Starting phenix.real_space_refine on Mon Aug 5 05:29:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb9_19029/08_2024/8rb9_19029.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb9_19029/08_2024/8rb9_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb9_19029/08_2024/8rb9_19029.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb9_19029/08_2024/8rb9_19029.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb9_19029/08_2024/8rb9_19029.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb9_19029/08_2024/8rb9_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 Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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 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 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: 7.62, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 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: 4.56 Conformation dependent library (CDL) restraints added in 2.0 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: 1.13 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: 3.37 Time building geometry restraints manager: 5.00 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 1.610 1.817 -0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C10 FMN C 500 " pdb=" C4A FMN C 500 " ideal model delta sigma weight residual 1.390 1.479 -0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C4A FMN C 500 " pdb=" N5 FMN C 500 " ideal model delta sigma weight residual 1.380 1.294 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C4A FMN D 413 " pdb=" N5 FMN D 413 " ideal model delta sigma weight residual 1.380 1.300 0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C4A FMN G 301 " pdb=" N5 FMN G 301 " ideal model delta sigma weight residual 1.380 1.301 0.079 2.00e-02 2.50e+03 1.57e+01 ... (remaining 13017 not shown) Histogram of bond angle deviations from ideal: 73.59 - 85.67: 50 85.67 - 97.76: 1 97.76 - 109.85: 1802 109.85 - 121.93: 13453 121.93 - 134.02: 2415 Bond angle restraints: 17721 Sorted by residual: angle pdb=" C2' FMN C 500 " pdb=" C1' FMN C 500 " pdb=" N10 FMN C 500 " ideal model delta sigma weight residual 109.47 123.88 -14.41 3.00e+00 1.11e-01 2.31e+01 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=" O1P FMN C 500 " pdb=" P FMN C 500 " pdb=" O5' FMN C 500 " ideal model delta sigma weight residual 108.20 97.96 10.24 3.00e+00 1.11e-01 1.17e+01 ... (remaining 17716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.17: 8003 34.17 - 68.35: 230 68.35 - 102.52: 87 102.52 - 136.70: 43 136.70 - 170.87: 2 Dihedral angle restraints: 8365 sinusoidal: 3836 harmonic: 4529 Sorted by residual: dihedral pdb=" C10 FMN D 413 " pdb=" C1' FMN D 413 " pdb=" N10 FMN D 413 " pdb=" C2' FMN D 413 " ideal model delta sinusoidal sigma weight residual 257.59 86.72 170.87 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C5' FMN G 301 " pdb=" O5' FMN G 301 " pdb=" P FMN G 301 " pdb=" O1P FMN G 301 " ideal model delta sinusoidal sigma weight residual 75.26 -143.02 -141.72 1 2.00e+01 2.50e-03 4.28e+01 dihedral pdb=" C5' FMN C 500 " pdb=" O5' FMN C 500 " pdb=" P FMN C 500 " pdb=" O1P FMN C 500 " ideal model delta sinusoidal sigma weight residual 75.26 -49.69 124.95 1 2.00e+01 2.50e-03 3.77e+01 ... (remaining 8362 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.004: 2164 1.004 - 2.008: 0 2.008 - 3.013: 0 3.013 - 4.017: 0 4.017 - 5.021: 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 -2.47 2.55 -5.02 2.00e-01 2.50e+01 6.30e+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 -2.47 2.42 -4.89 2.00e-01 2.50e+01 5.98e+02 ... (remaining 2165 not shown) Planarity restraints: 2121 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN G 301 " 0.097 2.00e-02 2.50e+03 2.73e-02 3.54e+01 pdb=" C10 FMN G 301 " -0.019 2.00e-02 2.50e+03 pdb=" C2 FMN G 301 " -0.009 2.00e-02 2.50e+03 pdb=" C4 FMN G 301 " 0.008 2.00e-02 2.50e+03 pdb=" C4A FMN G 301 " -0.009 2.00e-02 2.50e+03 pdb=" C5A FMN G 301 " -0.013 2.00e-02 2.50e+03 pdb=" C6 FMN G 301 " 0.001 2.00e-02 2.50e+03 pdb=" C7 FMN G 301 " 0.004 2.00e-02 2.50e+03 pdb=" C7M FMN G 301 " 0.024 2.00e-02 2.50e+03 pdb=" C8 FMN G 301 " -0.006 2.00e-02 2.50e+03 pdb=" C8M FMN G 301 " -0.017 2.00e-02 2.50e+03 pdb=" C9 FMN G 301 " -0.019 2.00e-02 2.50e+03 pdb=" C9A FMN G 301 " -0.021 2.00e-02 2.50e+03 pdb=" N1 FMN G 301 " -0.022 2.00e-02 2.50e+03 pdb=" N10 FMN G 301 " -0.014 2.00e-02 2.50e+03 pdb=" N3 FMN G 301 " 0.005 2.00e-02 2.50e+03 pdb=" N5 FMN G 301 " -0.010 2.00e-02 2.50e+03 pdb=" O2 FMN G 301 " -0.015 2.00e-02 2.50e+03 pdb=" O4 FMN G 301 " 0.034 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 " 0.028 2.00e-02 2.50e+03 1.15e-02 6.28e+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 " 