Starting phenix.real_space_refine on Thu Jun 4 01:17:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9umu_64322/06_2026/9umu_64322.cif Found real_map, /net/cci-nas-00/data/ceres_data/9umu_64322/06_2026/9umu_64322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9umu_64322/06_2026/9umu_64322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9umu_64322/06_2026/9umu_64322.map" model { file = "/net/cci-nas-00/data/ceres_data/9umu_64322/06_2026/9umu_64322.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9umu_64322/06_2026/9umu_64322.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.005 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: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 61 5.16 5 C 5813 2.51 5 N 1580 2.21 5 O 1781 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9240 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3372 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain: "B" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3371 Classifications: {'peptide': 430} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Chain: "J" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2437 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 298} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'GDP': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.37, per 1000 atoms: 0.26 Number of scatterers: 9240 At special positions: 0 Unit cell: (75.99, 104.3, 114.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 61 16.00 P 5 15.00 O 1781 8.00 N 1580 7.00 C 5813 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: 1.01 Conformation dependent library (CDL) restraints added in 357.0 milliseconds 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2170 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 49.1% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 74 through 81 Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 108 through 129 removed outlier: 3.876A pdb=" N GLU A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 118 " --> pdb=" O ILE A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.007A pdb=" N GLY A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE A 149 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.928A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.822A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.715A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 339 Processing helix chain 'A' and resid 383 through 401 removed outlier: 4.181A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.114A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 435 removed outlier: 3.796A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 41 through 45 Processing helix chain 'B' and resid 46 through 49 Processing helix chain 'B' and resid 71 through 78 Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 108 through 127 removed outlier: 3.774A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 159 removed outlier: 4.443A pdb=" N LEU B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 4.106A pdb=" N THR B 186 " --> pdb=" O PRO B 182 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 213 Processing helix chain 'B' and resid 221 through 242 removed outlier: 3.625A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N CYS B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 removed outlier: 3.896A pdb=" N LEU B 253 " --> pdb=" O ASP B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.679A pdb=" N THR B 290 " --> pdb=" O VAL B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.908A pdb=" N ASN B 298 " --> pdb=" O ASP B 295 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N MET B 299 " --> pdb=" O ALA B 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 295 through 299' Processing helix chain 'B' and resid 323 through 337 removed outlier: 3.844A pdb=" N MET B 330 " --> pdb=" O VAL B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 374 through 391 removed outlier: 3.927A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARG B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 399 removed outlier: 3.686A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.676A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 27 Processing helix chain 'J' and resid 58 through 64 Processing helix chain 'J' and resid 66 through 76 removed outlier: 4.194A pdb=" N ILE