residues: 104 loop : -1.29 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 96 HIS 0.006 0.001 HIS C 224 PHE 0.010 0.001 PHE A 70 TYR 0.015 0.001 TYR C 237 ARG 0.008 0.001 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8925 (mp) REVERT: E 121 ASN cc_start: 0.8508 (t0) cc_final: 0.8265 (t0) REVERT: E 147 MET cc_start: 0.7697 (mtp) cc_final: 0.7464 (mtm) REVERT: G 62 HIS cc_start: 0.8928 (p-80) cc_final: 0.8613 (p90) REVERT: G 111 ARG cc_start: 0.8206 (mmm-85) cc_final: 0.7817 (mmm-85) REVERT: G 188 VAL cc_start: 0.8300 (m) cc_final: 0.7887 (p) REVERT: H 63 LYS cc_start: 0.7965 (pptt) cc_final: 0.7560 (pptt) REVERT: B 26 PHE cc_start: 0.8731 (t80) cc_final: 0.8482 (m-80) REVERT: D 219 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8033 (mp0) REVERT: D 317 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7638 (tm-30) outliers start: 42 outliers final: 14 residues processed: 187 average time/residue: 0.2397 time to fit residues: 64.4543 Evaluate side-chains 148 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain G residue 125 ASN Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 79 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 151 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 422 HIS G 88 ASN ** G 125 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 = 0.3698 r_free = 0.3698 target = 0.095978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.063476 restraints weight = 33780.161| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.03 r_work: 0.2946 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12403 Z= 0.233 Angle : 0.644 8.922 16881 Z= 0.310 Chirality : 0.045 0.362 2023 Planarity : 0.005 0.067 2066 Dihedral : 10.304 88.008 2210 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.52 % Favored : 94.22 % Rotamer: Outliers : 2.37 % Allowed : 24.23 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.22), residues: 1541 helix: 1.49 (0.19), residues: 778 sheet: -0.86 (0.56), residues: 102 loop : -1.12 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 96 HIS 0.004 0.001 HIS C 224 PHE 0.027 0.001 PHE G 121 TYR 0.014 0.001 TYR C 237 ARG 0.005 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8844 (mmmt) cc_final: 0.8544 (mmtm) REVERT: A 73 ILE cc_start: 0.9159 (pt) cc_final: 0.8776 (tp) REVERT: A 89 MET cc_start: 0.6518 (tmm) cc_final: 0.6260 (tmm) REVERT: A 145 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8919 (mp) REVERT: E 121 ASN cc_start: 0.8497 (t0) cc_final: 0.8213 (t0) REVERT: G 62 HIS cc_start: 0.8905 (p-80) cc_final: 0.8572 (p-80) REVERT: G 136 MET cc_start: 0.6722 (pmm) cc_final: 0.6474 (pmm) REVERT: G 188 VAL cc_start: 0.8322 (m) cc_final: 0.7901 (p) REVERT: B 26 PHE cc_start: 0.8784 (t80) cc_final: 0.8538 (m-80) REVERT: B 117 ARG cc_start: 0.9225 (mtt180) cc_final: 0.8982 (tpp80) outliers start: 29 outliers final: 18 residues processed: 167 average time/residue: 0.2798 time to fit residues: 65.6425 Evaluate side-chains 155 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 41 optimal weight: 0.0870 chunk 74 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 130 optimal weight: 0.9980 chunk 137 optimal weight: 20.0000 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 105 HIS E 181 HIS G 125 ASN D 327 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.096252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.064234 restraints weight = 33432.165| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.99 r_work: 0.2965 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12403 Z= 0.185 Angle : 0.607 7.434 16881 Z= 0.293 Chirality : 0.043 0.343 2023 Planarity : 0.005 0.055 2066 Dihedral : 9.471 79.830 2210 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.52 % Favored : 94.29 % Rotamer: Outliers : 2.37 % Allowed : 24.23 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.22), residues: 1541 helix: 1.68 (0.19), residues: 783 sheet: -0.89 (0.56), residues: 102 loop : -1.06 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 96 HIS 0.003 0.001 HIS C 224 PHE 0.012 0.001 PHE A 143 TYR 0.015 0.001 TYR