Starting phenix.real_space_refine on Wed Jul 30 16:01:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rb9_19029/07_2025/8rb9_19029.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rb9_19029/07_2025/8rb9_19029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rb9_19029/07_2025/8rb9_19029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rb9_19029/07_2025/8rb9_19029.map" model { file = "/net/cci-nas-00/data/ceres_data/8rb9_19029/07_2025/8rb9_19029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rb9_19029/07_2025/8rb9_19029.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 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 97 5.16 5 C 8203 2.51 5 N 2067 2.21 5 O 2354 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12743 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: 3511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3511 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 37, 'TRANS': 438} Chain: "D" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2629 Classifications: {'peptide': 349} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 325} 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: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1489 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} 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: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 124 Unusual residues: {'FES': 1, 'LMT': 2, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'FMN': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 442 Unusual residues: {'FMN': 1, 'LMT': 11, 'RBF': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'LMT': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 184 SG CYS A 25 37.800 81.555 53.659 1.00 55.48 S ATOM 8343 SG CYS E 122 39.152 78.652 51.663 1.00 81.30 S ATOM 844 SG CYS A 113 41.722 82.081 48.664 1.00 63.79 S ATOM 7734 SG CYS E 39 40.476 84.999 51.135 1.00 69.20 S ATOM 4124 SG CYS C 376 42.296 92.711 92.548 1.00 44.59 S ATOM 4439 SG CYS C 419 37.916 94.279 93.154 1.00 26.17 S ATOM 4082 SG CYS C 370 39.028 93.363 86.489 1.00 27.74 S ATOM 4107 SG CYS C 373 41.835 98.038 90.225 1.00 31.60 S ATOM 4370 SG CYS C 409 43.613 82.286 97.462 1.00 36.12 S ATOM 4392 SG CYS C 412 45.419 87.269 101.448 1.00 30.47 S ATOM 4408 SG CYS C 415 43.048 88.555 96.202 1.00 36.09 S ATOM 4150 SG CYS C 380 48.328 87.195 96.044 1.00 37.59 S ATOM 11572 SG CYS B 119 27.592 44.867 96.228 1.00 71.98 S ATOM 11745 SG CYS B 145 22.006 46.170 96.213 1.00 82.52 S ATOM 11726 SG CYS B 142 26.078 48.099 91.350 1.00 74.81 S ATOM 11709 SG CYS B 139 25.334 51.568 96.502 1.00 42.56 S ATOM 11496 SG CYS B 109 19.456 40.963 105.636 1.00 91.32 S ATOM 11514 SG CYS B 112 18.525 36.556 100.470 1.00 87.95 S ATOM 11538 SG CYS B 115 22.899 41.220 100.778 1.00 80.72 S ATOM 11775 SG CYS B 149 16.079 41.125 99.925 1.00 99.88 S Time building chain proxies: 8.23, per 1000 atoms: 0.65 Number of scatterers: 12743 At special positions: 0 Unit cell: (82.82, 150.06, 150.06, 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 97 16.00 P 4 15.00 O 2354 8.00 N 2067 7.00 C 8203 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.94 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 201 " pdb="FE1 FES A 201 " - pdb=" SG CYS A 25 " pdb="FE1 FES A 201 " - pdb=" SG CYS E 122 " pdb="FE2 FES A 201 " - pdb=" SG CYS A 113 " pdb="FE2 FES A 201 " - pdb=" SG CYS E 39 " pdb=" SF4 B 201 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 142 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 145 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 139 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 119 " pdb=" SF4 B 202 " pdb="FE2 SF4 B 202 " - pdb=" SG CYS B 112 " pdb="FE3 SF4 B 202 " - pdb=" SG CYS B 115 " pdb="FE1 SF4 B 202 " - pdb=" SG CYS B 109 " pdb="FE4 SF4 B 202 " - pdb=" SG CYS B 149 " pdb=" SF4 C 501 " pdb="FE1 SF4 C 501 " - pdb=" SG CYS C 376 " pdb="FE2 SF4 C 501 " - pdb=" SG CYS C 419 " 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="FE2 SF4 C 502 " - pdb=" SG CYS C 412 " pdb="FE1 SF4 C 502 " - pdb=" SG CYS C 409 " pdb="FE4 SF4 C 502 " - pdb=" SG CYS C 380 " Number of angles added : 54 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2900 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 11 sheets defined 54.3% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 removed outlier: 3.681A pdb=" N PHE A 6 " --> pdb=" O GLU A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 31 removed outlier: 3.700A pdb=" N PHE A 27 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 31 " --> pdb=" O PHE A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 62 removed outlier: 3.665A 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 90 Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.540A pdb=" N THR A 110 " --> pdb=" O PRO A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 Proline residue: A 119 - end of helix removed outlier: 3.510A pdb=" N ARG A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 158 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: 3.557A pdb=" N LEU C 128 " --> pdb=" O ASP C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 157 removed outlier: 3.543A pdb=" N LYS C 150 " --> pdb=" O PRO C 146 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS C 157 " --> pdb=" O GLN C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 183 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: 4.036A pdb=" N GLY C 240 " --> pdb=" O TYR C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 250 removed outlier: 3.610A pdb=" N GLN C 247 " --> pdb=" O LYS C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 270 through 283 removed outlier: 3.796A pdb=" N TYR C 274 " --> pdb=" O ALA C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 319 removed outlier: 