J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS J 72 " --> pdb=" O MET J 68 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP J 73 " --> pdb=" O GLN J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 97 Processing helix chain 'J' and resid 107 through 121 removed outlier: 3.524A pdb=" N TYR J 121 " --> pdb=" O PHE J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 191 removed outlier: 3.594A pdb=" N ASN J 190 " --> pdb=" O GLU J 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 248 through 271 Processing helix chain 'J' and resid 282 through 289 Processing helix chain 'J' and resid 290 through 292 No H-bonds generated for 'chain 'J' and resid 290 through 292' Processing helix chain 'J' and resid 307 through 309 No H-bonds generated for 'chain 'J' and resid 307 through 309' Processing helix chain 'J' and resid 310 through 323 Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 93 removed outlier: 7.588A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N HIS A 139 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 9 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER A 165 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A 171 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.616A pdb=" N SER A 379 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLY A 354 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LEU A 317 " --> pdb=" O GLY A 354 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ASN A 356 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR A 319 " --> pdb=" O ASN A 356 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 63 through 66 removed outlier: 7.105A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AA6, first strand: chain 'B' and resid 199 through 200 removed outlier: 6.556A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 268 through 271 removed outlier: 4.496A pdb=" N THR B 312 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 51 through 53 removed outlier: 7.819A pdb=" N VAL J 12 " --> pdb=" O ARG J 51 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N PHE J 53 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N CYS J 14 " --> pdb=" O PHE J 53 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LYS J 11 " --> pdb=" O MET J 300 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE J 302 " --> pdb=" O LYS J 11 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU J 13 " --> pdb=" O ILE J 302 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE J 83 " --> pdb=" O PHE J 301 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N CYS J 303 " --> pdb=" O PHE J 83 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN J 222 " --> pdb=" O ASN J 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 127 through 129 Processing sheet with id=AB1, first strand: chain 'J' and resid 33 through 35 removed outlier: 3.643A pdb=" N ILE J 42 " --> pdb=" O LYS J 45 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1230 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: 1.64 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3064 1.34 - 1.46: 2042 1.46 - 1.58: 4230 1.58 - 1.69: 8 1.69 - 1.81: 96 Bond restraints: 9440 Sorted by residual: bond pdb=" C ILE J 31 " pdb=" N PRO J 32 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 2.04e+00 bond pdb=" N GLN B 280 " pdb=" CA GLN B 280 " ideal model delta sigma weight residual 1.458 1.481 -0.023 1.90e-02 2.77e+03 1.48e+00 bond pdb=" C GLN B 279 " pdb=" N GLN B 280 " ideal model delta sigma weight residual 1.329 1.346 -0.017 1.40e-02 5.10e+03 1.43e+00 bond pdb=" O5' GDP B 502 " pdb=" PA GDP B 502 " ideal model delta sigma weight residual 1.610 1.587 0.023 2.00e-02 2.50e+03 1.35e+00 bond pdb=" CA SER B 145 " pdb=" CB SER B 145 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.57e-02 4.06e+03 1.30e+00 ... (remaining 9435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 12657 2.15 - 4.30: 116 4.30 - 6.46: 16 6.46 - 8.61: 8 8.61 - 10.76: 2 Bond angle restraints: 12799 Sorted by residual: angle pdb=" C GLN B 279 " pdb=" N GLN B 280 " pdb=" CA GLN B 280 " ideal model delta sigma weight residual 121.70 132.46 -10.76 1.80e+00 3.09e-01 3.57e+01 angle pdb=" N ASP J 159 " pdb=" CA ASP J 159 " pdb=" C ASP J 159 " ideal model delta sigma weight residual 113.18 108.92 4.26 1.33e+00 5.65e-01 1.02e+01 angle pdb=" O5' GDP B 502 " pdb=" PA GDP B 502 " pdb=" O3A GDP B 502 " ideal model delta