Starting phenix.real_space_refine on Wed Feb 4 07:16:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nk8_49496/02_2026/9nk8_49496.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nk8_49496/02_2026/9nk8_49496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nk8_49496/02_2026/9nk8_49496.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nk8_49496/02_2026/9nk8_49496.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nk8_49496/02_2026/9nk8_49496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nk8_49496/02_2026/9nk8_49496.map" } resolution = 3.0 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= 0.004 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: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 5863 2.51 5 N 1551 2.21 5 O 1635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9064 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2430 Classifications: {'peptide': 311} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 285} Chain breaks: 1 Chain: "B" Number of atoms: 3529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3529 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 28, 'TRANS': 448} Chain: "C" Number of atoms: 2687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2687 Classifications: {'peptide': 354} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 326} Chain breaks: 4 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 70 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'UX8:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 232 Unusual residues: {'ERG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 116 Unusual residues: {'ERG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.57, per 1000 atoms: 0.17 Number of scatterers: 9064 At special positions: 0 Unit cell: (77.19, 107.9, 130.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 1635 8.00 N 1551 7.00 C 5863 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 328.4 milliseconds 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 7 sheets defined 43.1% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 16 through 25 removed outlier: 3.684A pdb=" N LEU A 20 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ARG A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N LEU A 23 " --> pdb=" O PRO A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 46 removed outlier: 3.713A pdb=" N SER A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 64 removed outlier: 3.838A pdb=" N LEU A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 82 removed outlier: 4.030A pdb=" N TRP A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 122 through 130 removed outlier: 3.520A pdb=" N LYS A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 150 through 162 removed outlier: 3.620A pdb=" N ALA A 155 " --> pdb=" O PRO A 151 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 178 through 187 Processing helix chain 'A' and resid 193 through 214 Processing helix chain 'A' and resid 230 through 234 Processing helix chain 'A' and resid 235 through 257 removed outlier: 3.820A pdb=" N SER A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 269 through 286 removed outlier: 4.024A pdb=" N TYR A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 308 removed outlier: 3.508A pdb=" N LYS A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 325 Processing helix chain 'B' and resid 37 through 42 removed outlier: 3.687A pdb=" N THR B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 72 removed outlier: 3.768A pdb=" N GLN B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 78 through 96 removed outlier: 3.927A pdb=" N GLN B 82 " --> pdb=" O THR B 78 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 211 through 214 Processing helix chain 'B' and resid 255 through 261 Processing helix chain 'B' and resid 446 through 462 removed outlier: 3.593A pdb=" N LEU B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 32 Processing helix chain 'C' and resid 43 through 47 Processing helix chain 'C' and resid 66 through 75 Processing helix chain 'C' and resid 105 through 122 Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 134 through 141 removed outlier: 3.628A pdb=" N ALA C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 148 Processing helix chain 'C' and resid 153 through 156 removed outlier: 3.922A pdb=" N TRP C 156 " --> pdb=" O PRO C 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 153 through 156' Processing helix chain 'C' and resid 157 through 170 removed outlier: 3.533A pdb=" N ALA C 161 " --> pdb=" O THR C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 174 Processing helix chain 'C' and resid 176 through 181 Processing helix chain 'C' and resid 234 through 254 removed outlier: 3.594A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 