0.001 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 " 0.032 2.00e-02 2.50e+03 pdb=" C8 FMN D 413 " -0.010 2.00e-02 2.50e+03 pdb=" C8M FMN D 413 " -0.013 2.00e-02 2.50e+03 pdb=" C9 FMN D 413 " -0.013 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 " -0.001 2.00e-02 2.50e+03 pdb=" O2 FMN D 413 " -0.007 2.00e-02 2.50e+03 pdb=" O4 FMN D 413 " -0.003 2.00e-02 2.50e+03 ... (remaining 2118 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 36.390 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.540 ------------------------------------------------------------------------------- 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 0.207 13022 Z= 0.455 Angle : 0.940 14.411 17721 Z= 0.392 Chirality : 0.219 5.021 2168 Planarity : 0.004 0.040 2121 Dihedral : 20.534 170.873 5465 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 *********************** 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 fitting. rotamer outliers: 25 poor density : 204 time to evaluate : 1.378 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: 0.2959 time to fit residues: 91.3169 Evaluate side-chains 150 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 139 time to evaluate : 1.482 ------------------------------------------------------------------------------- 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: 0.9990 chunk 142 optimal weight: 20.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 135 ASN E 228 GLN H 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13022 Z= 0.189 Angle : 0.688 13.719 17721 Z= 0.304 Chirality : 0.046 0.351 2168 Planarity : 0.004 0.038 2121 Dihedral : 17.989 177.622 2786 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.17 % Favored : 94.77 % Rotamer: Outliers : 2.78 % Allowed : 10.56 % Favored : 86.66 % 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: 0.79 (0.22), residues: 1587 helix: 1.69 (0.19), residues: 831 sheet: -0.36 (0.57), residues: 107 loop : -0.85 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 83 HIS 0.002 0.000 HIS A 60 PHE 0.018 0.001 PHE A 143 TYR 0.017 0.001 TYR H 7 ARG 0.007 0.001 ARG C 451 *********************** 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 fitting. rotamer outliers: 35 poor density : 160 time to evaluate : 1.410 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8376 (tm-30) cc_final: 0.8124 (tm-30) REVERT: A 125 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: E 19 GLN cc_start: 0.8396 (tm-30) cc_final: 0.7996 (tm-30) outliers start: 35 outliers final: 20 residues processed: 187 average time/residue: 0.2869 time to fit residues: 74.6803 Evaluate side-chains 161 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 140 time to evaluate : 1.490 ------------------------------------------------------------------------------- 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 79 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 142 optimal weight: 0.4980 chunk 154 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- 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 D 236 HIS ** E 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 13022 Z= 0.376 Angle : 0.738 13.515 17721 Z= 0.334 Chirality : 0.047 0.388 2168 Planarity : 0.005 0.046 2121 Dihedral : 14.448 176.041 2784 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.48 % Favored : 94.45 % Rotamer: Outliers : 3.34 % Allowed : 11.12 % Favored : 85.54 % 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: 1.73 (0.19), residues: 834 sheet: -0.45 (0.56), residues: 108 loop : -1.01 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 96 HIS 0.003 0.001 HIS A 14 PHE 0.013 0.002 PHE A 143 TYR 0.017 0.001 TYR H 7 ARG 0.010 0.001 ARG A 92 *********************** 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 195 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 153 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9012 (mm) REVERT: A 125 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: C 3 PHE cc_start: 0.6737 (OUTLIER) cc_final: 0.5446 (m-10) REVERT: C 140 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8678 (mt) REVERT: E 19 GLN cc_start: 0.8445 (tm-30) cc_final: 0.7985 (tm-30) REVERT: G 67 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7546 (tm-30) REVERT: H 18 CYS cc_start: 0.4630 (t) cc_final: 0.4386 (t) REVERT: H 32 GLN cc_start: 0.7340 (pt0) cc_final: 0.7016 (pt0) outliers start: 42 outliers final: 25 residues processed: 187 average time/residue: 0.2766 time to fit residues: 72.8367 Evaluate side-chains 169 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 140 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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 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 