Starting phenix.real_space_refine on Thu Jul 2 06:08:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1p_36798/07_2026/8k1p_36798.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1p_36798/07_2026/8k1p_36798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k1p_36798/07_2026/8k1p_36798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1p_36798/07_2026/8k1p_36798.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k1p_36798/07_2026/8k1p_36798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1p_36798/07_2026/8k1p_36798.map" } resolution = 3.4 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= 0.064 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians V 1 8.30 5 P 9 5.49 5 Mg 2 5.21 5 S 21 5.16 5 C 4558 2.51 5 N 1240 2.21 5 O 1308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7139 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3711 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 20, 'TRANS': 488} Chain breaks: 1 Chain: "B" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1606 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 8, 'TRANS': 204} Chain: "C" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1597 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 8, 'TRANS': 203} Chain: "A" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 160 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 40 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.27, per 1000 atoms: 0.18 Number of scatterers: 7139 At special positions: 0 Unit cell: (65.6, 87.74, 113.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) V 1 22.97 S 21 16.00 P 9 15.00 Mg 2 11.99 O 1308 8.00 N 1240 7.00 C 4558 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=0, symmetry=0 Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 377.0 milliseconds 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1652 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 57.8% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 25 through 35 Processing helix chain 'A' and resid 39 through 48 removed outlier: 3.869A pdb=" N LEU A 43 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 48 " --> pdb=" O TRP A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 61 removed outlier: 3.835A pdb=" N GLU A 61 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 79 removed outlier: 3.750A pdb=" N ALA A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 88 removed outlier: 3.962A pdb=" N LEU A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 87 " --> pdb=" O GLN A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 100 Processing helix chain 'A' and resid 101 through 104 Processing helix chain 'A' and resid 105 through 129 removed outlier: 3.514A pdb=" N LEU A 109 " --> pdb=" O MET A 105 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 111 " --> pdb=" O HIS A 107 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ASP A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 removed outlier: 4.181A pdb=" N LEU A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 168 removed outlier: 3.642A pdb=" N GLY A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 199 removed outlier: 3.750A pdb=" N SER A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 178 " --> pdb=" O PRO A 174 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 193 " --> pdb=" O MET A 189 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 228 removed outlier: 3.519A pdb=" N VAL A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.909A pdb=" N TRP A 235 " --> pdb=" O THR A 232 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS A 236 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 276 removed outlier: 3.995A pdb=" N LEU A 258 " --> pdb=" O TRP A 254 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 308 Processing helix chain 'A' and resid 308 through 327 removed outlier: 3.598A pdb=" N VAL A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 332 removed outlier: 3.911A pdb=" N HIS A 331 " --> pdb=" O SER A 328 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY A 332 " --> pdb=" O VAL A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 328 through 332' Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 365 through 381 Processing helix chain 'A' and resid 381 through 389 Processing helix chain 'A' and resid 390 through 397 removed outlier: 4.350A pdb=" N THR