284 removed outlier: 3.629A pdb=" N LEU C 281 " --> pdb=" O GLY C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 300 Processing helix chain 'C' and resid 300 through 315 Processing helix chain 'C' and resid 316 through 320 Processing helix chain 'C' and resid 324 through 327 Processing helix chain 'C' and resid 328 through 333 removed outlier: 3.971A pdb=" N ALA C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 337 Processing helix chain 'C' and resid 338 through 352 removed outlier: 3.739A pdb=" N ALA C 352 " --> pdb=" O ARG C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 377 removed outlier: 4.056A pdb=" N TRP C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 406 removed outlier: 4.059A pdb=" N PHE C 406 " --> pdb=" O ALA C 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 402 through 406' Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.108A pdb=" N ARG A 30 " --> pdb=" O LEU B 493 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.108A pdb=" N ARG A 30 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 470 " --> pdb=" O LEU B 489 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU B 468 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN B 402 " --> pdb=" O GLY B 336 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY B 318 " --> pdb=" O GLY B 337 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY B 288 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY B 263 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ASP B 196 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LEU B 197 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLU B 167 " --> pdb=" O ASN B 161 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE B 140 " --> pdb=" O LYS D 5 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 90 removed outlier: 3.587A pdb=" N PHE A 103 " --> pdb=" O TYR A 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 106 through 107 Processing sheet with id=AA5, first strand: chain 'B' and resid 106 through 107 removed outlier: 5.458A pdb=" N ILE B 46 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N ILE B 128 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N THR B 48 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N ILE B 130 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLU B 50 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 385 through 386 Processing sheet with id=AA7, first strand: chain 'C' and resid 37 through 41 465 hydrogen bonds defined for protein. 1293 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: 1.10 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2942 1.34 - 1.46: 1587 1.46 - 1.57: 4762 1.57 - 1.69: 0 1.69 - 1.81: 25 Bond restraints: 9316 Sorted by residual: bond pdb=" N VAL A 223 " pdb=" CA VAL A 223 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.30e-02 5.92e+03 8.50e+00 bond pdb=" N ILE A 222 " pdb=" CA ILE A 222 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.28e-02 6.10e+03 7.67e+00 bond pdb=" N HIS B 39 " pdb=" CA HIS B 39 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.30e-02 5.92e+03 5.63e+00 bond pdb=" N LEU B 41 " pdb=" CA LEU B 41 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.33e-02 5.65e+03 5.06e+00 bond pdb=" CA SER A 224 " pdb=" CB SER A 224 " ideal model delta sigma weight residual 1.534 1.505 0.029 1.34e-02 5.57e+03 4.70e+00 ... (remaining 9311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 12490 1.83 - 3.66: 221 3.66 - 5.49: 38 5.49 - 7.31: 12 7.31 - 9.14: 6 Bond angle restraints: 12767 Sorted by residual: angle pdb=" N VAL A 223 " pdb=" CA VAL A 223 " pdb=" C VAL A 223 " ideal model delta sigma weight residual 111.81 108.59 3.22 8.60e-01 1.35e+00 1.41e+01 angle pdb=" CB LYS C 380 " pdb=" CG LYS C 380 " pdb=" CD LYS C 380 " ideal model delta sigma weight residual 111.30 118.73 -7.43 2.30e+00 1.89e-01 1.04e+01 angle pdb=" CB MET B 283 " pdb=" CG MET B 283 " pdb=" SD MET B 283 " ideal model delta sigma weight residual 112.70 103.56 9.14 3.00e+00 1.11e-01 9.29e+00 angle pdb=" N VAL C 404 " pdb=" CA VAL C 404 " pdb=" C VAL C 404 " ideal model delta sigma weight residual 113.47 110.49 2.98 1.01e+00 9.80e-01 8.71e+00 angle pdb=" CA GLN C 317 " pdb=" C GLN C 317 " pdb=" O GLN C 317 " ideal model delta sigma weight residual 122.03 118.35 3.68 1.25e+00 6.40e-01 8.67e+00 ... (remaining 12762 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 5599 16.65 - 33.29: 376 33.29 - 49.94: 100 49.94 - 66.58: 20 66.58 - 83.23: 13 Dihedral angle restraints: 6108 sinusoidal: 2842 harmonic: 3266 Sorted by residual: dihedral pdb=" CA HIS B 478 " pdb=" C HIS B 478 " pdb=" N PRO B 479 " pdb=" CA PRO B 479 " ideal model delta harmonic sigma weight residual 180.00 -155.22 -24.78 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA PRO