3.720A 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: 3.649A pdb=" N TYR C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 removed outlier: 3.891A pdb=" N CYS C 419 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 478 Processing helix chain 'D' and resid 17 through 41 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 41 through 67 removed outlier: 3.570A pdb=" N ILE D 45 " --> pdb=" O GLY D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 75 removed outlier: 3.758A pdb=" N ASP D 75 " --> pdb=" O ARG D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.608A pdb=" N THR D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 106 removed outlier: 3.752A pdb=" N GLY D 98 " --> pdb=" O PRO D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 114 removed outlier: 3.627A pdb=" N GLY D 114 " --> pdb=" O GLN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 135 Processing helix chain 'D' and resid 155 through 164 Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 191 through 198 removed outlier: 3.613A pdb=" N ILE D 195 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY D 198 " --> pdb=" O GLU D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 208 Processing helix chain 'D' and resid 220 through 232 Processing helix chain 'D' and resid 237 through 258 Processing helix chain 'D' and resid 265 through 270 Processing helix chain 'D' and resid 273 through 281 Processing helix chain 'D' and resid 292 through 312 Processing helix chain 'D' and resid 318 through 337 Proline residue: D 331 - end of helix Processing helix chain 'E' and resid 17 through 27 removed outlier: 4.338A pdb=" N PHE E 21 " --> pdb=" O PRO E 17 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU E 25 " --> pdb=" O PHE E 21 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TRP E 26 " --> pdb=" O THR E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 44 removed outlier: 3.528A 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: 3.728A 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 104 removed outlier: 3.920A pdb=" N VAL E 92 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA E 102 " --> pdb=" O MET E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 removed outlier: 3.650A pdb=" N VAL E 110 " --> pdb=" O GLU E 106 " (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 removed outlier: 3.667A pdb=" N LEU E 177 " --> pdb=" O GLN E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 186 removed outlier: 4.481A pdb=" N TRP E 184 " --> pdb=" O HIS E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 228 removed outlier: 3.866A pdb=" N PHE E 206 " --> pdb=" O PRO E 202 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE E 207 " --> pdb=" O PRO E 203 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL E 208 " --> pdb=" O GLY E 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 79 removed outlier: 3.542A pdb=" N GLY G 40 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS G 47 " --> pdb=" O LEU G 43 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLY G 63 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N THR G 64 " --> pdb=" O MET G 60 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 86 Processing helix chain 'G' and resid 89 through 93 removed outlier: 3.826A pdb=" N ASP G 93 " --> pdb=" O PRO G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 172 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: 3.689A pdb=" N CYS H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.613A pdb=" N MET B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY B 12 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 19 " --> pdb=" O LEU B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 removed outlier: 3.549A pdb=" N LYS B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 Processing helix chain 'B' and resid 162 through 166 Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 28 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 38 removed outlier: 3.652A pdb=" N ALA C 84 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLU C 104 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ILE C 82 " --> pdb=" O GLU C 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 34 through 38 Processing sheet with id=AA4, first strand: chain 'C' and resid 48 through 49 Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 165 Processing sheet with id=AA6, first strand: chain 'C' and resid 206 through 208 Processing sheet with id=AA7, first strand: chain 'C' and resid 328 through 330 Processing sheet with id=AA8, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AA9, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.627A pdb=" N ALA G 118 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLU G 133 " --> pdb=" O LEU G 150 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY G 146 " --> pdb=" O SER G 137 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASP G 139 " --> pdb=" O ILE G 144 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE G 144 " --> pdb=" O ASP G 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 14 through 18 removed outlier: 6.214A pdb=" N SER H 4 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE H 70 " --> pdb=" O SER H 4 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL H 6 " --> pdb=" O ILE H 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 100 through 101 641 hydrogen bonds defined for protein. 