C 237 ARG 0.006 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8823 (mmmt) cc_final: 0.8523 (mmtm) REVERT: A 89 MET cc_start: 0.6533 (tmm) cc_final: 0.6231 (tmm) REVERT: A 145 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8917 (mp) REVERT: E 109 LYS cc_start: 0.8853 (mtmt) cc_final: 0.8553 (mtmm) REVERT: G 62 HIS cc_start: 0.8862 (p-80) cc_final: 0.8476 (p-80) REVERT: G 166 ARG cc_start: 0.9341 (mtp85) cc_final: 0.9054 (mtp85) REVERT: G 183 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8464 (pp) REVERT: G 188 VAL cc_start: 0.8690 (m) cc_final: 0.8388 (p) REVERT: B 26 PHE cc_start: 0.8802 (t80) cc_final: 0.8568 (m-80) REVERT: B 105 GLU cc_start: 0.8740 (mp0) cc_final: 0.8521 (mp0) REVERT: B 117 ARG cc_start: 0.9204 (mtt180) cc_final: 0.8976 (tpp80) REVERT: B 144 LYS cc_start: 0.8754 (mmtm) cc_final: 0.8429 (mmtm) outliers start: 29 outliers final: 15 residues processed: 165 average time/residue: 0.2536 time to fit residues: 59.5224 Evaluate side-chains 151 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 291 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 139 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 88 ASN G 125 ASN G 225 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.096330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.063951 restraints weight = 33667.948| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.03 r_work: 0.2962 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12403 Z= 0.180 Angle : 0.600 8.048 16881 Z= 0.290 Chirality : 0.043 0.288 2023 Planarity : 0.005 0.055 2066 Dihedral : 8.909 68.677 2210 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.65 % Favored : 94.16 % Rotamer: Outliers : 3.34 % Allowed : 23.65 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.23), residues: 1541 helix: 1.82 (0.19), residues: 785 sheet: -0.87 (0.55), residues: 104 loop : -0.95 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP D 96 HIS 0.007 0.001 HIS E 105 PHE 0.012 0.001 PHE A 143 TYR 0.015 0.001 TYR C 237 ARG 0.009 0.000 ARG B 146 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 148 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8810 (mmmt) cc_final: 0.8518 (mmtm) REVERT: A 89 MET cc_start: 0.6591 (tmm) cc_final: 0.6276 (tmm) REVERT: A 145 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8925 (mp) REVERT: C 110 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8535 (ttp80) REVERT: G 62 HIS cc_start: 0.8868 (p-80) cc_final: 0.8605 (p-80) REVERT: G 166 ARG cc_start: 0.9354 (mtp85) cc_final: 0.9055 (mtp85) REVERT: G 183 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8525 (pp) REVERT: G 225 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8158 (tm-30) REVERT: B 26 PHE cc_start: 0.8787 (t80) cc_final: 0.8555 (m-80) REVERT: B 117 ARG cc_start: 0.9235 (mtt180) cc_final: 0.8994 (tpp80) REVERT: B 144 LYS cc_start: 0.8779 (mmtm) cc_final: 0.8455 (mmtp) REVERT: B 159 GLN cc_start: 0.8745 (tp-100) cc_final: 0.8503 (tp-100) outliers start: 41 outliers final: 22 residues processed: 177 average time/residue: 0.2611 time to fit residues: 65.5627 Evaluate side-chains 161 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain E residue 132 CYS Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain G residue 125 ASN Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 225 GLN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 214 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 140 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 59 optimal weight: 0.4980 chunk 101 optimal weight: 0.2980 chunk 13 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 105 HIS G 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.096375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.064170 restraints weight = 33909.010| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.03 r_work: 0.2969 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12403 Z= 0.175 Angle : 0.602 8.852 16881 Z= 0.293 Chirality : 0.042 0.239 2023 Planarity : 0.005 0.054 2066 Dihedral : 8.512 66.888 2210 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.97 % Favored : 93.84 % Rotamer: Outliers : 2.85 % Allowed : 24.88 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.23), residues: 1541 helix: 1.89 (0.19), residues: 785 sheet: -0.89 (0.56), residues: 104 loop : -0.89 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP D 96 HIS 0.006 0.001 HIS E 105 PHE 0.013 0.001 PHE A 143 TYR 0.014 0.001 TYR C 237 ARG 0.006 0.000 ARG B 146 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8507 (mmtm) REVERT: A 89 MET cc_start: 0.6579 (tmm) cc_final: 0.6273 (tmm) REVERT: A 145 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8939 (mp) REVERT: G 62 HIS cc_start: 0.8879 (p-80) cc_final: 0.8490 (p-80) REVERT: G 166 ARG cc_start: 0.9353 (mtp85) cc_final: 0.9058 (mtp85) REVERT: G 183 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8366 (tt) REVERT: B 26 PHE cc_start: 0.8784 (t80) cc_final: 0.8555 (m-80) REVERT: B 105 GLU cc_start: 0.8934 (mp0) cc_final: 0.8662 (mp0) REVERT: B 117 ARG cc_start: 0.9233 (mtt180) cc_final: 0.8976 (tpp80) REVERT: B 144 LYS cc_start: 0.8814 (mmtm) cc_final: 0.8544 (mmtm) REVERT: B 159 GLN cc_start: 0.8779 (tp-100) cc_final: 0.8555 (tp-100) outliers start: 35 outliers final: 23 residues processed: 165 average time/residue: 0.2591 time to fit residues: 60.6612 Evaluate side-chains 158 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 79 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 129 optimal weight: 0.0060 chunk 5 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 125 ASN ** G 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.096594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.064448 restraints weight = 33654.820| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.01 r_work: 0.2974 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12403 Z= 0.171 Angle : 0.596 9.286 16881 Z= 0.288 Chirality : 0.042 0.189 2023 Planarity : 0.004 0.053 2066 Dihedral : 8.082 64.208 2210 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.84 % Favored : 93.96 % Rotamer: Outliers : 3.02 % Allowed : 24.47 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.23), residues: 1541 helix: 1.97 (0.19), residues: 785 sheet: -0.99 (0.55), residues: 104 loop : -0.81 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP D 96 HIS 0.003 0.000 HIS E 105 PHE 0.017 0.001 PHE G 95 TYR 0.016 0.001 TYR B 116 ARG 0.008 0.000 ARG B 146 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8797 (mmmt) cc_final: 0.8503 (mmtm) REVERT: A 89 MET cc_start: 0.6559 (tmm) cc_final: 0.6277 (tmm) REVERT: A 145 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8953 (mp) REVERT: G 62 HIS cc_start: 0.8875 (p-80) cc_final: 0.8609 (p-80) REVERT: G 65 ILE cc_start: 0.9481 (mt) cc_final: 0.9258 (mm) REVERT: G 166 ARG cc_start: 0.9369 (mtp85) cc_final: 0.9076 (mtp85) REVERT: G 183 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8436 (tt) REVERT: B 105 GLU cc_start: 0.8903 (mp0) cc_final: 0.8661 (mp0) REVERT: B 117 ARG cc_start: 0.9208 (mtt180) cc_final: 0.8953 (tpp80) REVERT: B 144 LYS cc_start: 0.8822 (mmtm) cc_final: 0.8480 (mmtp) REVERT: B 159 GLN cc_start: 0.8820 (tp-100) cc_final: 0.8601 (tp-100) REVERT: D 327 ASN cc_start: 0.9075 (m110) cc_final: 0.8854 (m110) outliers start: 37 outliers final: 25 residues processed: 172 average time/residue: 0.2588 time to fit residues: 63.1844 Evaluate side-chains 167 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain E residue 132 CYS Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 125 ASN Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 31 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 chunk 120 optimal weight: 4.9990 chunk 105 optimal weight: 20.0000 chunk 119 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 148 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN ** G 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.094301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.061891 restraints weight = 34195.797| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.99 r_work: 0.2848 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12403 