C 151 " pdb=" C PRO C 151 " pdb=" N LEU C 152 " pdb=" CA LEU C 152 " ideal model delta harmonic sigma weight residual -180.00 -157.91 -22.09 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ASN B 423 " pdb=" CB ASN B 423 " pdb=" CG ASN B 423 " pdb=" OD1 ASN B 423 " ideal model delta sinusoidal sigma weight residual 120.00 -170.44 -69.56 2 2.00e+01 2.50e-03 1.05e+01 ... (remaining 6105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1144 0.046 - 0.092: 223 0.092 - 0.138: 73 0.138 - 0.184: 6 0.184 - 0.230: 2 Chirality restraints: 1448 Sorted by residual: chirality pdb=" CA ILE A 222 " pdb=" N ILE A 222 " pdb=" C ILE A 222 " pdb=" CB ILE A 222 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C20 ERG B 601 " pdb=" C17 ERG B 601 " pdb=" C21 ERG B 601 " pdb=" C22 ERG B 601 " both_signs ideal model delta sigma weight residual False 2.58 2.39 0.19 2.00e-01 2.50e+01 8.76e-01 chirality pdb=" CA PRO B 479 " pdb=" N PRO B 479 " pdb=" C PRO B 479 " pdb=" CB PRO B 479 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.94e-01 ... (remaining 1445 not shown) Planarity restraints: 1601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 14 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO C 15 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 15 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 15 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 159 " -0.024 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO C 160 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 160 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 160 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 405 " 0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO B 406 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 406 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 406 " 0.016 5.00e-02 4.00e+02 ... (remaining 1598 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2595 2.81 - 3.34: 8433 3.34 - 3.86: 14259 3.86 - 4.38: 17199 4.38 - 4.90: 29525 Nonbonded interactions: 72011 Sorted by model distance: nonbonded pdb=" N SER B 45 " pdb=" O THR B 124 " model vdw 2.293 3.120 nonbonded pdb=" NE1 TRP D 1 " pdb=" O9 UX8 D 3 " model vdw 2.304 2.496 nonbonded pdb=" NE2 GLN B 246 " pdb=" OD1 ASP B 264 " model vdw 2.321 3.120 nonbonded pdb=" NH1 ARG A 62 " pdb=" OE1 GLU B 441 " model vdw 2.333 3.120 nonbonded pdb=" OH TYR B 421 " pdb=" OG SER B 488 " model vdw 2.341 3.040 ... (remaining 72006 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.360 Find NCS groups from input model: 0.050 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:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 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 : 0.004 0.074 9318 Z= 0.205 Angle : 0.652 9.144 12767 Z= 0.337 Chirality : 0.042 0.230 1448 Planarity : 0.004 0.038 1601 Dihedral : 12.413 83.229 4010 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.33 % Allowed : 11.59 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 1.04 (0.25), residues: 1128 helix: 0.82 (0.27), residues: 375 sheet: 1.38 (0.36), residues: 204 loop : 0.47 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 96 TYR 0.018 0.001 TYR C 138 PHE 0.017 0.001 PHE D 7 TRP 0.008 0.001 TRP C 8 HIS 0.007 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 9316) covalent geometry : angle 0.65206 (12767) hydrogen bonds : bond 0.22491 ( 463) hydrogen bonds : angle 7.55462 ( 1293) Misc. bond : bond 0.05228 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 LEU cc_start: 0.9337 (pp) cc_final: 0.9120 (tm) outliers start: 3 outliers final: 3 residues processed: 73 average time/residue: 0.4963 time to fit residues: 39.1457 Evaluate side-chains 60 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain D residue 1 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 211 GLN B 52 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.095996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.064316 restraints weight = 19370.988| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 3.33 r_work: 0.2767 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9318 Z= 0.129 Angle : 0.615 10.997 12767 Z= 0.297 Chirality : 0.042 0.190 1448 Planarity : 0.005 0.042 1601 Dihedral : 6.826 72.116 2060 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.78 % Allowed : 11.93 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 1.27 (0.25), residues: 1128 helix: 1.42 (0.26), residues: 399 sheet: 1.30 (0.36), residues: 203 loop : 0.31 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 96 TYR 0.017 0.001 TYR C 138 PHE 0.017 0.001 PHE B 163 TRP 0.007 0.001 TRP C 360 HIS 0.006 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9316) covalent geometry : angle 0.61464 (12767) hydrogen bonds : bond 0.04217 ( 463) hydrogen bonds : angle 