1821 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: 3.41 Time building geometry restraints manager: 4.20 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: 5097 1.42 - 1.63: 7750 1.63 - 1.85: 123 1.85 - 2.07: 0 2.07 - 2.28: 52 Bond restraints: 13022 Sorted by residual: bond pdb=" O5' FMN C 500 " pdb=" P FMN C 500 " ideal model delta sigma weight residual 1.676 1.817 -0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" C1' FMN C 500 " pdb=" N10 FMN C 500 " ideal model delta sigma weight residual 1.473 1.566 -0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" O5' FMN D 413 " pdb=" P FMN D 413 " ideal model delta sigma weight residual 1.676 1.591 0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" O5' FMN G 301 " pdb=" P FMN G 301 " ideal model delta sigma weight residual 1.676 1.596 0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C5' FMN C 500 " pdb=" O5' FMN C 500 " ideal model delta sigma weight residual 1.418 1.339 0.079 2.00e-02 2.50e+03 1.57e+01 ... (remaining 13017 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 17189 2.32 - 4.64: 380 4.64 - 6.96: 92 6.96 - 9.28: 46 9.28 - 11.60: 14 Bond angle restraints: 17721 Sorted by residual: angle pdb=" C ASN A 112 " pdb=" N CYS A 113 " pdb=" CA CYS A 113 " ideal model delta sigma weight residual 121.54 129.22 -7.68 1.91e+00 2.74e-01 1.62e+01 angle pdb=" N THR G 202 " pdb=" CA THR G 202 " pdb=" C THR G 202 " ideal model delta sigma weight residual 114.04 109.15 4.89 1.24e+00 6.50e-01 1.55e+01 angle pdb=" C ALA D 170 " pdb=" CA ALA D 170 " pdb=" CB ALA D 170 " ideal model delta sigma weight residual 115.89 110.74 5.15 1.32e+00 5.74e-01 1.52e+01 angle pdb=" C2' FMN C 500 " pdb=" C1' FMN C 500 " pdb=" N10 FMN C 500 " ideal model delta sigma weight residual 112.28 123.88 -11.60 3.00e+00 1.11e-01 1.50e+01 angle pdb=" C1' FMN C 500 " pdb=" N10 FMN C 500 " pdb=" C10 FMN C 500 " ideal model delta sigma weight residual 117.86 128.02 -10.16 3.00e+00 1.11e-01 1.15e+01 ... (remaining 17716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.90: 7734 23.90 - 47.79: 411 47.79 - 71.68: 115 71.68 - 95.58: 48 95.58 - 119.47: 61 Dihedral angle restraints: 8369 sinusoidal: 3840 harmonic: 4529 Sorted by residual: dihedral pdb=" CA ILE D 106 " pdb=" C ILE D 106 " pdb=" N GLY D 107 " pdb=" CA GLY D 107 " ideal model delta harmonic sigma weight residual -180.00 -157.28 -22.72 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ALA G 223 " pdb=" C ALA G 223 " pdb=" N GLU G 224 " pdb=" CA GLU G 224 " ideal model delta harmonic sigma weight residual 180.00 159.91 20.09 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" C3 PTY A 204 " pdb=" O11 PTY A 204 " pdb=" P1 PTY A 204 " pdb=" O12 PTY A 204 " ideal model delta sinusoidal sigma weight residual -59.77 -179.24 119.47 1 3.00e+01 1.11e-03 1.59e+01 ... (remaining 8366 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.015: 2164 1.015 - 2.029: 0 2.029 - 3.044: 0 3.044 - 4.059: 0 4.059 - 5.074: 4 Chirality restraints: 2168 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 -2.52 2.55 -5.07 2.00e-01 2.50e+01 6.44e+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 -2.45 5.00 2.00e-01 2.50e+01 6.26e+02 chirality pdb=" C4' FMN D 413 " pdb=" C3' FMN D 413 " pdb=" C5' FMN D 413 " pdb=" O4' FMN D 413 " both_signs ideal model delta sigma weight residual False -2.50 2.42 -4.92 2.00e-01 2.50e+01 6.06e+02 ... (remaining 2165 not shown) Planarity restraints: 2124 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN G 301 " 0.090 2.00e-02 2.50e+03 2.63e-02 3.11e+01 pdb=" C10 FMN G 301 " -0.018 2.00e-02 2.50e+03 pdb=" C2 FMN G 301 " -0.006 2.00e-02 2.50e+03 pdb=" C4 FMN G 301 " 0.019 2.00e-02 2.50e+03 pdb=" C4A FMN G 301 " -0.003 2.00e-02 2.50e+03 pdb=" C5A FMN G 301 " -0.008 2.00e-02 2.50e+03 pdb=" C6 FMN G 301 " 0.007 2.00e-02 2.50e+03 pdb=" C7 FMN G 301 " 0.007 2.00e-02 2.50e+03 pdb=" C7M FMN G 301 " 0.029 2.00e-02 2.50e+03 pdb=" C8 FMN G 301 " -0.009 2.00e-02 2.50e+03 pdb=" C8M FMN G 301 " -0.023 2.00e-02 2.50e+03 pdb=" C9 FMN G 301 " -0.023 2.00e-02 2.50e+03 pdb=" C9A FMN G 301 " -0.022 2.00e-02 2.50e+03 pdb=" N1 FMN G 301 " -0.022 2.00e-02 2.50e+03 pdb=" N10 FMN G 301 " -0.016 2.00e-02 2.50e+03 pdb=" N3 FMN G 301 " 0.013 2.00e-02 2.50e+03 pdb=" N5 FMN G 301 " -0.002 2.00e-02 2.50e+03 pdb=" O2 FMN G 301 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 223 " -0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C ALA G 223 " 0.061 2.00e-02 2.50e+03 pdb=" O ALA G 223 " -0.023 2.00e-02 2.50e+03 pdb=" N GLU G 224 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN D 413 " 0.029 2.00e-02 2.50e+03 1.18e-02 6.25e+00 pdb=" C10 FMN D 413 " 0.004 2.00e-02 2.50e+03 pdb=" C2 FMN D 413 " -0.000 2.00e-02 2.50e+03 pdb=" C4 FMN D 413 " -0.000 2.00e-02 2.50e+03 pdb=" C4A FMN D 413 " 0.003 2.00e-02 2.50e+03 pdb=" C5A FMN D 413 " -0.007 2.00e-02 2.50e+03 pdb=" C6 FMN D 413 " -0.004 2.00e-02 2.50e+03 pdb=" C7 FMN D 413 " -0.004 2.00e-02 2.50e+03 pdb=" C7M FMN D 413 " 0.031 2.00e-02 2.50e+03 pdb=" C8 FMN D 413 " -0.010 2.00e-02 2.50e+03 pdb=" C8M FMN D 413 " -0.012 2.00e-02 2.50e+03 pdb=" C9 FMN D 413 " -0.012 2.00e-02 2.50e+03 pdb=" C9A FMN D 413 " -0.010 2.00e-02 2.50e+03 pdb=" N1 FMN D 413 " 0.003 2.00e-02 2.50e+03 pdb=" N10 FMN D 413 " 0.001 2.00e-02 2.50e+03 pdb=" N3 FMN D 413 " -0.000 2.00e-02 2.50e+03 pdb=" N5 FMN D 413 " -0.002 2.00e-02 2.50e+03 pdb=" O2 FMN D 413 " -0.007 2.00e-02 2.50e+03 ... (remaining 2121 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 294 2.70 - 3.25: 12457 3.25 - 3.80: 19683 3.80 - 4.35: 25092 4.35 - 4.90: 43295 Nonbonded interactions: 100821 Sorted by model distance: nonbonded pdb=" OD1 ASN D 119 " pdb=" O5' RBF D 403 " model vdw 2.148 3.040 nonbonded pdb=" O LYS C 243 " pdb=" OH TYR D 342 " model vdw 2.221 3.040 nonbonded pdb=" OE2 GLU E 79 " pdb=" NE2 GLN G 39 " model vdw 2.227 3.120 nonbonded pdb=" O LEU C 140 " pdb=" ND2 ASN C 269 " model vdw 2.250 3.120 nonbonded pdb=" OG1 THR D 191 " pdb=" OE1 GLU D 194 " model vdw 2.251 3.040 ... (remaining 100816 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 33.930 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 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 : 0.007 0.141 13044 Z= 0.348 Angle : 1.159 39.574 17775 Z= 0.390 Chirality : 0.220 5.074 2168 Planarity : 0.004 0.040 2124 Dihedral : 20.165 119.475 5469 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.98 % Favored : 94.90 % Rotamer: Outliers : 1.99 % Allowed : 5.80 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 0.54 (0.22), residues: 1587 helix: 1.46 (0.19), residues: 821 sheet: -0.59 (0.56), residues: 109 loop : -0.87 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 83 HIS 0.002 0.001 HIS C 268 PHE 0.012 0.001 PHE D 298 TYR 0.009 0.001 TYR C 428 ARG 0.002 0.000 ARG E 227 Details of bonding type rmsd hydrogen bonds : bond 0.14986 ( 637) hydrogen bonds : angle 6.15500 ( 1821) metal coordination : bond 0.00989 ( 20) metal coordination : angle 12.90994 ( 54) covalent geometry : bond 0.00675 (13022) covalent geometry : angle 0.91606 (17721) Misc. bond : bond 0.06948 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7994 (mp0) REVERT: C 449 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8877 (tt) REVERT: E 19 GLN cc_start: 0.8429 (tm-30) cc_final: 0.8051 (tm-30) outliers start: 25 outliers final: 9 residues processed: 225 average time/residue: 0.3079 time to fit residues: 95.3780 Evaluate side-chains 149 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain G residue 202 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 142 optimal weight: 20.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 111 GLN E 34 GLN E 194 GLN E 228 GLN ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.091078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.062619 restraints weight = 31055.308| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.60 r_work: 0.2871 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13044 Z= 0.128 Angle : 0.980 39.360 17775 Z= 0.310 Chirality : 0.045 0.329 2168 Planarity : 0.004 0.038 2124 Dihedral : 18.314 118.158 2790 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.17 % Favored : 94.77 % Rotamer: Outliers : 2.78 % Allowed : 10.64 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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 (0.22), residues: 1587 helix: 1.63 (0.19), residues: 843 sheet: -0.37 (0.57), residues: 107 loop : -0.92 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 96 HIS 0.002 0.000 HIS A 60 PHE 0.019 0.001 PHE A 143 TYR 0.016 0.001 TYR H 7 ARG 0.006 0.000 ARG C 451 Details of bonding type rmsd hydrogen bonds : bond 0.04172 ( 637) hydrogen bonds : angle 4.54170 ( 1821) metal coordination : bond 0.01126 ( 20) metal coordination : angle 12.73044 ( 54) covalent geometry : bond 0.00280 (13022) covalent geometry : angle 0.68502 (17721) Misc. bond : bond 0.00219 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 1.479 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8193 (tm-30) REVERT: A 92 ARG cc_start: 0.8495 (ttp-110) cc_final: 0.8259 (ttp-110) REVERT: A 124 ARG cc_start: 0.9033 (mtp180) cc_final: 0.8721 (ttm170) REVERT: A 125 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: D 75 ASP cc_start: 0.8703 (p0) cc_final: 0.8432 (p0) REVERT: D 173 MET cc_start: 0.8452 (mtt) cc_final: 0.8249 (mtm) REVERT: E 19 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8141 (tm-30) REVERT: E 106 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8961 (mm-30) REVERT: G 67 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7652 (tm-30) outliers start: 35 outliers final: 20 residues processed: 188 average time/residue: 0.3231 time to fit residues: 84.8770 Evaluate side-chains 161 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain B residue 162 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 147 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 154 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 GLN ** E 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 ASN E 194 GLN ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.090212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.061443 restraints weight = 31762.359| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.63 r_work: 0.2844 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13044 Z= 0.149 Angle : 1.036 40.852 17775 Z= 0.309 Chirality : 0.045 0.387 2168 Planarity : 0.004 0.042 2124 Dihedral : 13.571 110.513 2788 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.85 % Favored : 95.09 % Rotamer: Outliers : 2.70 % Allowed : 11.28 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 0.90 (0.22), residues: 1587 helix: 1.85 (0.19), residues: 831 sheet: -0.36 (0.57), residues: 108 loop : -0.90 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 166 HIS 0.002 0.001 HIS A 60 PHE 0.014 0.001 PHE A 143 TYR 0.017 0.001 TYR H 7 ARG 0.007 0.000 ARG C 451 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 637) hydrogen bonds : angle 4.31304 ( 1821) metal coordination : bond 0.01354 ( 20) metal coordination : angle 14.26317 ( 54) covalent geometry : bond 0.00339 (13022) covalent geometry : angle 0.67529 (17721) Misc. bond : bond 0.00045 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9091 (tm-30) cc_final: 0.8876 (tm-30) REVERT: A 92 ARG cc_start: 0.8652 (ttp-110) cc_final: 0.8343 (ttp-110) REVERT: A 100 ARG cc_start: 0.8573 (tpp80) cc_final: 0.8277 (tpp80) REVERT: A 125 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8207 (mp0) REVERT: C 297 CYS cc_start: 0.8978 (m) cc_final: 0.8283 (t) REVERT: C 344 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8413 (pm20) REVERT: D 75 ASP cc_start: 0.8671 (p0) cc_final: 0.8443 (p0) REVERT: D 194 GLU cc_start: 0.8619 (mp0) cc_final: 0.8285 (pm20) REVERT: D 260 GLU cc_start: 0.9281 (mt-10) cc_final: 0.8960 (mm-30) REVERT: E 19 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8077 (tm-30) REVERT: E 106 GLU cc_start: 0.9216 (mm-30) cc_final: 0.9001 (mm-30) REVERT: G 67 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7526 (tm-30) REVERT: H 9 ASP cc_start: 0.7699 (t0) cc_final: 0.7407 (t0) outliers start: 34 outliers final: 22 residues processed: 181 average time/residue: 0.3215 time to fit residues: 83.4525 Evaluate side-chains 163 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain C residue 4 ASN Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain B residue 83 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 138 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 HIS ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.087474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.058894 restraints weight = 31736.174| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.58 r_work: 0.2791 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 13044 Z= 0.239 Angle : 1.087 45.250 17775 Z= 0.333 Chirality : 0.047 0.383 2168 Planarity : 0.005 0.051 2124 Dihedral : 11.721 105.066 2788 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.67 % Favored : 94.27 % Rotamer: Outliers : 3.34 % Allowed : 11.83 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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 (0.22), residues: 1587 helix: 1.86 (0.19), residues: 833 sheet: -0.49 (0.56), residues: 108 loop : -0.94 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 96 HIS 0.003 0.001 HIS A 14 PHE 0.014 0.001 PHE E 193 TYR 0.027 0.001 TYR H 7 ARG 0.004 0.000 ARG C 459 Details of bonding type rmsd hydrogen bonds : bond 0.04467 ( 637) hydrogen bonds : angle 4.31158 ( 1821) metal coordination : bond 0.02340 ( 20) metal coordination : angle 14.79609 ( 54) covalent geometry : bond 0.00567 (13022) covalent geometry : angle 0.71929 (17721) Misc. bond : bond 0.00118 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 1.539 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8861 (tm-30) REVERT: A 92 ARG cc_start: 0.8598 (ttp-110) cc_final: 0.8333 (ttp-110) REVERT: A 100 ARG cc_start: 0.8639 (tpp80) cc_final: 0.8354 (tpp80) REVERT: A 125 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8213 (mp0) REVERT: A 161 ASN cc_start: 0.9124 (t0) cc_final: 0.8749 (t0) REVERT: C 3 PHE cc_start: 0.7474 (OUTLIER) cc_final: 0.5880 (m-10) REVERT: C 140 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9039 (mt) REVERT: C 344 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8414 (pm20) REVERT: D 75 ASP cc_start: 0.8745 (p0) cc_final: 0.8517 (p0) REVERT: D 260 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8997 (mm-30) REVERT: D 326 MET cc_start: 0.9275 (mmt) cc_final: 0.8799 (mmt) REVERT: E 19 GLN cc_start: 0.8590 (tm-30) cc_final: 0.8083 (tm-30) REVERT: G 59 ILE cc_start: 0.9541 (tp) cc_final: 0.9307 (tp) REVERT: G 133 GLU cc_start: 0.9245 (OUTLIER) cc_final: 0.8995 (tp30) REVERT: H 9 ASP cc_start: 0.8224 (t0) cc_final: 0.7926 (t0) REVERT: H 12 LYS cc_start: 0.8450 (mmmt) cc_final: 0.8067 (mtpp) REVERT: B 100 MET cc_start: 0.8881 (mmp) cc_final: 0.8397 (tpp) REVERT: B 159 GLN cc_start: 0.8117 (tp-100) cc_final: 0.7916 (tp-100) REVERT: B 169 ASP cc_start: 0.8964 (p0) cc_final: 0.8644 (p0) outliers start: 42 outliers final: 25 residues processed: 184 average time/residue: 0.2869 time to fit residues: 76.0270 Evaluate side-chains 171 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 1.407 ------------------------------------------------------------------------------- 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 125 GLU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 4 ASN Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 162 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 28 optimal weight: 8.9990 chunk 135 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 ASN ** E 29 ASN ** 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 = 0.3401 r_free = 0.3401 target = 0.084107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.056934 restraints weight = 29866.042| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.80 r_work: 0.2661 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13044 Z= 0.119 Angle : 0.996 43.119 17775 Z= 0.287 Chirality : 0.042 0.305 2168 Planarity : 0.004 0.047 2124 Dihedral : 10.599 89.413 2787 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.47 % Favored : 95.46 % Rotamer: Outliers : 2.46 % Allowed : 13.19 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 1.07 (0.22), residues: 1587 helix: 2.03 (0.19), residues: 832 sheet: -0.28 (0.58), residues: 106 loop : -0.88 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 96 HIS 0.002 0.000 HIS C 17 PHE 0.015 0.001 PHE A 143 TYR 0.016 0.001 TYR C 237 ARG 0.005 0.000 ARG B 167 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 637) hydrogen bonds : angle 4.13930 ( 1821) metal coordination : bond 0.00998 ( 20) metal coordination : angle 14.35283 ( 54) covalent geometry : bond 0.00269 (13022) covalent geometry : angle 0.60573 (17721) Misc. bond : bond 0.00020 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8582 (tm-30) REVERT: A 92 ARG cc_start: 0.8785 (ttp-110) cc_final: 0.8402 (ttp-110) REVERT: A 100 ARG cc_start: 0.8698 (tpp80) cc_final: 0.8407 (tpp80) REVERT: A 125 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: A 161 ASN cc_start: 0.9013 (t0) cc_final: 0.8700 (t0) REVERT: C 3 PHE cc_start: 0.7592 (OUTLIER) cc_final: 0.5972 (m-10) REVERT: C 297 CYS cc_start: 0.9090 (m) cc_final: 0.8264 (t) REVERT: C 344 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8529 (pm20) REVERT: D 75 ASP cc_start: 0.8508 (p0) cc_final: 0.8259 (p0) REVERT: D 194 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8254 (pm20) REVERT: D 260 GLU cc_start: 0.9320 (mt-10) cc_final: 0.8927 (mm-30) REVERT: D 326 MET cc_start: 0.9085 (mmt) cc_final: 0.8808 (mmt) REVERT: E 19 GLN