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 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 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 162 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 141 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 143 optimal weight: 7.9990 chunk 151 optimal weight: 7.9990 chunk 135 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13022 Z= 0.188 Angle : 0.643 14.041 17721 Z= 0.291 Chirality : 0.043 0.361 2168 Planarity : 0.004 0.039 2121 Dihedral : 12.132 172.976 2784 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.73 % Favored : 95.21 % Rotamer: Outliers : 2.22 % Allowed : 12.63 % Favored : 85.15 % 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: 1.00 (0.22), residues: 1587 helix: 1.92 (0.19), residues: 838 sheet: -0.37 (0.57), residues: 108 loop : -0.85 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 96 HIS 0.001 0.000 HIS C 17 PHE 0.015 0.001 PHE A 143 TYR 0.016 0.001 TYR C 237 ARG 0.007 0.000 ARG A 92 *********************** 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 181 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 153 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7639 (mp0) REVERT: D 326 MET cc_start: 0.8455 (mmt) cc_final: 0.8136 (mmt) REVERT: E 19 GLN cc_start: 0.8392 (tm-30) cc_final: 0.7896 (tm-30) REVERT: G 59 ILE cc_start: 0.9528 (tp) cc_final: 0.9280 (tp) REVERT: G 67 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7524 (tm-30) REVERT: H 32 GLN cc_start: 0.7383 (pt0) cc_final: 0.7083 (pt0) outliers start: 28 outliers final: 19 residues processed: 174 average time/residue: 0.2657 time to fit residues: 65.1426 Evaluate side-chains 160 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 140 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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 319 CYS 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 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 173 PHE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain B residue 155 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 86 optimal weight: 7.9990 chunk 2 optimal weight: 0.0870 chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 104 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 0.5980 chunk 136 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- 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 228 GLN G 134 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13022 Z= 0.153 Angle : 0.591 13.148 17721 Z= 0.275 Chirality : 0.041 0.257 2168 Planarity : 0.004 0.051 2121 Dihedral : 10.870 172.820 2783 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.60 % Favored : 95.34 % Rotamer: Outliers : 2.38 % Allowed : 13.19 % Favored : 84.43 % 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: 1.22 (0.22), residues: 1587 helix: 2.16 (0.19), residues: 821 sheet: -0.24 (0.58), residues: 106 loop : -0.77 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 166 HIS 0.005 0.000 HIS A 60 PHE 0.018 0.001 PHE A 143 TYR 0.015 0.001 TYR C 237 ARG 0.004 0.000 ARG B 167 *********************** 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 187 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 157 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: C 3 PHE cc_start: 0.6638 (OUTLIER) cc_final: 0.5288 (m-10) REVERT: E 19 GLN cc_start: 0.8402 (tm-30) cc_final: 0.7872 (tm-30) REVERT: G 67 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7518 (tm-30) REVERT: B 105 GLU cc_start: 0.7237 (mp0) cc_final: 0.6391 (mp0) outliers start: 30 outliers final: 16 residues processed: 180 average time/residue: 0.2666 time to fit residues: 67.8337 Evaluate side-chains 159 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 319 CYS 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 D residue 214 LEU Chi-restraints excluded: chain D residue 269 LEU 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 136 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 151 optimal weight: 20.0000 chunk 126 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13022 Z= 0.285 Angle : 0.638 12.014 17721 Z= 0.298 Chirality : 0.043 0.225 2168 Planarity : 0.004 0.050 2121 Dihedral : 10.559 175.855 2779 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.10 % Favored : 94.83 % Rotamer: Outliers : 2.62 % Allowed : 13.58 % Favored : 83.80 % 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: 1.23 (0.22), residues: 1587 helix: 2.14 (0.19), residues: 826 sheet: -0.20 (0.58), residues: 106 loop : -0.75 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 166 HIS 0.003 0.001 HIS A 60 PHE 0.014 0.001 PHE A 143 TYR 0.014 0.001 TYR C 237 ARG 0.006 0.000 ARG A 92 *********************** 