sigma weight residual 102.60 112.09 -9.49 3.00e+00 1.11e-01 1.00e+01 angle pdb=" PA GDP B 502 " pdb=" O3A GDP B 502 " pdb=" PB GDP B 502 " ideal model delta sigma weight residual 120.50 112.17 8.33 3.00e+00 1.11e-01 7.71e+00 angle pdb=" C5' GDP B 502 " pdb=" O5' GDP B 502 " pdb=" PA GDP B 502 " ideal model delta sigma weight residual 120.50 112.42 8.08 3.00e+00 1.11e-01 7.25e+00 ... (remaining 12794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 5564 35.47 - 70.95: 74 70.95 - 106.42: 6 106.42 - 141.89: 3 141.89 - 177.37: 1 Dihedral angle restraints: 5648 sinusoidal: 2268 harmonic: 3380 Sorted by residual: dihedral pdb=" CA SER B 145 " pdb=" C SER B 145 " pdb=" N GLY B 146 " pdb=" CA GLY B 146 " ideal model delta harmonic sigma weight residual -180.00 -132.68 -47.32 0 5.00e+00 4.00e-02 8.96e+01 dihedral pdb=" C8 GTP B 501 " pdb=" C1' GTP B 501 " pdb=" N9 GTP B 501 " pdb=" O4' GTP B 501 " ideal model delta sinusoidal sigma weight residual 104.59 -72.77 177.37 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2B GDP B 502 " pdb=" O3A GDP B 502 " pdb=" PB GDP B 502 " pdb=" PA GDP B 502 " ideal model delta sinusoidal sigma weight residual 180.00 38.82 141.18 1 2.00e+01 2.50e-03 4.27e+01 ... (remaining 5645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 978 0.036 - 0.072: 315 0.072 - 0.108: 94 0.108 - 0.144: 22 0.144 - 0.180: 3 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CA GLN B 280 " pdb=" N GLN B 280 " pdb=" C GLN B 280 " pdb=" CB GLN B 280 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" C3' GDP B 502 " pdb=" C4' GDP B 502 " pdb=" O3' GDP B 502 " pdb=" C2' GDP B 502 " both_signs ideal model delta sigma weight residual False -2.51 -2.67 0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CA GLU A 183 " pdb=" N GLU A 183 " pdb=" C GLU A 183 " pdb=" CB GLU A 183 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 1409 not shown) Planarity restraints: 1664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 145 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C SER B 145 " 0.028 2.00e-02 2.50e+03 pdb=" O SER B 145 " -0.010 2.00e-02 2.50e+03 pdb=" N GLY B 146 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 146 " -0.007 2.00e-02 2.50e+03 1.45e-02 2.10e+00 pdb=" C GLY A 146 " 0.025 2.00e-02 2.50e+03 pdb=" O GLY A 146 " -0.009 2.00e-02 2.50e+03 pdb=" N SER A 147 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 105 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C ARG A 105 " -0.025 2.00e-02 2.50e+03 pdb=" O ARG A 105 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY A 106 " 0.008 2.00e-02 2.50e+03 ... (remaining 1661 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 245 2.68 - 3.24: 9815 3.24 - 3.79: 15383 3.79 - 4.35: 19877 4.35 - 4.90: 31283 Nonbonded interactions: 76603 Sorted by model distance: nonbonded pdb=" O TYR J 279 " pdb=" OG1 THR J 285 " model vdw 2.126 3.040 nonbonded pdb=" O VAL B 49 " pdb=" NH2 ARG B 62 " model vdw 2.138 3.120 nonbonded pdb=" O ILE J 138 " pdb=" OG SER J 205 " model vdw 2.150 3.040 nonbonded pdb=" N GLY B 13 " pdb=" OG SER B 138 " model vdw 2.178 3.120 nonbonded pdb=" ND2 ASN A 102 " pdb=" OE1 GLU A 411 " model vdw 2.208 3.120 ... (remaining 76598 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 group one per residue 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: 6.010 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.990 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 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 : 0.003 0.040 9442 Z= 0.156 Angle : 0.580 10.761 12799 Z= 0.293 Chirality : 0.040 0.180 1412 Planarity : 0.003 0.030 1664 Dihedral : 13.062 177.368 3478 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.19 % Allowed : 7.76 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.25), residues: 1162 helix: 1.50 (0.24), residues: 503 sheet: -0.99 (0.41), residues: 165 loop : -1.87 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 214 TYR 0.012 0.001 TYR A 172 PHE 0.009 0.001 PHE A 138 TRP 0.011 0.002 TRP A 21 HIS 0.006 0.001 HIS B 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.16 ( 9440) covalent geometry : angle 0.57989 / 0.29 (12799) hydrogen bonds : bond 0.17935 / 11.73 ( 424) hydrogen bonds : angle 6.98989 / 4.67 ( 1230) Misc. bond : bond 0.00371 / 0.19 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.7870 (mpp) cc_final: 0.7393 (tpp) REVERT: B 257 MET cc_start: 0.8812 (mmp) cc_final: 0.8499 (mmm) REVERT: J 78 TYR cc_start: 0.9760 (m-10) cc_final: 0.9473 (m-80) REVERT: J 94 HIS cc_start: 0.9788 (m90) cc_final: 0.9469 (t-170) REVERT: J 123 MET cc_start: 0.4994 (pmm) cc_final: 0.4670 (pmm) REVERT: J 319 MET cc_start: 0.8702 (ttt) cc_final: 0.8321 (ptm) outliers start: 22 outliers final: 5 residues processed: 76 average time/residue: 0.0904 time to fit residues: 10.3807 Evaluate side-chains 48 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 30.0000 chunk 97 optimal weight: 50.0000 chunk 113 optimal weight: 0.4980 chunk 53 optimal weight: 50.0000 chunk 5 optimal weight: 50.0000 chunk 33 optimal weight: 0.0670 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 40.0000 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 50.0000 overall best weight: 3.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 176 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 ASN J 322 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.049557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.033793 restraints weight = 116497.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.034235 restraints weight = 85871.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.034670 restraints weight = 69368.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.034835 restraints weight = 57085.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.034835 restraints weight = 52687.640| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9442 Z= 0.124 Angle : 0.592 10.211 12799 Z= 0.301 Chirality : 0.042 0.187 1412 Planarity : 0.004 0.037 1664 Dihedral : 9.695 179.809 1292 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.25), residues: 1162 helix: 1.53 (0.24), residues: 498 sheet: -0.69 (0.42), residues: 161 loop : -1.88 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 84 TYR 0.020 0.001 TYR J 135 PHE 0.011 0.001 PHE J 209 TRP 0.009 0.001 TRP B 21 HIS 0.009 0.001 HIS J 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 9440) covalent geometry : angle 0.59162 / 0.30 (12799) hydrogen bonds : bond 0.03760 / 2.52 ( 424) hydrogen bonds : angle 5.26013 / 3.60 ( 1230) Misc. bond : bond 0.00490 / 0.26 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 282 TYR cc_start: 0.9540 (m-80) cc_final: 0.9325 (m-80) REVERT: A 398 MET cc_start: 0.9437 (mmp) cc_final: 0.9164 (mmm) REVERT: B 257 MET cc_start: 0.9538 (mmp) cc_final: 0.9165 (mmm) REVERT: B 300 MET cc_start: 0.9820 (mmp) cc_final: 0.9521 (mmt) REVERT: B 307 HIS cc_start: 0.8966 (t70) cc_final: 0.8732 (t70) REVERT: B 323 MET cc_start: 0.9372 (mpp) cc_final: 0.8903 (mpp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0887 time to fit residues: 6.8409 Evaluate side-chains 42 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 43 optimal weight: 50.0000 chunk 99 optimal weight: 40.0000 chunk 116 optimal weight: 7.9990 chunk 61 optimal weight: 40.0000 chunk 81 optimal weight: 30.0000 chunk 91 optimal weight: 50.0000 chunk 73 optimal weight: 30.0000 chunk 97 optimal weight: 30.0000 overall best weight: 15.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN B 14 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 424 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.047192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.030869 restraints weight = 102594.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.031180 restraints weight = 80857.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.031506 restraints weight = 65362.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.032105 restraints weight = 60013.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.032105 restraints weight = 53729.146| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9442 Z= 0.223 Angle : 0.637 10.434 12799 Z= 0.331 Chirality : 0.040 0.162 1412 Planarity : 0.004 0.038 1664 Dihedral : 10.010 171.610 1292 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.20 % Allowed : 2.89 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.25), residues: 1162 helix: 1.20 (0.24), residues: 489 sheet: -0.79 (0.40), residues: 163 loop : -1.88 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 84 TYR 0.015 0.002 TYR J 135 PHE 0.014 0.002 PHE B 294 TRP 0.008 0.002 TRP A 346 HIS 0.008 0.002 HIS J 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.22 ( 9440) covalent geometry : angle 0.63728 / 