Z= 0.304 Angle : 0.664 11.120 16881 Z= 0.322 Chirality : 0.044 0.201 2023 Planarity : 0.005 0.056 2066 Dihedral : 8.115 59.926 2210 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.36 % Favored : 93.45 % Rotamer: Outliers : 3.43 % Allowed : 24.63 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.23), residues: 1541 helix: 1.89 (0.19), residues: 791 sheet: -0.97 (0.56), residues: 100 loop : -0.80 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 237 HIS 0.003 0.001 HIS C 196 PHE 0.011 0.001 PHE E 206 TYR 0.016 0.001 TYR C 237 ARG 0.004 0.000 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 142 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8857 (mmmt) cc_final: 0.8534 (mmtm) REVERT: A 89 MET cc_start: 0.6464 (tmm) cc_final: 0.6200 (tmm) REVERT: A 145 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8869 (mp) REVERT: E 106 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8301 (pm20) REVERT: G 62 HIS cc_start: 0.8928 (p-80) cc_final: 0.8537 (p90) REVERT: G 65 ILE cc_start: 0.9502 (mt) cc_final: 0.9254 (mm) REVERT: G 111 ARG cc_start: 0.8358 (mpp80) cc_final: 0.8150 (mpp80) REVERT: G 166 ARG cc_start: 0.9438 (mtp85) cc_final: 0.9154 (mtp85) REVERT: G 183 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8475 (tt) REVERT: G 206 ARG cc_start: 0.8522 (mmm-85) cc_final: 0.8048 (mmm160) REVERT: H 9 ASP cc_start: 0.9133 (t70) cc_final: 0.8403 (t0) REVERT: H 31 GLN cc_start: 0.9270 (mm110) cc_final: 0.8968 (mm-40) REVERT: B 105 GLU cc_start: 0.8889 (mp0) cc_final: 0.8629 (mp0) REVERT: B 117 ARG cc_start: 0.9304 (mtt180) cc_final: 0.9035 (tpp80) REVERT: B 144 LYS cc_start: 0.8966 (mmtm) cc_final: 0.8593 (mmtp) REVERT: B 159 GLN cc_start: 0.8892 (tp-100) cc_final: 0.8667 (tp-100) REVERT: D 317 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8153 (tm-30) REVERT: D 327 ASN cc_start: 0.9090 (m110) cc_final: 0.8860 (m110) outliers start: 42 outliers final: 27 residues processed: 169 average time/residue: 0.2632 time to fit residues: 62.6852 Evaluate side-chains 163 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 132 CYS Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 71 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 0.0980 chunk 83 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 125 ASN ** G 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.095257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.063335 restraints weight = 33867.561| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.99 r_work: 0.2943 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12403 Z= 0.197 Angle : 0.634 10.036 16881 Z= 0.307 Chirality : 0.042 0.193 2023 Planarity : 0.004 0.054 2066 Dihedral : 7.886 59.494 2210 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.78 % Favored : 94.03 % Rotamer: Outliers : 2.45 % Allowed : 25.37 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.23), residues: 1541 helix: 1.97 (0.19), residues: 785 sheet: -0.93 (0.55), residues: 102 loop : -0.77 (0.26), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 96 HIS 0.002 0.000 HIS C 224 PHE 0.013 0.001 PHE A 143 TYR 0.015 0.001 TYR C 237 ARG 0.006 0.000 ARG B 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8869 (mmmt) cc_final: 0.8568 (mmtm) REVERT: A 89 MET cc_start: 0.6544 (tmm) cc_final: 0.6290 (tmm) REVERT: A 145 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8916 (mp) REVERT: E 106 GLU cc_start: 0.8518 (mp0) cc_final: 0.8156 (pm20) REVERT: G 62 HIS cc_start: 0.8889 (p-80) cc_final: 0.8617 (p-80) REVERT: G 65 ILE cc_start: 0.9485 (mt) cc_final: 0.9263 (mm) REVERT: G 111 ARG cc_start: 0.8328 (mpp80) cc_final: 0.8095 (mpp80) REVERT: G 166 ARG cc_start: 0.9400 (mtp85) cc_final: 0.9128 (mtp85) REVERT: G 183 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8495 (tt) REVERT: H 9 ASP cc_start: 0.9185 (t70) cc_final: 0.8487 (t0) REVERT: H 31 GLN cc_start: 0.9255 (mm110) cc_final: 0.8964 (mm-40) REVERT: B 105 GLU cc_start: 0.8898 (mp0) cc_final: 0.8675 (mp0) REVERT: B 117 ARG cc_start: 0.9236 (mtt180) cc_final: 0.8984 (tpp80) REVERT: B 144 LYS cc_start: 