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 176 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 143 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: C 3 PHE cc_start: 0.6740 (OUTLIER) cc_final: 0.5377 (m-10) REVERT: E 19 GLN cc_start: 0.8444 (tm-30) cc_final: 0.7863 (tm-30) REVERT: G 59 ILE cc_start: 0.9564 (tp) cc_final: 0.9295 (tp) REVERT: G 67 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7636 (tm-30) outliers start: 33 outliers final: 19 residues processed: 172 average time/residue: 0.2565 time to fit residues: 63.1927 Evaluate side-chains 160 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 139 time to evaluate : 1.431 ------------------------------------------------------------------------------- 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 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 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 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 H residue 64 ASP Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 83 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 85 optimal weight: 0.8980 chunk 127 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13022 Z= 0.165 Angle : 0.586 11.254 17721 Z= 0.275 Chirality : 0.041 0.191 2168 Planarity : 0.004 0.052 2121 Dihedral : 10.243 172.901 2779 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.60 % Favored : 95.34 % Rotamer: Outliers : 1.99 % Allowed : 14.46 % Favored : 83.56 % 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: 2.20 (0.19), residues: 832 sheet: -0.06 (0.59), residues: 106 loop : -0.67 (0.25), 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 0.019 0.001 PHE A 143 TYR 0.022 0.001 TYR H 7 ARG 0.004 0.000 ARG B 167 *********************** 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 171 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 146 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: C 3 PHE cc_start: 0.6710 (OUTLIER) cc_final: 0.5280 (m-10) REVERT: E 19 GLN cc_start: 0.8419 (tm-30) cc_final: 0.7814 (tm-30) REVERT: G 59 ILE cc_start: 0.9554 (tp) cc_final: 0.9267 (tp) REVERT: G 67 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7611 (tm-30) REVERT: G 179 GLU cc_start: 0.8456 (pm20) cc_final: 0.8235 (pm20) outliers start: 25 outliers final: 19 residues processed: 167 average time/residue: 0.2612 time to fit residues: 62.1463 Evaluate side-chains 162 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 1.438 ------------------------------------------------------------------------------- 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 3 PHE Chi-restraints excluded: chain C residue 198 LEU 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 214 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 75 THR 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 H residue 56 VAL Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 162 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 96 optimal weight: 0.5980 chunk 103 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 137 optimal weight: 0.5980 chunk 144 optimal weight: 30.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** H 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13022 Z= 0.159 Angle : 0.587 9.494 17721 Z= 0.279 Chirality : 0.041 0.262 2168 Planarity : 0.004 0.050 2121 Dihedral : 9.932 172.455 2779 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.54 % Favored : 95.40 % Rotamer: Outliers : 1.83 % Allowed : 15.17 % 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: 1.44 (0.22), residues: 1587 helix: 2.30 (0.19), residues: 825 sheet: 0.16 (0.62), residues: 96 loop : -0.67 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 166 HIS 0.002 0.000 HIS C 13 PHE 0.021 0.001 PHE A 143 TYR 0.013 0.001 TYR C 237 ARG 0.007 0.000 ARG A 92 *********************** 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 174 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 151 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: C 3 PHE cc_start: 0.6738 (OUTLIER) cc_final: 0.5311 (m-10) REVERT: E 19 GLN cc_start: 0.8391 (tm-30) cc_final: 0.7819 (tm-30) REVERT: G 67 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7607 (tm-30) REVERT: G 179 GLU cc_start: 0.8495 (pm20) cc_final: 0.8278 (pm20) outliers start: 23 outliers final: 18 residues processed: 168 average time/residue: 0.2657 time to fit residues: 63.0337 Evaluate side-chains 163 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 143 time to evaluate : 1.335 ------------------------------------------------------------------------------- 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 3 PHE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 75 THR 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 H residue 