cc_start: 0.8525 (tm-30) cc_final: 0.7975 (tm-30) REVERT: E 106 GLU cc_start: 0.9261 (mm-30) cc_final: 0.8978 (mm-30) REVERT: G 59 ILE cc_start: 0.9443 (tp) cc_final: 0.9216 (tp) REVERT: G 67 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7669 (tm-30) REVERT: G 133 GLU cc_start: 0.9253 (OUTLIER) cc_final: 0.8843 (tp30) REVERT: G 179 GLU cc_start: 0.9122 (pt0) cc_final: 0.8709 (pm20) REVERT: H 9 ASP cc_start: 0.7963 (t0) cc_final: 0.7521 (t0) REVERT: H 12 LYS cc_start: 0.8465 (mmmt) cc_final: 0.8106 (mtpt) REVERT: B 105 GLU cc_start: 0.7856 (mp0) cc_final: 0.7065 (mp0) REVERT: B 155 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8973 (mp) REVERT: B 169 ASP cc_start: 0.9012 (p0) cc_final: 0.8695 (p0) outliers start: 31 outliers final: 18 residues processed: 176 average time/residue: 0.3097 time to fit residues: 79.2796 Evaluate side-chains 167 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 1.339 ------------------------------------------------------------------------------- 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 125 GLU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 155 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 137 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 29 optimal weight: 0.0030 chunk 53 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 228 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.084598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.058060 restraints weight = 30093.482| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.78 r_work: 0.2682 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13044 Z= 0.109 Angle : 0.958 41.002 17775 Z= 0.277 Chirality : 0.041 0.207 2168 Planarity : 0.004 0.053 2124 Dihedral : 9.765 75.415 2787 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.60 % Favored : 95.34 % Rotamer: Outliers : 2.38 % Allowed : 13.58 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 1.30 (0.22), residues: 1587 helix: 2.23 (0.19), residues: 825 sheet: -0.17 (0.59), residues: 106 loop : -0.76 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 166 HIS 0.002 0.000 HIS C 17 PHE 0.017 0.001 PHE A 143 TYR 0.016 0.001 TYR C 237 ARG 0.003 0.000 ARG B 167 Details of bonding type rmsd hydrogen bonds : bond 0.03387 ( 637) hydrogen bonds : angle 4.05290 ( 1821) metal coordination : bond 0.00895 ( 20) metal coordination : angle 13.92849 ( 54) covalent geometry : bond 0.00241 (13022) covalent geometry : angle 0.57378 (17721) Misc. bond : bond 0.00022 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9106 (tm-30) cc_final: 0.8540 (tm-30) REVERT: A 92 ARG cc_start: 0.8796 (ttp-110) cc_final: 0.8422 (ttp-110) REVERT: A 100 ARG cc_start: 0.8716 (tpp80) cc_final: 0.8468 (tpp80) REVERT: A 125 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8061 (mp0) REVERT: A 161 ASN cc_start: 0.9030 (t0) cc_final: 0.8638 (t0) REVERT: C 3 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.6029 (m-10) REVERT: C 297 CYS cc_start: 0.9061 (m) cc_final: 0.8204 (t) REVERT: C 344 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8553 (pm20) REVERT: D 75 ASP cc_start: 0.8393 (p0) cc_final: 0.8159 (p0) REVERT: D 194 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8257 (pm20) REVERT: D 260 GLU cc_start: 0.9327 (mt-10) cc_final: 0.8934 (mm-30) REVERT: D 326 MET cc_start: 0.9052 (mmt) cc_final: 0.8850 (mmt) REVERT: E 19 GLN cc_start: 0.8506 (tm-30) cc_final: 0.7930 (tm-30) REVERT: E 106 GLU cc_start: 0.9278 (mm-30) cc_final: 0.9018 (mm-30) REVERT: E 173 GLN cc_start: 0.8695 (pm20) cc_final: 0.8404 (pm20) REVERT: G 59 ILE cc_start: 0.9437 (tp) cc_final: 0.9207 (tp) REVERT: G 67 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7588 (tm-30) REVERT: G 133 GLU cc_start: 0.9231 (OUTLIER) cc_final: 0.8821 (tp30) REVERT: G 179 GLU cc_start: 0.9142 (pt0) cc_final: 0.8757 (pm20) REVERT: H 9 ASP cc_start: 0.7898 (t0) cc_final: 0.7397 (t0) REVERT: H 12 LYS cc_start: 0.8515 (mmmt) cc_final: 0.8066 (mtpp) REVERT: B 169 ASP cc_start: 0.8953 (p0) cc_final: 0.8646 (p0) outliers start: 30 outliers final: 18 residues processed: 175 average time/residue: 0.2829 time to fit residues: 71.2340 Evaluate side-chains 164 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 1.383 ------------------------------------------------------------------------------- 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 125 GLU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain B residue 155 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 31 optimal weight: 3.9990 chunk 152 optimal weight: 20.0000 chunk 148 optimal weight: 20.0000 chunk 141 optimal weight: 20.0000 chunk 82 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.085548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.060249 restraints weight = 29978.214| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.29 r_work: 0.2769 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13044 Z= 0.118 Angle : 0.953 41.049 17775 Z= 0.278 Chirality : 0.041 0.189 2168 Planarity : 0.004 0.056 2124 Dihedral : 9.411 64.867 2786 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.54 % Favored : 95.40 % Rotamer: Outliers : 2.38 % Allowed : 14.22 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 1.35 (0.22), residues: 1587 helix: 2.27 (0.19), residues: 825 sheet: -0.14 (0.59), residues: 106 loop : -0.74 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 166 HIS 0.002 0.000 HIS C 17 PHE 0.019 0.001 PHE A 143 TYR 0.015 0.001 TYR C 237 ARG 0.003 0.000 ARG B 167 Details of bonding type rmsd hydrogen bonds : bond 0.03464 ( 637) hydrogen bonds : angle 4.03972 ( 1821) metal coordination : bond 0.01059 ( 20) metal coordination : angle 13.82491 ( 54) covalent geometry : bond 0.00270 (13022) covalent geometry : angle 0.57316 (17721) Misc. bond : bond 0.00034 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 3.