0.8953 (mmtm) cc_final: 0.8582 (mmtp) REVERT: D 317 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8149 (tm-30) REVERT: D 327 ASN cc_start: 0.9057 (m110) cc_final: 0.8825 (m110) outliers start: 30 outliers final: 25 residues processed: 167 average time/residue: 0.2756 time to fit residues: 64.8304 Evaluate side-chains 166 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain E residue 132 CYS Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 125 ASN Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 84 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 132 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 chunk 82 optimal weight: 0.0670 chunk 72 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 overall best weight: 1.5324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 125 ASN ** G 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.095315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.063213 restraints weight = 33856.747| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.00 r_work: 0.2882 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12403 Z= 0.221 Angle : 0.645 10.448 16881 Z= 0.314 Chirality : 0.043 0.199 2023 Planarity : 0.004 0.054 2066 Dihedral : 7.809 59.874 2210 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.10 % Favored : 93.71 % Rotamer: Outliers : 2.61 % Allowed : 25.29 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.23), residues: 1541 helix: 1.97 (0.19), residues: 785 sheet: -0.92 (0.55), residues: 102 loop : -0.79 (0.26), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 96 HIS 0.002 0.000 HIS C 224 PHE 0.012 0.001 PHE A 143 TYR 0.015 0.001 TYR C 237 ARG 0.007 0.000 ARG B 146 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8815 (mmmt) cc_final: 0.8514 (mmtm) REVERT: A 89 MET cc_start: 0.6502 (tmm) cc_final: 0.6247 (tmm) REVERT: A 145 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8879 (mp) REVERT: E 106 GLU cc_start: 0.8501 (mp0) cc_final: 0.8104 (pm20) REVERT: G 62 HIS cc_start: 0.8917 (p-80) cc_final: 0.8635 (p-80) REVERT: G 65 ILE cc_start: 0.9496 (mt) cc_final: 0.9288 (mm) REVERT: G 111 ARG cc_start: 0.8384 (mpp80) cc_final: 0.8159 (mpp80) REVERT: G 166 ARG cc_start: 0.9433 (mtp85) cc_final: 0.9154 (mtp85) REVERT: G 183 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8463 (tt) REVERT: H 9 ASP cc_start: 0.9197 (t70) cc_final: 0.8516 (t0) REVERT: H 31 GLN cc_start: 0.9270 (mm110) cc_final: 0.8978 (mm-40) REVERT: H 71 TYR cc_start: 0.6642 (OUTLIER) cc_final: 0.5080 (p90) REVERT: B 105 GLU cc_start: 0.8874 (mp0) cc_final: 0.8618 (mp0) REVERT: B 117 ARG cc_start: 0.9284 (mtt180) cc_final: 0.9009 (tpp80) REVERT: D 327 ASN cc_start: 0.9072 (m110) cc_final: 0.8849 (m110) outliers start: 32 outliers final: 25 residues processed: 163 average time/residue: 0.2484 time to fit residues: 57.7361 Evaluate side-chains 166 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain E residue 132 CYS Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 71 TYR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 152 optimal weight: 0.3980 chunk 23 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.095503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.063479 restraints weight = 33820.096| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.99 r_work: 0.2889 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12403 Z= 0.213 Angle : 0.643 10.948 16881 Z= 0.314 Chirality : 0.043 0.191 2023 Planarity : 0.004 0.054 2066 Dihedral : 7.648 59.475 2210 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.91 % Favored : 93.90 % Rotamer: Outliers : 2.37 % Allowed : 25.86 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.23), residues: 1541 helix: 1.98 (0.19), residues: 792 sheet: -0.87 (0.55), residues: 102 loop : -0.78 (0.26), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 96 HIS 0.002 0.000 HIS C 224 PHE 0.012 0.001 PHE A 143 TYR 0.015 0.001 TYR C 237 ARG 0.006 0.000 ARG B 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5733.08 seconds wall clock time: 102 minutes 25.12 seconds (6145.12 seconds total)