0.33 (12799) hydrogen bonds : bond 0.03780 / 2.50 ( 424) hydrogen bonds : angle 5.18844 / 3.57 ( 1230) Misc. bond : bond 0.00459 / 0.24 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 398 MET cc_start: 0.9397 (mmp) cc_final: 0.9143 (mmm) REVERT: B 257 MET cc_start: 0.9397 (mmp) cc_final: 0.8806 (tpt) REVERT: B 267 MET cc_start: 0.8953 (tpp) cc_final: 0.8712 (tpp) REVERT: B 300 MET cc_start: 0.9809 (mmp) cc_final: 0.9556 (mmp) REVERT: B 307 HIS cc_start: 0.8781 (t70) cc_final: 0.8529 (t70) REVERT: B 323 MET cc_start: 0.9280 (mpp) cc_final: 0.8846 (mpp) outliers start: 2 outliers final: 0 residues processed: 48 average time/residue: 0.0798 time to fit residues: 6.0573 Evaluate side-chains 42 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 113 optimal weight: 4.9990 chunk 59 optimal weight: 30.0000 chunk 60 optimal weight: 9.9990 chunk 95 optimal weight: 40.0000 chunk 0 optimal weight: 60.0000 chunk 98 optimal weight: 50.0000 chunk 71 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 35 optimal weight: 40.0000 chunk 105 optimal weight: 9.9990 chunk 6 optimal weight: 0.4980 overall best weight: 6.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 GLN ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.046782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.032207 restraints weight = 120440.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.032927 restraints weight = 90643.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.033331 restraints weight = 69336.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.033470 restraints weight = 59277.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.033470 restraints weight = 54337.205| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9442 Z= 0.125 Angle : 0.561 10.367 12799 Z= 0.285 Chirality : 0.041 0.160 1412 Planarity : 0.003 0.037 1664 Dihedral : 9.795 172.987 1292 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.25), residues: 1162 helix: 1.32 (0.24), residues: 482 sheet: -0.58 (0.41), residues: 159 loop : -1.75 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 84 TYR 0.020 0.001 TYR A 408 PHE 0.011 0.001 PHE B 294 TRP 0.009 0.001 TRP A 407 HIS 0.005 0.001 HIS J 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.13 ( 9440) covalent geometry : angle 0.56108 / 0.29 (12799) hydrogen bonds : bond 0.03282 / 2.21 ( 424) hydrogen bonds : angle 4.95540 / 3.44 ( 1230) Misc. bond : bond 0.00420 / 0.22 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.9265 (mmp) cc_final: 0.9018 (mmm) REVERT: B 257 MET cc_start: 0.9388 (mmp) cc_final: 0.8623 (mmm) REVERT: B 300 MET cc_start: 0.9813 (mmp) cc_final: 0.9544 (mmt) REVERT: B 307 HIS cc_start: 0.8686 (t70) cc_final: 0.8423 (t70) REVERT: B 323 MET cc_start: 0.9349 (mpp) cc_final: 0.8897 (mpp) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0802 time to fit residues: 6.3193 Evaluate side-chains 42 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 6 optimal weight: 0.0010 chunk 61 optimal weight: 9.9990 chunk 44 optimal weight: 50.0000 chunk 49 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 40 optimal weight: 40.0000 chunk 10 optimal weight: 40.0000 chunk 53 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 overall best weight: 5.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 GLN ** 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 = 0.3388 r_free = 0.3388 target = 0.047064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.032474 restraints weight = 115071.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.033260 restraints weight = 83762.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.033657 restraints weight = 64068.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.034198 restraints weight = 53995.