Starting phenix.real_space_refine on Fri Oct 10 15:29:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1p_36798/10_2025/8k1p_36798.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1p_36798/10_2025/8k1p_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8k1p_36798/10_2025/8k1p_36798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1p_36798/10_2025/8k1p_36798.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1p_36798/10_2025/8k1p_36798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1p_36798/10_2025/8k1p_36798.cif" } 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-2.0-5842/lib/python3.9/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: 2.00, per 1000 atoms: 0.28 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: 0.66 Conformation dependent library (CDL) restraints added in 394.9 milliseconds Enol-peptide restraints added in 12.4 microseconds 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: 0.22 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: 1.05 Time building geometry restraints manager: 0.87 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=" OB3 CDL A 601 " pdb=" PB2 CDL A 601 " ideal model delta sigma weight residual 1.529 1.495 0.034 1.00e-02 1.00e+04 1.14e+01 ... (remaining 7259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 9767 3.55 - 7.11: 81 7.11 - 10.66: 8 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: 4036 25.51 - 51.02: 244 51.02 - 76.53: 46 76.53 - 102.04: 5 102.04 - 127.54: 1 Dihedral angle restraints: 4332 sinusoidal: 1735 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 4329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 983 0.060 - 0.119: 159 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=" CA4 CDL A 601 " pdb=" CA3 CDL A 601 " pdb=" CA6 CDL A 601 " pdb=" OA6 CDL A 601 " both_signs ideal model delta sigma weight residual False -2.57 -2.38 -0.19 2.00e-01 2.50e+01 9.19e-01 ... (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: 3.580 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.360 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 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= 0.321 Angle : 0.862 17.768 9859 Z= 0.511 Chirality : 0.047 0.298 1164 Planarity : 0.005 0.070 1220 Dihedral : 16.577 127.544 2680 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 aren 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 covalent geometry : bond 0.00650 ( 7264) covalent geometry : angle 0.86168 ( 9859) hydrogen bonds : bond 0.16534 ( 327) hydrogen bonds : angle 6.61112 ( 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 : 0.236 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 0.0855 time to fit residues: 10.3037 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 : 0.253 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 331 HIS C 193 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.114460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.095337 restraints weight = 8908.499| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.53 r_work: 0.2807 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1005 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 7.078 9859 Z= 0.296 Chirality : 0.042 0.144 1164 Planarity : 0.005 0.050 1220 Dihedral : 13.732 91.768 1202 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.06 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 aren not related in a simple way. whole: -1.20 (0.28), residues: 926 helix: 0.34 (0.24), residues: 520 sheet: -2.16 (1.11), residues: 23 loop : -2.36 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 402 TYR 0.016 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 covalent geometry : bond 0.00315 ( 7264) covalent geometry : angle 0.59316 ( 9859) hydrogen bonds : bond 0.03936 ( 327) hydrogen bonds : angle 4.41257 ( 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 : 0.217 Fit side-chains REVERT: A 430 LEU cc_start: 0.8099 (tt) cc_final: 0.7869 (tp) REVERT: C 26 ASP cc_start: 0.7852 (t0) cc_final: 0.7605 (t0) outliers start: 3 outliers final: 2 residues processed: 80 average time/residue: 0.0835 time to fit residues: 9.2594 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 : 0.260 ------------------------------------------------------------------------------- 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: 2.