A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 395 " --> pdb=" O ARG A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 437 removed outlier: 3.958A pdb=" N HIS A 409 " --> pdb=" O TRP A 405 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N MET A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 452 removed outlier: 4.394A pdb=" N THR A 445 " --> pdb=" O GLY A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 468 removed outlier: 4.547A pdb=" N LEU A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER A 461 " --> pdb=" O VAL A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 476 Proline residue: A 476 - end of helix Processing helix chain 'A' and resid 477 through 496 removed outlier: 4.865A pdb=" N SER A 493 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 540 removed outlier: 3.808A pdb=" N LEU A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 removed outlier: 3.515A pdb=" N THR B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU B 52 " --> pdb=" O LYS B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 108 removed outlier: 3.650A pdb=" N ILE B 103 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP B 104 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 126 removed outlier: 3.890A pdb=" N ALA B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 151 removed outlier: 3.505A pdb=" N LYS B 143 " --> pdb=" O GLY B 139 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 182 removed outlier: 3.745A pdb=" N GLN B 175 " --> pdb=" O GLU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 196 through 202 removed outlier: 3.717A pdb=" N ALA B 200 " --> pdb=" O ALA B 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.778A pdb=" N ARG C 82 " --> pdb=" O ASP C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 111 Processing helix chain 'C' and resid 114 through 126 removed outlier: 3.519A pdb=" N GLU C 120 " --> pdb=" O ALA C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 removed outlier: 3.667A pdb=" N TYR C 136 " --> pdb=" O ALA C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 151 removed outlier: 3.799A pdb=" N VAL C 144 " --> pdb=" O ASN C 140 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER C 145 " --> pdb=" O ARG C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 184 Processing helix chain 'C' and resid 194 through 202 removed outlier: 3.561A pdb=" N THR C 198 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU C 199 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA C 200 " --> pdb=" O ALA C 196 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 23 through 31 removed outlier: 3.550A pdb=" N LEU B 25 " --> pdb=" O LYS B 17 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LEU B 15 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASP B 29 " --> pdb=" O ARG B 13 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ARG B 13 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR B 31 " --> pdb=" O GLU B 11 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLU B 11 " --> pdb=" O THR B 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 85 through 87 removed outlier: 7.056A pdb=" N ALA B 85 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU B 157 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 215 " --> pdb=" O ILE B 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 15 through 18 removed outlier: 5.847A pdb=" N LEU C 15 " --> pdb=" O GLY C 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 37 through 39 removed outlier: 6.209A pdb=" N HIS C 38 " --> pdb=" O LEU C 190 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 85 through 87 removed outlier: 6.829A pdb=" N ALA C 85 " --> pdb=" O LEU C 158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 205 through 208 removed outlier: 6.750A pdb=" N VAL C 205 " --> pdb=" O SER C 216 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER C 216 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE C 207 " --> pdb=" O VAL C 214 " (cutoff:3.500A) 327 hydrogen bonds defined for protein. 