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.034288 restraints weight = 49240.697| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9442 Z= 0.118 Angle : 0.559 10.238 12799 Z= 0.282 Chirality : 0.041 0.190 1412 Planarity : 0.004 0.074 1664 Dihedral : 9.759 174.707 1292 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.25), residues: 1162 helix: 1.43 (0.24), residues: 481 sheet: -0.58 (0.41), residues: 161 loop : -1.75 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 84 TYR 0.017 0.001 TYR A 408 PHE 0.009 0.001 PHE B 294 TRP 0.008 0.001 TRP A 21 HIS 0.005 0.001 HIS J 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 ( 9440) covalent geometry : angle 0.55880 / 0.28 (12799) hydrogen bonds : bond 0.03123 / 2.09 ( 424) hydrogen bonds : angle 4.81026 / 3.34 ( 1230) Misc. bond : bond 0.00368 / 0.19 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.9232 (mmp) cc_final: 0.8995 (mmm) REVERT: B 257 MET cc_start: 0.9324 (mmp) cc_final: 0.8852 (mmm) REVERT: B 300 MET cc_start: 0.9724 (mmp) cc_final: 0.9512 (mmt) REVERT: B 307 HIS cc_start: 0.8590 (t70) cc_final: 0.8310 (t70) REVERT: B 323 MET cc_start: 0.9317 (mpp) cc_final: 0.8866 (mpp) REVERT: B 415 MET cc_start: 0.9719 (ppp) cc_final: 0.9466 (ppp) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0782 time to fit residues: 6.1524 Evaluate side-chains 41 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 10 optimal weight: 6.9990 chunk 67 optimal weight: 20.0000 chunk 12 optimal weight: 50.0000 chunk 112 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 54 optimal weight: 50.0000 chunk 91 optimal weight: 50.0000 chunk 48 optimal weight: 9.9990 chunk 88 optimal weight: 0.0170 chunk 43 optimal weight: 40.0000 overall best weight: 3.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 254 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.046914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.031978 restraints weight = 117058.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.032242 restraints weight = 81556.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.032976 restraints weight = 67745.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.033219 restraints weight = 57368.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.033446 restraints weight = 51117.183| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9442 Z= 0.102 Angle : 0.547 10.200 12799 Z= 0.274 Chirality : 0.041 0.157 1412 Planarity : 0.003 0.037 1664 Dihedral : 9.696 175.861 1292 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.25), residues: 1162 helix: 1.50 (0.24), residues: 488 sheet: -0.34 (0.40), residues: 178 loop : -1.69 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 308 TYR 0.017 0.001 TYR A 408 PHE 0.010 0.001 PHE A 53 TRP 0.008 0.001 TRP A 21 HIS 0.005 0.001 HIS J 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 9440) covalent geometry : angle 0.54680 / 0.27 (12799) hydrogen bonds : bond 0.02973 / 1.98 ( 424) hydrogen bonds : angle 4.64952 / 3.25 ( 1230) Misc. bond : bond 0.00331 / 0.17 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.9262 (mmp) cc_final: 0.9011 (mmm) REVERT: B 257 MET cc_start: 0.9392 (mmp) cc_final: 0.8905 (mmm) REVERT: B 307 HIS cc_start: 0.8572 (t70) cc_final: 0.8304 (t70) REVERT: B 323 MET cc_start: 0.9343 (mpp) cc_final: 0.8880 (mpp) REVERT: B 415 MET cc_start: 0.9698 (ppp) cc_final: 0.9435 (ppp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0851 time to fit residues: 6.6555 Evaluate side-chains 43 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 11 optimal weight: 30.0000 chunk 0 optimal weight: 60.0000 chunk 81 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 48 optimal weight: 0.5980 chunk 104 optimal weight: 50.0000 chunk 79 optimal weight: 20.0000 chunk 42 optimal weight: 0.0770 chunk 1 optimal weight: 50.0000 chunk 78 optimal weight: 10.0000 overall best weight: 6.1348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 GLN ** 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 = 0.3398 r_free = 0.3398 target = 0.047123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.031712 restraints weight = 109961.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.032072 restraints weight = 80675.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.032929 restraints weight = 69136.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.033003 restraints weight = 58546.