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.113999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.095056 restraints weight = 8918.079| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.48 r_work: 0.2804 rms_B_bonded: 2.12 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: 0.8541 moved from start: 0.1285 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= 0.138 Angle : 0.568 6.794 9859 Z= 0.283 Chirality : 0.041 0.130 1164 Planarity : 0.004 0.048 1220 Dihedral : 12.698 74.833 1202 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.71 % Allowed : 9.07 % Favored : 90.23 % 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 aren not related in a simple way. whole: -0.98 (0.28), residues: 926 helix: 0.54 (0.24), residues: 520 sheet: -2.03 (1.06), residues: 23 loop : -2.29 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 35 TYR 0.009 0.001 TYR A 489 PHE 0.012 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 covalent geometry : bond 0.00339 ( 7264) covalent geometry : angle 0.56837 ( 9859) hydrogen bonds : bond 0.03830 ( 327) hydrogen bonds : angle 4.16012 ( 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: 5 poor density : 69 time to evaluate : 0.251 Fit side-chains REVERT: B 33 ARG cc_start: 0.8288 (mtp-110) cc_final: 0.7869 (ttm-80) REVERT: C 26 ASP cc_start: 0.7894 (t0) cc_final: 0.7617 (t0) outliers start: 5 outliers final: 3 residues processed: 72 average time/residue: 0.0966 time to fit residues: 9.3845 Evaluate side-chains 64 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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: 0.9990 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 chunk 69 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 14 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.115004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.095618 restraints weight = 8970.014| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.54 r_work: 0.2812 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1514 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= 0.121 Angle : 0.545 7.322 9859 Z= 0.269 Chirality : 0.040 0.129 1164 Planarity : 0.004 0.044 1220 Dihedral : 12.029 73.330 1202 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.13 % Allowed : 10.48 % 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 aren not related in a simple way. whole: -0.77 (0.28), residues: 926 helix: 0.68 (0.24), residues: 521 sheet: -1.91 (1.03), residues: 23 loop : -2.15 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 35 TYR 0.007 0.001 TYR A 489 PHE 0.009 0.001 PHE A 191 TRP 0.018 0.001 TRP A 44 HIS 0.003 0.001 HIS B 81 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 7264) covalent geometry : angle 0.54535 ( 9859) hydrogen bonds : bond 0.03388 ( 327) hydrogen bonds : angle 3.92464 ( 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 81 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.274 Fit side-chains REVERT: A 35 ARG cc_start: 0.8564 (ttt90) cc_final: 0.7694 (ttp-170) REVERT: B 33 ARG cc_start: 0.8312 (mtp-110) cc_final: 0.7946 (tpp-160) REVERT: C 26 ASP cc_start: 0.7847 (t0) cc_final: 0.7587 (t0) REVERT: C 67 ARG cc_start: 0.7958 (ttp80) cc_final: 0.7551 (ttm-80) REVERT: C 170 MET cc_start: 0.7482 (mmp) cc_final: 0.7271 (mmt) outliers start: 8 outliers final: 3 residues processed: 79 average time/residue: 0.0955 time to fit residues: 10.1380 Evaluate side-chains 70 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU 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: 0.7980 chunk 85 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 72 optimal weight: 0.0000 chunk 27 optimal weight: 0.0370 chunk 83 optimal weight: 2.9990 overall best weight: 0.4662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.116314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.097832 restraints weight = 8861.998| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.44 r_work: 0.2844 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1692 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= 0.105 Angle : 0.519 6.095 9859 Z= 0.258 Chirality : 0.039 0.122 1164 Planarity : 0.004 0.043 1220 Dihedral : 11.594 79.305 1202 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % 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 aren not related in a simple way. whole: -0.53 (0.28), residues: 926 helix: 0.92 (0.24), residues: 518 sheet: -1.79 (1.04), residues: 23 loop : -2.11 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 35 TYR 0.006 0.001 TYR A 489 PHE 0.008 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 covalent geometry : bond 0.00248 ( 7264) covalent geometry : angle 0.51942 ( 9859) hydrogen bonds : bond 0.03082 ( 327) hydrogen bonds : angle 3.79095 ( 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 82 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.316 Fit side-chains REVERT: A 35 ARG cc_start: 0.8585 (ttt90) cc_final: 0.7742 (ttp-170) REVERT: B 33 ARG cc_start: 0.8305 (mtp-110) cc_final: 0.7918 (tpp-160) REVERT: C 26 ASP cc_start: 0.7857 (t0) cc_final: 0.7656 (t0) REVERT: C 67 ARG cc_start: 0.7926 (ttp80) cc_final: 0.7557 (ttm-80) outliers start: 7 outliers final: 4 residues processed: 80 average time/residue: 0.0929 time to fit residues: 10.0824 Evaluate side-chains 70 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 60 optimal weight: 0.0010 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 48 optimal weight: 0.