954 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: 0.70 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 1805 1.33 - 1.48: 2215 1.48 - 1.62: 3204 1.62 - 1.76: 0 1.76 - 1.91: 40 Bond restraints: 7264 Sorted by residual: bond pdb=" C4 ADP B 402 " pdb=" C5 ADP B 402 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C5 ADP B 402 " pdb=" C6 ADP B 402 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" CA ALA A 281 " pdb=" CB ALA A 281 " ideal model delta sigma weight residual 1.531 1.478 0.053 1.48e-02 4.57e+03 1.27e+01 bond pdb=" CA SER B 49 " pdb=" CB SER B 49 " ideal model delta sigma weight residual 1.532 1.475 0.057 1.62e-02 3.81e+03 1.23e+01 bond pdb=" N VAL C 59 " pdb=" CA VAL C 59 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.14e-02 7.69e+03 8.74e+00 ... (remaining 7259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 9757 3.55 - 7.11: 90 7.11 - 10.66: 9 10.66 - 14.21: 2 14.21 - 17.77: 1 Bond angle restraints: 9859 Sorted by residual: angle pdb=" PB ATP C 402 " pdb=" O3B ATP C 402 " pdb=" PG ATP C 402 " ideal model delta sigma weight residual 139.87 122.10 17.77 1.00e+00 1.00e+00 3.16e+02 angle pdb=" N VAL A 60 " pdb=" CA VAL A 60 " pdb=" C VAL A 60 " ideal model delta sigma weight residual 113.71 107.82 5.89 9.50e-01 1.11e+00 3.84e+01 angle pdb=" C ARG A 402 " pdb=" CA ARG A 402 " pdb=" CB ARG A 402 " ideal model delta sigma weight residual 111.22 118.60 -7.38 1.24e+00 6.50e-01 3.54e+01 angle pdb=" PA ATP C 402 " pdb=" O3A ATP C 402 " pdb=" PB ATP C 402 " ideal model delta sigma weight residual 136.83 131.11 5.72 1.00e+00 1.00e+00 3.27e+01 angle pdb=" N ARG A 402 " pdb=" CA ARG A 402 " pdb=" C ARG A 402 " ideal model delta sigma weight residual 113.20 106.40 6.80 1.36e+00 5.41e-01 2.50e+01 ... (remaining 9854 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.51: 4105 25.51 - 51.02: 221 51.02 - 76.53: 31 76.53 - 102.04: 5 102.04 - 127.54: 2 Dihedral angle restraints: 4364 sinusoidal: 1767 harmonic: 2597 Sorted by residual: dihedral pdb=" C5' ADP B 402 " pdb=" O5' ADP B 402 " pdb=" PA ADP B 402 " pdb=" O2A ADP B 402 " ideal model delta sinusoidal sigma weight residual 300.00 172.46 127.54 1 2.00e+01 2.50e-03 3.86e+01 dihedral pdb=" CA CYS B 202 " pdb=" C CYS B 202 " pdb=" N GLU B 203 " pdb=" CA GLU B 203 " ideal model delta harmonic sigma weight residual 180.00 159.20 20.80 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA SER C 191 " pdb=" C SER C 191 " pdb=" N SER C 192 " pdb=" CA SER C 192 " ideal model delta harmonic sigma weight residual -180.00 -160.15 -19.85 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 4361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 984 0.060 - 0.119: 158 0.119 - 0.179: 17 0.179 - 0.238: 4 0.238 - 0.298: 1 Chirality restraints: 1164 Sorted by residual: chirality pdb=" CA VAL C 59 " pdb=" N VAL C 59 " pdb=" C VAL C 59 " pdb=" CB VAL C 59 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB VAL A 279 " pdb=" CA VAL A 279 " pdb=" CG1 VAL A 279 " pdb=" CG2 VAL A 279 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB4 CDL A 601 " pdb=" CB3 CDL A 601 " pdb=" CB6 CDL A 601 " pdb=" OB6 CDL A 601 " both_signs ideal model delta sigma weight residual False -2.61 -2.39 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1161 not shown) Planarity restraints: 1220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 400 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C VAL A 400 " 0.056 2.00e-02 2.50e+03 pdb=" O VAL A 400 " -0.022 2.00e-02 2.50e+03 pdb=" N SER A 401 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 138 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C LYS C 138 " -0.055 2.00e-02 2.50e+03 pdb=" O LYS C 138 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY C 139 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 58 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.14e+00 pdb=" C LEU C 58 " 0.039 2.00e-02 2.50e+03 pdb=" O LEU C 58 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL C 59 " -0.014 2.00e-02 2.50e+03 ... (remaining 1217 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 59 2.63 - 3.20: 6188 3.20 - 3.76: 10039 3.76 - 4.33: 14156 4.33 - 4.90: 24804 Nonbonded interactions: 55246 Sorted by model distance: nonbonded pdb=" OG SER C 49 " pdb="MG MG C 401 " model vdw 2.062 2.170 nonbonded pdb="MG MG B 401 " pdb=" O2 VO4 B 403 " model vdw 2.127 2.170 nonbonded pdb=" O SER C 163 " pdb=" OG SER C 163 " model vdw 2.301 3.040 nonbonded pdb=" OE2 GLU A 132 " pdb=" NH1 ARG C 53 " model vdw 2.305 3.120 nonbonded pdb=" O ILE B 147 " pdb=" OG SER B 151 " model vdw 2.320 3.040 ... (remaining 55241 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 Found NCS groups: ncs_group { reference = (chain 'B' and resid 8 through 401) selection = (chain 'C' and resid 8 through 401) } 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: 3.