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9108 (tm-30) cc_final: 0.8689 (tm-30) REVERT: A 92 ARG cc_start: 0.8571 (ttp-110) cc_final: 0.8365 (ttp-110) REVERT: A 100 ARG cc_start: 0.8642 (tpp80) cc_final: 0.8320 (tpp80) REVERT: A 105 TYR cc_start: 0.8455 (m-80) cc_final: 0.7998 (m-80) REVERT: A 125 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8304 (mp0) REVERT: A 161 ASN cc_start: 0.9150 (t0) cc_final: 0.8903 (t0) REVERT: C 3 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.5847 (m-10) REVERT: C 297 CYS cc_start: 0.9027 (m) cc_final: 0.8461 (t) REVERT: C 344 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8635 (pm20) REVERT: E 19 GLN cc_start: 0.8613 (tm-30) cc_final: 0.8022 (tm-30) REVERT: G 59 ILE cc_start: 0.9571 (tp) cc_final: 0.9286 (tp) REVERT: G 67 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7872 (tm-30) REVERT: G 179 GLU cc_start: 0.9011 (pt0) cc_final: 0.8788 (pm20) REVERT: H 9 ASP cc_start: 0.8129 (t0) cc_final: 0.7622 (t0) REVERT: H 12 LYS cc_start: 0.8663 (mmmt) cc_final: 0.8224 (mtpp) REVERT: B 169 ASP cc_start: 0.8987 (p0) cc_final: 0.8756 (p0) outliers start: 30 outliers final: 19 residues processed: 174 average time/residue: 0.4796 time to fit residues: 123.2599 Evaluate side-chains 164 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 1.491 ------------------------------------------------------------------------------- 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 125 GLU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 155 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 154 optimal weight: 0.0030 chunk 91 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 overall best weight: 2.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 ASN ** E 29 ASN ** 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 = 0.3393 r_free = 0.3393 target = 0.083532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.058041 restraints weight = 30174.336| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.30 r_work: 0.2722 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13044 Z= 0.198 Angle : 1.011 43.747 17775 Z= 0.313 Chirality : 0.043 0.190 2168 Planarity : 0.004 0.056 2124 Dihedral : 9.472 59.018 2786 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.36 % Favored : 94.58 % Rotamer: Outliers : 2.22 % Allowed : 14.38 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 1.19 (0.22), residues: 1587 helix: 2.10 (0.19), residues: 832 sheet: -0.14 (0.58), residues: 106 loop : -0.80 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 166 HIS 0.003 0.001 HIS A 14 PHE 0.017 0.001 PHE A 143 TYR 0.012 0.001 TYR C 237 ARG 0.013 0.000 ARG B 103 Details of bonding type rmsd hydrogen bonds : bond 0.04131 ( 637) hydrogen bonds : angle 4.17361 ( 1821) metal coordination : bond 0.01943 ( 20) metal coordination : angle 14.19660 ( 54) covalent geometry : bond 0.00474 (13022) covalent geometry : angle 0.64066 (17721) Misc. bond : bond 0.00099 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9147 (tm-30) cc_final: 0.8886 (tm-30) REVERT: A 92 ARG cc_start: 0.8618 (ttp-110) cc_final: 0.8400 (ttp-110) REVERT: A 125 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8273 (mp0) REVERT: A 161 ASN cc_start: 0.9158 (t0) cc_final: 0.8886 (t0) REVERT: C 3 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.5851 (m-10) REVERT: C 297 CYS cc_start: 0.9044 (m) cc_final: 0.8485 (t) REVERT: C 344 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8624 (pm20) REVERT: D 75 ASP cc_start: 0.8827 (p0) cc_final: 0.8594 (p0) REVERT: E 19 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8031 (tm-30) REVERT: G 38 TYR cc_start: 0.7581 (t80) cc_final: 0.7191 (t80) REVERT: G 59 ILE cc_start: 0.9586 (tp) cc_final: 0.9306 (tp) REVERT: G 67 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7967 (tm-30) REVERT: G 106 GLU cc_start: 0.8638 (tp30) cc_final: 0.8305 (tp30) REVERT: G 179 GLU cc_start: 0.9057 (pt0) cc_final: 0.8786 (pm20) REVERT: H 9 ASP cc_start: 0.8104 (t0) cc_final: 0.7587 (t0) REVERT: H 12 LYS cc_start: 0.8673 (mmmt) cc_final: 0.8193 (mtpp) REVERT: B 169 ASP cc_start: 0.9084 (p0) cc_final: 0.8838 (p0) outliers start: 28 outliers final: 20 residues processed: 169 average time/residue: 0.2488 time to fit residues: 60.0062 Evaluate side-chains 164 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 1.415 ------------------------------------------------------------------------------- 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 125 GLU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 155 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 48 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 98 optimal weight: 0.1980 chunk 106 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 145 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 125 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 ASN ** E 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.085148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.059871 restraints weight = 29877.527| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.28 r_work: 0.2766 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13044 Z= 0.120 Angle : 0.961 42.028 17775 Z= 0.292 Chirality : 0.041 0.183 2168 Planarity : 0.004 0.057 2124 Dihedral : 9.188 59.560 2786 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.35 % Favored : 95.59 % Rotamer: Outliers : 1.83 % Allowed : 14.85 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 1.36 (0.22), residues: 1587 helix: 2.23 (0.19), residues: 826 sheet: -0.22 (0.56), residues: 116 loop : -0.65 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 96 HIS 0.002 0.000 HIS C 13 PHE 0.022 0.001 PHE A 143 TYR 0.017 0.001 TYR C 201 ARG 0.008 0.000 ARG