56 VAL Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 162 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 0.3980 chunk 141 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 140 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13022 Z= 0.162 Angle : 0.579 9.093 17721 Z= 0.278 Chirality : 0.040 0.238 2168 Planarity : 0.004 0.058 2121 Dihedral : 9.591 172.624 2778 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.54 % Favored : 95.40 % Rotamer: Outliers : 1.99 % Allowed : 15.09 % Favored : 82.92 % 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: 1.52 (0.22), residues: 1587 helix: 2.37 (0.19), residues: 820 sheet: 0.19 (0.62), residues: 96 loop : -0.61 (0.25), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 166 HIS 0.002 0.000 HIS C 422 PHE 0.020 0.001 PHE A 143 TYR 0.014 0.001 TYR C 237 ARG 0.013 0.000 ARG B 103 *********************** 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 173 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: E 19 GLN cc_start: 0.8395 (tm-30) cc_final: 0.7820 (tm-30) REVERT: G 67 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7662 (tm-30) REVERT: G 179 GLU cc_start: 0.8499 (pm20) cc_final: 0.8271 (pm20) outliers start: 25 outliers final: 18 residues processed: 166 average time/residue: 0.2740 time to fit residues: 64.4002 Evaluate side-chains 165 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 1.512 ------------------------------------------------------------------------------- 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 198 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 214 LEU 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 162 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 149 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 143 optimal weight: 20.0000 chunk 124 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 98 optimal weight: 0.4980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 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 : 0.003 0.036 13022 Z= 0.170 Angle : 0.596 12.087 17721 Z= 0.288 Chirality : 0.041 0.233 2168 Planarity : 0.004 0.057 2121 Dihedral : 9.407 172.697 2778 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.54 % Favored : 95.40 % Rotamer: Outliers : 1.43 % Allowed : 16.12 % Favored : 82.45 % 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: 1.56 (0.22), residues: 1587 helix: 2.40 (0.19), residues: 821 sheet: 0.21 (0.62), residues: 96 loop : -0.61 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 166 HIS 0.002 0.000 HIS C 422 PHE 0.026 0.001 PHE A 143 TYR 0.018 0.001 TYR H 7 ARG 0.014 0.000 ARG A 92 ********************** 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 166 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7738 (mp0) REVERT: E 19 GLN cc_start: 0.8359 (tm-30) cc_final: 0.7787 (tm-30) REVERT: E 106 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8361 (mm-30) REVERT: G 67 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7655 (tm-30) REVERT: G 179 GLU cc_start: 0.8499 (pm20) cc_final: 0.8267 (pm20) outliers start: 18 outliers final: 17 residues processed: 163 average time/residue: 0.2720 time to fit residues: 63.0369 Evaluate side-chains 165 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 147 time to evaluate : 1.418 ------------------------------------------------------------------------------- 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 198 LEU Chi-restraints excluded: chain C residue 352 THR 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 162 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 109 optimal weight: 0.1980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 GLN ** 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 = 0.3532 r_free = 0.3532 target = 0.090244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.062185 restraints weight = 31380.107| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.61 r_work: 0.2861 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13022 Z= 0.190 Angle : 0.589 9.285 17721 Z= 0.286 Chirality : 0.041 0.205 2168 Planarity : 0.004 0.061 2121 Dihedral : 9.301 173.398 2778 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.73 % Favored : 95.21 % Rotamer: Outliers : 1.75 % Allowed : 15.81 % Favored : 82.45 % 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: 1.56 (0.22), residues: 1587 helix: 2.41 (0.19), residues: 820 sheet: 0.30 (0.62), residues: 96 loop : -0.63 (0.25), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 166 HIS 0.002 0.000 HIS C 422 PHE 0.028 0.001 PHE A 143 TYR 0.014 0.001 TYR C 237 ARG 0.014 0.000 ARG A 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2683.97 seconds wall clock time: 48 minutes 34.35 seconds (2914.35 seconds total)