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.600 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 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 0.109 7264 Z= 0.341 Angle : 0.885 17.768 9859 Z= 0.507 Chirality : 0.047 0.298 1164 Planarity : 0.005 0.070 1220 Dihedral : 15.657 127.544 2712 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 0.14 % Allowed : 0.28 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.68 (0.27), residues: 926 helix: -0.11 (0.24), residues: 506 sheet: -2.30 (1.17), residues: 23 loop : -2.40 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 402 TYR 0.013 0.002 TYR A 64 PHE 0.022 0.002 PHE C 40 TRP 0.020 0.001 TRP A 44 HIS 0.005 0.001 HIS A 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00703 / 0.34 ( 7264) covalent geometry : angle 0.88460 / 0.51 ( 9859) hydrogen bonds : bond 0.16534 / 11.49 ( 327) hydrogen bonds : angle 6.61112 / 4.66 ( 954) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.199 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 0.0762 time to fit residues: 9.3325 Evaluate side-chains 75 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 193 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.114332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.095259 restraints weight = 8943.816| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.52 r_work: 0.2806 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7264 Z= 0.132 Angle : 0.593 6.872 9859 Z= 0.294 Chirality : 0.042 0.133 1164 Planarity : 0.004 0.049 1220 Dihedral : 11.874 90.664 1234 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.42 % Allowed : 5.10 % Favored : 94.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.21 (0.28), residues: 926 helix: 0.33 (0.24), residues: 521 sheet: -2.16 (1.11), residues: 23 loop : -2.37 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 402 TYR 0.017 0.001 TYR A 489 PHE 0.012 0.001 PHE C 40 TRP 0.019 0.001 TRP A 44 HIS 0.003 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 7264) covalent geometry : angle 0.59262 / 0.29 ( 9859) hydrogen bonds : bond 0.03965 / 2.59 ( 327) hydrogen bonds : angle 4.41376 / 3.17 ( 954) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.182 Fit side-chains REVERT: C 26 ASP cc_start: 0.7878 (t0) cc_final: 0.7628 (t0) outliers start: 3 outliers final: 2 residues processed: 80 average time/residue: 0.0719 time to fit residues: 7.8818 Evaluate side-chains 58 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 216 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 47 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 308 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.114073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.095071 restraints weight = 8963.998| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.49 r_work: 0.2804 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7264 Z= 0.135 Angle : 0.566 6.704 9859 Z= 0.281 Chirality : 0.041 0.128 1164 Planarity : 0.004 0.048 1220 Dihedral : 11.466 88.388 1234 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.85 % Allowed : 8.64 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.96 (0.28), residues: 926 helix: 0.55 (0.24), residues: 520 sheet: -1.98 (1.06), residues: 23 loop : -2.29 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 35 TYR 0.009 0.001 TYR A 489 PHE 0.010 0.001 PHE C 40 TRP 0.018 0.001 TRP A 44 HIS 0.003 0.001 HIS A 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 7264) covalent geometry : angle 0.56627 / 0.28 ( 9859) hydrogen bonds : bond 0.03774 / 2.46 ( 327) hydrogen bonds : angle 4.15402 / 2.99 ( 954) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.187 Fit side-chains REVERT: B 33 ARG cc_start: 0.8284 (mtp-110) cc_final: 0.7856 (ttm-80) REVERT: C 26 ASP cc_start: 0.7881 (t0) cc_final: 0.7606 (t0) outliers start: 6 outliers final: 3 residues processed: 72 average time/residue: 0.0782 time to fit residues: 7.6105 Evaluate side-chains 63 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain B residue 216 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 3 optimal weight: 0.0670 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 69 