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.033163 restraints weight = 54281.901| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9442 Z= 0.116 Angle : 0.546 10.072 12799 Z= 0.275 Chirality : 0.040 0.181 1412 Planarity : 0.003 0.036 1664 Dihedral : 9.687 177.806 1292 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.25), residues: 1162 helix: 1.51 (0.24), residues: 487 sheet: -0.39 (0.39), residues: 178 loop : -1.62 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 308 TYR 0.015 0.001 TYR A 408 PHE 0.015 0.001 PHE A 53 TRP 0.007 0.001 TRP A 21 HIS 0.004 0.001 HIS J 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 ( 9440) covalent geometry : angle 0.54581 / 0.28 (12799) hydrogen bonds : bond 0.02938 / 1.96 ( 424) hydrogen bonds : angle 4.60286 / 3.22 ( 1230) Misc. bond : bond 0.00311 / 0.16 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.9236 (mmp) cc_final: 0.8976 (mmm) REVERT: B 257 MET cc_start: 0.9318 (mmp) cc_final: 0.8811 (mmm) REVERT: B 299 MET cc_start: 0.6519 (pmm) cc_final: 0.6270 (pmm) REVERT: B 307 HIS cc_start: 0.8714 (t70) cc_final: 0.8459 (t70) REVERT: B 323 MET cc_start: 0.9322 (mpp) cc_final: 0.8885 (mpp) REVERT: B 415 MET cc_start: 0.9712 (ppp) cc_final: 0.9454 (ppp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0770 time to fit residues: 6.0204 Evaluate side-chains 42 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 58 optimal weight: 8.9990 chunk 114 optimal weight: 8.9990 chunk 60 optimal weight: 50.0000 chunk 57 optimal weight: 9.9990 chunk 101 optimal weight: 40.0000 chunk 8 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 78 optimal weight: 3.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.046489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.030678 restraints weight = 105229.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.031211 restraints weight = 77879.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.031883 restraints weight = 64831.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.031883 restraints weight = 53654.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.031883 restraints weight = 53654.942| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9442 Z= 0.133 Angle : 0.562 10.168 12799 Z= 0.284 Chirality : 0.041 0.178 1412 Planarity : 0.003 0.036 1664 Dihedral : 9.745 179.283 1292 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.25), residues: 1162 helix: 1.46 (0.24), residues: 488 sheet: -0.28 (0.40), residues: 169 loop : -1.59 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 213 TYR 0.014 0.001 TYR A 408 PHE 0.014 0.001 PHE B 133 TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 9440) covalent geometry : angle 0.56175 / 0.28 (12799) hydrogen bonds : bond 0.02905 / 1.93 ( 424) hydrogen bonds : angle 4.61672 / 3.25 ( 1230) Misc. bond : bond 0.00301 / 0.16 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.9259 (mmp) cc_final: 0.8991 (mmm) REVERT: B 257 MET cc_start: 0.9274 (mmp) cc_final: 0.8762 (mmm) REVERT: B 299 MET cc_start: 0.6805 (pmm) cc_final: 0.6477 (pmm) REVERT: B 307 HIS cc_start: 0.8729 (t70) cc_final: 0.8504 (t70) REVERT: B 323 MET cc_start: 0.8951 (mpp) cc_final: 0.8453 (mpp) REVERT: B 415 MET cc_start: 0.9712 (ppp) cc_final: 0.9457 (ppp) REVERT: J 139 TYR cc_start: 0.8415 (t80) cc_final: 0.8214 (t80) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0932 time to fit residues: 7.0390 Evaluate side-chains 42 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 98 optimal weight: 50.0000 chunk 104 optimal weight: 7.9990 chunk 25 optimal weight: 30.0000 chunk 5 optimal weight: 50.0000 chunk 103 optimal weight: 9.9990 chunk 57 optimal weight: 0.5980 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.046698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.030954 restraints weight = 103148.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.031444 restraints weight = 75938.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.031989 restraints weight = 62063.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.032118 restraints weight = 51171.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.032291 restraints weight = 50439.432| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9442 Z= 0.112 Angle : 0.549 10.198 12799 Z= 0.275 Chirality : 0.041 0.170 1412 Planarity : 0.003 0.036 1664 Dihedral : 9.878 179.735 1292 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.26), residues: 1162 helix: 1.58 (0.24), residues: 486 sheet: -0.28 (0.39), residues: 183 loop : -1.58 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 84 TYR 0.029 0.001 TYR A 408 PHE 0.009 0.001 PHE B 294 TRP 0.006 0.001 TRP B 21 HIS 0.004 0.001 HIS J 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 9440) covalent geometry : angle 0.54906 / 0.27 (12799) hydrogen bonds : bond 0.02852 / 1.89 ( 424) hydrogen bonds : angle 4.57810 / 3.22 ( 1230) Misc. bond : bond 0.00292 / 0.15 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.9256 (mmp) cc_final: 0.8987 (mmm) REVERT: B 257 MET cc_start: 0.9265 (mmp) cc_final: 0.8616 (mmm) REVERT: B 299 MET cc_start: 0.6598 (pmm) cc_final: 0.6283 (pmm) REVERT: B 323 MET cc_start: 0.9086 (mpp) cc_final: 0.8669 (mpp) REVERT: B 415 MET cc_start: 0.9710 (ppp) cc_final: 0.9450 (ppp) REVERT: J 139 TYR cc_start: 0.8440 (t80) cc_final: 0.8235 (t80) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0781 time to fit residues: 5.9887 Evaluate side-chains 42 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 81 optimal weight: 40.0000 chunk 87 optimal weight: 50.0000 chunk 15 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 50.0000 chunk 62 optimal weight: 50.0000 chunk 44 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 103 optimal weight: 20.0000 chunk 46 optimal weight: 0.4980 overall best weight: 9.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.046550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.030408 restraints weight = 104368.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.031305 restraints weight = 76431.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.031743 restraints weight = 59880.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.031743 restraints weight = 51772.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.031743 restraints weight = 51772.027| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9442 Z= 0.141 Angle : 0.568 10.192 12799 Z= 0.288 Chirality : 0.041 0.173 1412 Planarity : 0.004 0.036 1664 Dihedral : 9.823 178.026 1292 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.25), residues: 1162 helix: 1.51 (0.24), residues: 480 sheet: -0.34 (0.40), residues: 169 loop : -1.52 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 306 TYR 0.025 0.001 TYR A 408 PHE 0.011 0.001 PHE B 294 TRP 0.008 0.001 TRP A 346 HIS 0.010 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 ( 9440) covalent geometry : angle 0.56839 / 0.29 (12799) hydrogen bonds : bond 0.02938 / 1.94 ( 424) hydrogen bonds : angle 4.61367 / 3.25 ( 1230) Misc. bond : bond 0.00316 / 0.16 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.9252 (mmp) cc_final: 0.8988 (mmm) REVERT: B 257 MET cc_start: 0.9217 (mmp) cc_final: 0.8778 (mmm) REVERT: B 299 MET cc_start: 0.6811 (pmm) cc_final: 0.6485 (pmm) REVERT: B 323 MET cc_start: 0.9119 (mpp) cc_final: 0.8733 (mpp) REVERT: B 415 MET cc_start: 0.9737 (ppp) cc_final: 0.9473 (ppp) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0850 time to fit residues: 6.4700 Evaluate side-chains 40 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 46 optimal weight: 7.9990 chunk 116 optimal weight: 50.0000 chunk 9 optimal weight: 50.0000 chunk 101 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 5 optimal weight: 30.0000 chunk 33 optimal weight: 20.0000 chunk 105 optimal weight: 30.0000 chunk 48 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 51 optimal weight: 0.0770 overall best weight: 5.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 HIS ** J 61 GLN ** 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 = 0.3382 r_free = 0.3382 target = 0.046264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.030606 restraints weight = 104689.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.030677 restraints weight = 77648.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.030677 restraints weight = 71429.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.030677 restraints weight = 71429.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.030677 restraints weight = 71429.206| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9442 Z= 0.105 Angle : 0.541 10.225 12799 Z= 0.271 Chirality : 0.041 0.171 1412 Planarity : 0.003 0.036 1664 Dihedral : 9.779 178.829 1292 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.25), residues: 1162 helix: 1.63 (0.24), residues: 480 sheet: -0.28 (0.39), residues: 182 loop : -1.50 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 306 TYR 0.025 0.001 TYR A 408 PHE 0.009 0.001 PHE B 294 TRP 0.007 0.001 TRP B 21 HIS 0.005 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 ( 9440) covalent geometry : angle 0.54141 / 0.27 (12799) hydrogen bonds : bond 0.02821 / 1.86 ( 424) hydrogen bonds : angle 4.55415 / 3.22 ( 1230) Misc. bond : bond 0.00269 / 0.14 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1960.66 seconds wall clock time: 34 minutes 42.62 seconds (2082.62 seconds total)