B 103 Details of bonding type rmsd hydrogen bonds : bond 0.03528 ( 637) hydrogen bonds : angle 4.08017 ( 1821) metal coordination : bond 0.01051 ( 20) metal coordination : angle 13.75101 ( 54) covalent geometry : bond 0.00277 (13022) covalent geometry : angle 0.59177 (17721) Misc. bond : bond 0.00031 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8685 (tm-30) REVERT: A 92 ARG cc_start: 0.8515 (ttp-110) cc_final: 0.8294 (ttp-110) REVERT: A 125 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8294 (mp0) REVERT: A 161 ASN cc_start: 0.9134 (t0) cc_final: 0.8895 (t0) REVERT: C 297 CYS cc_start: 0.9013 (m) cc_final: 0.8487 (t) REVERT: C 344 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8630 (pm20) REVERT: E 19 GLN cc_start: 0.8578 (tm-30) cc_final: 0.7993 (tm-30) REVERT: G 38 TYR cc_start: 0.7640 (t80) cc_final: 0.7237 (t80) REVERT: G 59 ILE cc_start: 0.9580 (tp) cc_final: 0.9292 (tp) REVERT: G 67 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7955 (tm-30) REVERT: G 106 GLU cc_start: 0.8634 (tp30) cc_final: 0.8319 (tp30) REVERT: G 179 GLU cc_start: 0.9015 (pt0) cc_final: 0.8779 (pm20) REVERT: H 9 ASP cc_start: 0.8038 (t0) cc_final: 0.7534 (t0) REVERT: H 12 LYS cc_start: 0.8732 (mmmt) cc_final: 0.8274 (mtpp) REVERT: B 169 ASP cc_start: 0.9027 (p0) cc_final: 0.8797 (p0) outliers start: 23 outliers final: 19 residues processed: 167 average time/residue: 0.2775 time to fit residues: 65.5706 Evaluate side-chains 164 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 71 ILE Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 162 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 150 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 13 optimal weight: 7.9990 chunk 141 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 ASN ** E 29 ASN ** 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 = 0.3429 r_free = 0.3429 target = 0.085664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.060420 restraints weight = 29855.365| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.30 r_work: 0.2782 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13044 Z= 0.114 Angle : 0.944 40.656 17775 Z= 0.289 Chirality : 0.040 0.177 2168 Planarity : 0.004 0.057 2124 Dihedral : 8.908 59.690 2786 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.60 % Favored : 95.34 % Rotamer: Outliers : 1.59 % Allowed : 14.93 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 1.50 (0.22), residues: 1587 helix: 2.37 (0.19), residues: 821 sheet: -0.04 (0.59), residues: 106 loop : -0.62 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 166 HIS 0.002 0.000 HIS C 17 PHE 0.022 0.001 PHE A 143 TYR 0.017 0.001 TYR C 201 ARG 0.009 0.000 ARG B 167 Details of bonding type rmsd hydrogen bonds : bond 0.03400 ( 637) hydrogen bonds : angle 4.01651 ( 1821) metal coordination : bond 0.00937 ( 20) metal coordination : angle 13.48028 ( 54) covalent geometry : bond 0.00260 (13022) covalent geometry : angle 0.58322 (17721) Misc. bond : bond 0.00027 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8668 (tm-30) REVERT: A 92 ARG cc_start: 0.8496 (ttp-110) cc_final: 0.8281 (ttp-110) REVERT: A 105 TYR cc_start: 0.8433 (m-80) cc_final: 0.7994 (m-80) REVERT: A 125 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8310 (mp0) REVERT: A 161 ASN cc_start: 0.9154 (t0) cc_final: 0.8908 (t0) REVERT: C 297 CYS cc_start: 0.9040 (m) cc_final: 0.8480 (t) REVERT: C 344 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8609 (pm20) REVERT: E 106 GLU cc_start: 0.9316 (mm-30) cc_final: 0.9076 (mm-30) REVERT: E 173 GLN cc_start: 0.9039 (pm20) cc_final: 0.8786 (pm20) REVERT: G 38 TYR cc_start: 0.7670 (t80) cc_final: 0.7262 (t80) REVERT: G 59 ILE cc_start: 0.9568 (tp) cc_final: 0.9272 (tp) REVERT: G 67 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7948 (tm-30) REVERT: G 106 GLU cc_start: 0.8644 (tp30) cc_final: 0.8324 (tp30) REVERT: G 179 GLU cc_start: 0.8995 (pt0) cc_final: 0.8779 (pm20) REVERT: H 9 ASP cc_start: 0.7899 (t0) cc_final: 0.7294 (t0) REVERT: H 12 LYS cc_start: 0.8744 (mmmt) cc_final: 0.8305 (mtpp) REVERT: B 169 ASP cc_start: 0.9032 (p0) cc_final: 0.8796 (p0) outliers start: 20 outliers final: 17 residues processed: 165 average time/residue: 0.2730 time to fit residues: 64.1174 Evaluate side-chains 163 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 162 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 0.1980 chunk 107 optimal weight: 7.9990 chunk 149 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 110 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.086426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.061360 restraints weight = 29769.785| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.29 r_work: 0.2795 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13044 Z= 0.105 Angle : 0.931 39.553 17775 Z= 0.286 Chirality : 0.040 0.172 2168 Planarity : 0.004 0.057 2124 Dihedral : 8.669 59.954 2783 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.41 % Favored : 95.53 % Rotamer: Outliers : 1.67 % Allowed : 15.33 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 1.57 (0.22), residues: 1587 helix: 2.44 (0.19), residues: 818 sheet: 0.02 (0.59), residues: 106 loop : -0.61 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 96 HIS 0.002 0.000 HIS C 17 PHE 0.026 0.001 PHE A 143 TYR 0.019 0.001 TYR C 201 ARG 0.009 0.000 ARG B 167 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 637) hydrogen bonds : angle 3.96539 ( 1821) metal coordination : bond 0.00750 ( 20) metal coordination : angle 13.32800 ( 54) covalent geometry : bond 0.00234 (13022) covalent geometry : angle 0.57212 (17721) Misc. bond : bond 0.00014 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7803.97 seconds wall clock time: 140 minutes 51.62 seconds (8451.62 seconds total)