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.116138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.096674 restraints weight = 8978.494| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.55 r_work: 0.2827 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7264 Z= 0.103 Angle : 0.530 6.357 9859 Z= 0.262 Chirality : 0.040 0.123 1164 Planarity : 0.004 0.045 1220 Dihedral : 10.904 84.947 1234 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.27 % Allowed : 10.34 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.72 (0.28), residues: 926 helix: 0.75 (0.24), residues: 520 sheet: -2.08 (0.83), residues: 32 loop : -2.14 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 35 TYR 0.011 0.001 TYR A 64 PHE 0.009 0.001 PHE A 191 TRP 0.018 0.001 TRP A 44 HIS 0.002 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 ( 7264) covalent geometry : angle 0.52994 / 0.26 ( 9859) hydrogen bonds : bond 0.03140 / 2.04 ( 327) hydrogen bonds : angle 3.89435 / 2.81 ( 954) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.204 Fit side-chains REVERT: A 35 ARG cc_start: 0.8568 (ttt90) cc_final: 0.7690 (ttp-170) REVERT: A 83 GLN cc_start: 0.8683 (tp-100) cc_final: 0.8482 (tp40) REVERT: B 33 ARG cc_start: 0.8295 (mtp-110) cc_final: 0.7924 (tpp-160) REVERT: C 26 ASP cc_start: 0.7815 (t0) cc_final: 0.7552 (t0) REVERT: C 67 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7545 (ttm-80) REVERT: C 170 MET cc_start: 0.7447 (mmp) cc_final: 0.7240 (mmt) outliers start: 9 outliers final: 4 residues processed: 82 average time/residue: 0.0742 time to fit residues: 8.2458 Evaluate side-chains 71 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain C residue 193 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 0.0070 chunk 27 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.115510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.096083 restraints weight = 8926.851| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.54 r_work: 0.2816 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7264 Z= 0.116 Angle : 0.534 7.792 9859 Z= 0.264 Chirality : 0.040 0.123 1164 Planarity : 0.004 0.044 1220 Dihedral : 10.730 84.396 1234 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.99 % Allowed : 11.76 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.54 (0.28), residues: 926 helix: 0.89 (0.24), residues: 517 sheet: -1.84 (1.02), residues: 23 loop : -2.07 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 35 TYR 0.007 0.001 TYR A 432 PHE 0.008 0.001 PHE A 191 TRP 0.017 0.001 TRP A 44 HIS 0.002 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 7264) covalent geometry : angle 0.53374 / 0.26 ( 9859) hydrogen bonds : bond 0.03302 / 2.15 ( 327) hydrogen bonds : angle 3.83455 / 2.76 ( 954) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.266 Fit side-chains REVERT: A 35 ARG cc_start: 0.8564 (ttt90) cc_final: 0.7660 (ttp-170) REVERT: B 33 ARG cc_start: 0.8363 (mtp-110) cc_final: 0.7932 (tpp-160) REVERT: C 26 ASP cc_start: 0.7891 (t0) cc_final: 0.7626 (t0) REVERT: C 67 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7551 (ttm-80) outliers start: 7 outliers final: 6 residues processed: 81 average time/residue: 0.0669 time to fit residues: 7.4841 Evaluate side-chains 73 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 204 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 35 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.114990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.095735 restraints weight = 9053.547| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.51 r_work: 0.2810 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7264 Z= 0.124 Angle : 0.544 8.068 9859 Z= 0.267 Chirality : 0.040 0.123 1164 Planarity : 0.004 0.046 1220 Dihedral : 10.629 84.150 1234 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.27 % Allowed : 11.76 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.49 (0.28), residues: 926 helix: 0.97 (0.24), residues: 517 sheet: -2.02 (0.81), residues: 32 loop : -2.06 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 70 TYR 0.012 0.001 TYR A 64 PHE 0.009 0.001 PHE A 191 TRP 0.017 0.001 TRP A 44 HIS 0.003 0.001 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.12 ( 7264) covalent geometry : angle 0.54363 / 0.27 ( 9859) hydrogen bonds : bond 0.03377 / 2.20 ( 327) hydrogen bonds : angle 3.81682 / 2.75 ( 954) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.174 Fit side-chains REVERT: A 35 ARG cc_start: 0.8470 (ttt90) cc_final: 0.7609 (ttp-170) REVERT: B 33 ARG cc_start: 0.8322 (mtp-110) cc_final: 0.7947 (tpp-160) REVERT: C 67 ARG cc_start: 0.7964 (ttp80) cc_final: 0.7569 (ttm-80) REVERT: C 170 MET cc_start: 0.7526 (mmp) cc_final: 0.7303 (mmt) outliers start: 9 outliers final: 6 residues processed: 81 average time/residue: 0.0715 time to fit residues: 7.9240 Evaluate side-chains 75 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 204 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 83 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.111427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.091792 restraints weight = 9058.621| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.55 r_work: 0.2752 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 7264 Z= 0.220 Angle : 0.636 8.738 9859 Z= 0.313 Chirality : 0.044 0.141 1164 Planarity : 0.005 0.062 1220 Dihedral : 11.251 89.310 1234 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 1.13 % Allowed : 13.17 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.61 (0.28), residues: 926 helix: 0.80 (0.24), residues: 521 sheet: -1.62 (0.83), residues: 37 loop : -2.10 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 70 TYR 0.010 0.002 TYR B 86 PHE 0.012 0.002 PHE A 375 TRP 0.015 0.001 TRP A 44 HIS 0.005 0.001 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.22 ( 7264) covalent geometry : angle 0.63622 / 0.31 ( 9859) hydrogen bonds : bond 0.04527 / 2.94 ( 327) hydrogen bonds : angle 4.04544 / 2.90 ( 954) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.186 Fit side-chains REVERT: A 35 ARG cc_start: 0.8481 (ttt90) cc_final: 0.7638 (ttp-170) REVERT: B 33 ARG cc_start: 0.8395 (mtp-110) cc_final: 0.7952 (tpp-160) REVERT: C 67 ARG cc_start: 0.8031 (ttp80) cc_final: 0.7562 (ttm-80) outliers start: 8 outliers final: 5 residues processed: 75 average time/residue: 0.0696 time to fit residues: 7.0124 Evaluate side-chains 70 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain C residue 198 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 29 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 81 optimal weight: 0.0270 chunk 8 optimal weight: 0.0060 chunk 91 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.3454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.116419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.096831 restraints weight = 8930.071| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.53 r_work: 0.2828 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7264 Z= 0.099 Angle : 0.536 7.934 9859 Z= 0.265 Chirality : 0.039 0.124 1164 Planarity : 0.004 0.051 1220 Dihedral : 10.505 88.971 1234 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.99 % Allowed : 13.31 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.29 (0.28), residues: 926 helix: 1.17 (0.24), residues: 508 sheet: -1.73 (1.00), residues: 23 loop : -2.00 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 35 TYR 0.006 0.001 TYR A 64 PHE 0.008 0.001 PHE A 191 TRP 0.021 0.001 TRP A 44 HIS 0.002 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 7264) covalent geometry : angle 0.53595 / 0.26 ( 9859) hydrogen bonds : bond 0.02987 / 1.94 ( 327) hydrogen bonds : angle 3.78286 / 2.72 ( 954) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.169 Fit side-chains REVERT: A 35 ARG cc_start: 0.8464 (ttt90) cc_final: 0.7537 (ttp-170) REVERT: B 33 ARG cc_start: 0.8323 (mtp-110) cc_final: 0.7938 (tpp-160) REVERT: C 67 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7525 (ttm-80) REVERT: C 170 MET cc_start: 0.7497 (mmp) cc_final: 0.7126 (mmt) outliers start: 7 outliers final: 6 residues processed: 74 average time/residue: 0.0652 time to fit residues: 6.5770 Evaluate side-chains 72 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 204 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 57 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.0970 chunk 53 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 0.3980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.115861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.096430 restraints weight = 8864.466| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.53 r_work: 0.2821 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7264 Z= 0.111 