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.116236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.097709 restraints weight = 8976.225| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.45 r_work: 0.2843 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1811 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= 0.105 Angle : 0.518 8.080 9859 Z= 0.256 Chirality : 0.039 0.123 1164 Planarity : 0.004 0.042 1220 Dihedral : 11.461 85.827 1202 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.13 % Allowed : 12.32 % Favored : 86.54 % 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 aren not related in a simple way. whole: -0.41 (0.28), residues: 926 helix: 1.05 (0.24), residues: 518 sheet: -1.91 (0.84), residues: 32 loop : -2.07 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 35 TYR 0.016 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 covalent geometry : bond 0.00250 ( 7264) covalent geometry : angle 0.51758 ( 9859) hydrogen bonds : bond 0.03061 ( 327) hydrogen bonds : angle 3.73469 ( 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 86 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.315 Fit side-chains REVERT: A 35 ARG cc_start: 0.8532 (ttt90) cc_final: 0.7693 (ttp-170) REVERT: B 33 ARG cc_start: 0.8273 (mtp-110) cc_final: 0.7939 (tpp-160) REVERT: C 67 ARG cc_start: 0.7911 (ttp80) cc_final: 0.7553 (ttm-80) outliers start: 8 outliers final: 6 residues processed: 84 average time/residue: 0.0940 time to fit residues: 10.7039 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 : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.0070 chunk 74 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 0.0870 chunk 56 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.116020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.096749 restraints weight = 8885.994| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.53 r_work: 0.2827 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1845 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= 0.112 Angle : 0.532 7.953 9859 Z= 0.261 Chirality : 0.040 0.123 1164 Planarity : 0.004 0.050 1220 Dihedral : 11.417 88.673 1202 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.13 % Allowed : 12.89 % Favored : 85.98 % 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 aren not related in a simple way. whole: -0.32 (0.28), residues: 926 helix: 1.10 (0.24), residues: 523 sheet: -1.77 (0.84), residues: 32 loop : -2.05 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 35 TYR 0.013 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 C 38 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7264) covalent geometry : angle 0.53182 ( 9859) hydrogen bonds : bond 0.03146 ( 327) hydrogen bonds : angle 3.72623 ( 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 83 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.257 Fit side-chains REVERT: A 35 ARG cc_start: 0.8486 (ttt90) cc_final: 0.7639 (ttp-170) REVERT: B 33 ARG cc_start: 0.8257 (mtp-110) cc_final: 0.7897 (tpp-160) REVERT: C 67 ARG cc_start: 0.7935 (ttp80) cc_final: 0.7532 (ttm-80) REVERT: C 170 MET cc_start: 0.7561 (mmp) cc_final: 0.7292 (mmt) outliers start: 8 outliers final: 7 residues processed: 81 average time/residue: 0.0945 time to fit residues: 10.3912 Evaluate side-chains 74 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 28 LEU Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 204 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 81 optimal weight: 0.0870 chunk 8 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 46 optimal weight: 0.1980 chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.116816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.097600 restraints weight = 8903.286| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.52 r_work: 0.2838 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1947 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= 0.105 Angle : 0.527 7.734 9859 Z= 0.260 Chirality : 0.039 0.122 1164 Planarity : 0.004 0.047 1220 Dihedral : 11.265 87.295 1202 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.27 % Allowed : 13.03 % 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 aren not related in a simple way. whole: -0.20 (0.28), residues: 926 helix: 1.20 (0.24), residues: 522 sheet: -1.47 (1.05), residues: 23 loop : -2.03 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 35 TYR 0.016 0.001 TYR A 432 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 covalent geometry : bond 0.00248 ( 7264) covalent geometry : angle 0.52735 ( 9859) hydrogen bonds : bond 0.02972 ( 327) hydrogen bonds : angle 3.68597 ( 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 77 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.250 Fit side-chains REVERT: A 35 ARG cc_start: 0.8470 (ttt90) cc_final: 0.7566 (ttp-170) REVERT: B 33 ARG cc_start: 0.8249 (mtp-110) cc_final: 0.7915 (tpp-160) REVERT: C 67 ARG cc_start: 0.7943 (ttp80) cc_final: 0.7529 (ttm-80) REVERT: C 170 MET cc_start: 0.7507 (mmp) cc_final: 0.7291 (mmt) outliers start: 9 outliers final: 7 residues processed: 75 average time/residue: 0.0968 time to fit residues: 9.8537 Evaluate side-chains 74 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 28 LEU Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 198 THR 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: 0.0030 chunk 48 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 74 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 0.0270 overall best weight: 0.3048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.118278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.099215 restraints weight = 8774.880| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.51 r_work: 0.2863 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2082 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= 0.094 Angle : 0.513 7.451 9859 Z= 0.253 Chirality : 0.039 0.119 1164 Planarity : 0.004 0.046 1220 Dihedral : 10.966 80.726 1202 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.99 % Allowed : 13.46 % Favored : 85.55 % 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 aren not related in a simple way. whole: -0.06 (0.28), residues: 926 helix: 1.37 (0.24), residues: 519 sheet: -1.38 (1.05), residues: 23 loop : -2.03 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 35 TYR 0.015 0.001 TYR A 432 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 covalent geometry : bond 0.00214 ( 7264) covalent geometry : angle 0.51341 ( 9859) hydrogen bonds : bond 0.02673 ( 327) hydrogen bonds : angle 3.59656 ( 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 78 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.254 Fit side-chains REVERT: A 35 ARG cc_start: 0.8461 (ttt90) cc_final: 0.7500 (ttp-170) REVERT: B 33 ARG cc_start: 0.8211 (mtp-110) cc_final: 0.7908 (tpp-160) REVERT: C 67 ARG cc_start: 0.7883 (ttp80) cc_final: 0.7420 (ttm-80) outliers start: 7 outliers final: 6 residues processed: 76 average time/residue: 0.0938 time to fit residues: 9.5980 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 : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 28 LEU Chi-restraints excluded: chain C residue 193 HIS 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: 1.9990 chunk 52 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 4 optimal weight: 0.1980 chunk 68 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.115810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.096558 restraints weight = 8878.541| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.52 r_work: 0.2821 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2003 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= 0.120 Angle : 0.533 7.907 9859 Z= 0.264 Chirality : 0.040 0.123 1164 Planarity : 0.004 0.046 1220 Dihedral : 11.160 88.702 1202 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.71 % Allowed : 14.31 % Favored : 84.99 % 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 aren not related in a simple way. whole: -0.09 (0.28), residues: 926 helix: 1.30 (0.24), residues: 522 sheet: -1.38 (1.05), residues: 23 loop : -2.00 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 35 TYR 0.013 0.001 TYR A 432 PHE 0.007 0.001 PHE A 191 TRP 0.016 0.001 TRP A 44 HIS 0.003 0.001 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7264) covalent geometry : angle 0.53315 ( 9859) hydrogen bonds : bond 0.03210 ( 327) hydrogen bonds : angle 3.69120 ( 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 : 0.248 Fit side-chains REVERT: A 35 ARG cc_start: 0.8470 (ttt90) cc_final: 0.7513 (ttp-170) REVERT: B 33 ARG cc_start: 0.8216 (mtp-110) cc_final: 0.7910 (tpp-160) REVERT: C 67 ARG cc_start: 0.7917 (ttp80) cc_final: 0.7451 (ttm-80) outliers start: 5 outliers final: 5 residues processed: 71 average time/residue: 0.0983 time to fit residues: 9.4106 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 : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 198 THR 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: 2.9990 chunk 65 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 chunk 18 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 48 optimal weight: 0.4980 chunk 57 optimal weight: 0.0370 chunk 45 optimal weight: 1.9990 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.117513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.099149 restraints weight = 8830.410| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.42 r_work: 0.2862 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2095 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= 0.101 Angle : 0.527 7.924 9859 Z= 0.259 Chirality : 0.039 0.123 1164 Planarity : 0.004 0.045 1220 Dihedral : 10.937 84.157 1202 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.71 % Allowed : 14.45 % Favored : 84.84 % 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 aren not related in a simple way. whole: 0.02 (0.28), residues: 926 helix: 1.43 (0.24), residues: 520 sheet: -1.23 (1.05), residues: 23 loop : -2.00 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 35 TYR 0.014 0.001 TYR A 432 PHE 0.007 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 covalent geometry : bond 0.00236 ( 7264) covalent geometry : angle 0.52659 ( 9859) hydrogen bonds : bond 0.02831 ( 327) hydrogen bonds : angle 3.57498 ( 954) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1842.03 seconds wall clock time: 32 minutes 15.13 seconds (1935.13 seconds total)