Angle : 0.541 8.095 9859 Z= 0.267 Chirality : 0.040 0.123 1164 Planarity : 0.004 0.053 1220 Dihedral : 10.356 88.544 1234 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.99 % Allowed : 13.74 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.16 (0.28), residues: 926 helix: 1.25 (0.24), residues: 514 sheet: -1.70 (0.99), residues: 23 loop : -1.94 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 35 TYR 0.014 0.001 TYR A 64 PHE 0.008 0.001 PHE A 191 TRP 0.018 0.001 TRP A 44 HIS 0.002 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 7264) covalent geometry : angle 0.54131 / 0.27 ( 9859) hydrogen bonds : bond 0.03153 / 2.05 ( 327) hydrogen bonds : angle 3.75681 / 2.70 ( 954) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.158 Fit side-chains REVERT: A 35 ARG cc_start: 0.8448 (ttt90) cc_final: 0.7513 (ttp-170) REVERT: B 33 ARG cc_start: 0.8280 (mtp-110) cc_final: 0.7949 (tpp-160) REVERT: C 67 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7506 (ttm-80) REVERT: C 170 MET cc_start: 0.7473 (mmp) cc_final: 0.7105 (mmt) outliers start: 7 outliers final: 5 residues processed: 74 average time/residue: 0.0692 time to fit residues: 6.9959 Evaluate side-chains 74 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 204 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 86 optimal weight: 0.0870 chunk 75 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.114259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.095035 restraints weight = 8964.178| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.50 r_work: 0.2802 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7264 Z= 0.140 Angle : 0.568 8.315 9859 Z= 0.279 Chirality : 0.041 0.127 1164 Planarity : 0.004 0.053 1220 Dihedral : 10.499 85.320 1234 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.71 % Allowed : 14.02 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.21 (0.28), residues: 926 helix: 1.20 (0.24), residues: 514 sheet: -1.67 (0.99), residues: 23 loop : -1.96 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 70 TYR 0.008 0.001 TYR A 64 PHE 0.009 0.001 PHE A 191 TRP 0.017 0.001 TRP A 44 HIS 0.003 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 ( 7264) covalent geometry : angle 0.56815 / 0.28 ( 9859) hydrogen bonds : bond 0.03551 / 2.30 ( 327) hydrogen bonds : angle 3.81800 / 2.74 ( 954) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.164 Fit side-chains REVERT: A 35 ARG cc_start: 0.8467 (ttt90) cc_final: 0.7569 (ttp-170) REVERT: B 33 ARG cc_start: 0.8286 (mtp-110) cc_final: 0.7982 (tpp-160) REVERT: C 67 ARG cc_start: 0.7968 (ttp80) cc_final: 0.7509 (ttm-80) REVERT: C 170 MET cc_start: 0.7505 (mmp) cc_final: 0.7275 (mmt) outliers start: 5 outliers final: 5 residues processed: 72 average time/residue: 0.0740 time to fit residues: 7.2397 Evaluate side-chains 73 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 204 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.4980 chunk 65 optimal weight: 0.0040 chunk 41 optimal weight: 0.0170 chunk 18 optimal weight: 0.6980 chunk 51 optimal weight: 0.3980 chunk 84 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 57 optimal weight: 0.0370 chunk 45 optimal weight: 0.9990 overall best weight: 0.1908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.119429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.099964 restraints weight = 8772.772| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.51 r_work: 0.2875 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7264 Z= 0.090 Angle : 0.516 7.605 9859 Z= 0.254 Chirality : 0.038 0.120 1164 Planarity : 0.004 0.049 1220 Dihedral : 9.721 76.778 1234 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.57 % Allowed : 14.31 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.01 (0.29), residues: 926 helix: 1.41 (0.24), residues: 520 sheet: -1.54 (0.99), residues: 23 loop : -1.99 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 274 TYR 0.007 0.001 TYR A 432 PHE 0.009 0.001 PHE A 191 TRP 0.022 0.001 TRP A 44 HIS 0.002 0.000 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 ( 7264) covalent geometry : angle 0.51583 / 0.25 ( 9859) hydrogen bonds : bond 0.02484 / 1.62 ( 327) hydrogen bonds : angle 3.59705 / 2.59 ( 954) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1385.25 seconds wall clock time: 24 minutes 23.15 seconds (1463.15 seconds total)