5.15791 ( 1293) Misc. bond : bond 0.00073 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6349 (OUTLIER) REVERT: B 108 PHE cc_start: 0.8762 (m-10) cc_final: 0.8476 (m-10) REVERT: B 246 GLN cc_start: 0.9100 (tt0) cc_final: 0.8814 (tt0) outliers start: 16 outliers final: 8 residues processed: 80 average time/residue: 0.4242 time to fit residues: 36.9312 Evaluate side-chains 64 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 1 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 111 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN B 56 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.095181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.063911 restraints weight = 19288.420| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.25 r_work: 0.2753 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 9318 Z= 0.255 Angle : 0.650 8.822 12767 Z= 0.312 Chirality : 0.044 0.207 1448 Planarity : 0.005 0.044 1601 Dihedral : 7.066 72.227 2058 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.12 % Allowed : 12.93 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 1.24 (0.25), residues: 1128 helix: 1.58 (0.27), residues: 402 sheet: 1.07 (0.35), residues: 219 loop : 0.20 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 86 TYR 0.018 0.002 TYR C 138 PHE 0.014 0.001 PHE B 163 TRP 0.008 0.001 TRP C 360 HIS 0.004 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00594 ( 9316) covalent geometry : angle 0.64964 (12767) hydrogen bonds : bond 0.04024 ( 463) hydrogen bonds : angle 4.81121 ( 1293) Misc. bond : bond 0.00098 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6445 (OUTLIER) REVERT: B 108 PHE cc_start: 0.8774 (m-10) cc_final: 0.8463 (m-10) REVERT: B 246 GLN cc_start: 0.9159 (tt0) cc_final: 0.8885 (tt0) REVERT: B 373 ASP cc_start: 0.8749 (m-30) cc_final: 0.8472 (m-30) outliers start: 19 outliers final: 10 residues processed: 74 average time/residue: 0.4036 time to fit residues: 32.7559 Evaluate side-chains 65 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain D residue 6 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 48 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.096110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.064821 restraints weight = 19546.962| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.27 r_work: 0.2785 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9318 Z= 0.134 Angle : 0.612 9.518 12767 Z= 0.287 Chirality : 0.042 0.205 1448 Planarity : 0.004 0.043 1601 Dihedral : 6.797 71.795 2056 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.01 % Allowed : 13.49 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 1.34 (0.25), residues: 1128 helix: 1.77 (0.27), residues: 400 sheet: 1.01 (0.35), residues: 216 loop : 0.23 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.017 0.001 TYR B 183 PHE 0.012 0.001 PHE B 396 TRP 0.038 0.001 TRP D 1 HIS 0.004 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9316) covalent geometry : angle 0.61224 (12767) hydrogen bonds : bond 0.03264 ( 463) hydrogen bonds : angle 4.62362 ( 1293) Misc. bond : bond 0.00434 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6448 (OUTLIER) REVERT: B 108 PHE cc_start: 0.8789 (m-10) cc_final: 0.8414 (m-10) REVERT: B 246 GLN cc_start: 0.9120 (tt0) cc_final: 0.8827 (tt0) REVERT: B 373 ASP cc_start: 0.8666 (m-30) cc_final: 0.8400 (m-30) REVERT: C 317 GLN cc_start: 0.8224 (tm-30) cc_final: 0.7797 (tm-30) outliers start: 18 outliers final: 10 residues processed: 75 average time/residue: 0.3973 time to fit residues: 32.6287 Evaluate side-chains 66 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 1 TRP Chi-restraints excluded: chain D residue 6 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 72 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.096285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.064810 restraints weight = 19502.827| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.31 r_work: 0.2752 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9318 Z= 0.167 Angle : 0.617 8.960 12767 Z= 0.290 Chirality : 0.042 0.204 1448 Planarity : 0.004 0.043 1601 Dihedral : 6.812 71.841 2056 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.45 % Allowed : 13.38 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 1.33 (0.25), residues: 1128 helix: 1.81 (0.27), residues: 403 sheet: 0.93 (0.34), residues: 218 loop : 0.20 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.013 0.001 TYR B 183 PHE 0.012 0.001 PHE B 396 TRP 0.040 0.001 TRP D 1 HIS 0.004 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 9316) covalent geometry : angle 0.61677 (12767) hydrogen bonds : bond 0.03175 ( 463) hydrogen bonds : angle 4.48463 ( 1293) Misc. bond : bond 0.00423 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6499 (OUTLIER) REVERT: B 108 PHE cc_start: 0.8881 (m-10) cc_final: 0.8434 (m-10) REVERT: B 204 LEU cc_start: 0.9134 (tp) cc_final: 0.8816 (pp) REVERT: B 246 GLN cc_start: 0.9112 (tt0) cc_final: 0.8825 (tt0) REVERT: B 283 MET cc_start: 0.8949 (tpt) cc_final: 0.8708 (tpt) REVERT: B 373 ASP cc_start: 0.8689 (m-30) cc_final: 0.8385 (m-30) REVERT: C 317 GLN cc_start: 0.8242 (tm-30) cc_final: 0.7737 (tm-30) outliers start: 22 outliers final: 13 residues processed: 80 average time/residue: 0.3305 time to fit residues: 29.1469 Evaluate side-chains 71 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 1 TRP Chi-restraints excluded: chain D residue 6 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 40 optimal weight: 3.9990 chunk 77 optimal weight: 0.0270 chunk 11 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 chunk 80 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 overall best weight: 0.8442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.097305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.065867 restraints weight = 19363.374| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.29 r_work: 0.2794 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9318 Z= 0.127 Angle : 0.596 8.897 12767 Z= 0.279 Chirality : 0.042 0.201 1448 Planarity : 0.004 0.042 1601 Dihedral : 6.735 71.751 2056 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.01 % Allowed : 14.27 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 1.41 (0.26), residues: 1128 helix: 1.86 (0.27), residues: 405 sheet: 1.00 (0.34), residues: 218 loop : 0.24 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 417 TYR 0.011 0.001 TYR B 183 PHE 0.012 0.001 PHE B 396 TRP 0.040 0.001 TRP D 1 HIS 0.004 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9316) covalent geometry : angle 0.59581 (12767) hydrogen bonds : bond 0.02876 ( 463) hydrogen bonds : angle 4.37532 ( 1293) Misc. bond : bond 0.00343 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.6500 (OUTLIER) REVERT: B 108 PHE cc_start: 0.8859 (m-10) cc_final: 0.8562 (m-10) REVERT: B 204 LEU cc_start: 0.9105 (tp) cc_final: 0.8860 (pp) REVERT: B 246 GLN cc_start: 0.9106 (tt0) cc_final: 0.8816 (tt0) REVERT: B 283 MET cc_start: 0.8996 (tpt) cc_final: 0.8730 (tpt) REVERT: C 317 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7731 (tm-30) outliers start: 18 outliers final: 11 residues processed: 77 average time/residue: 0.3316 time to fit residues: 28.1994 Evaluate side-chains 73 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 1 TRP Chi-restraints excluded: chain D residue 6 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 53 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 112 optimal weight: 8.9990 chunk 57 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.097096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.065583 restraints weight = 19429.923| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.29 r_work: 0.2786 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9318 Z= 0.144 Angle : 0.610 11.090 12767 Z= 0.283 Chirality : 0.042 0.199 1448 Planarity : 0.004 0.042 1601 Dihedral : 6.751 71.872 2056 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.01 % Allowed : 14.49 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 1.39 (0.26), residues: 1128 helix: 1.88 (0.27), residues: 406 sheet: 0.99 (0.34), residues: 218 loop : 0.19 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 417 TYR 0.016 0.001 TYR C 138 PHE 0.012 0.001 PHE B 396 TRP 0.040 0.001 TRP D 1 HIS 0.005 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9316) covalent geometry : angle 0.60985 (12767) hydrogen bonds : bond 0.02915 ( 463) hydrogen bonds : angle 4.32868 ( 1293) Misc. bond : bond 0.00343 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6529 (OUTLIER) REVERT: B 108 PHE cc_start: 0.8945 (m-10) cc_final: 0.8578 (m-10) REVERT: B 204 LEU cc_start: 0.9112 (tp) cc_final: 0.8874 (pp) REVERT: B 246 GLN cc_start: 0.9119 (tt0) cc_final: 0.8833 (tt0) REVERT: B 283 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8789 (tpt) REVERT: C 317 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7712 (tm-30) outliers start: 18 outliers final: 13 residues processed: 80 average time/residue: 0.3095 time to fit residues: 27.4430 Evaluate side-chains 76 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 1 TRP Chi-restraints excluded: chain D residue 6 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 71 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.096085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.064520 restraints weight = 19515.397| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.28 r_work: 0.2764 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 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 : 0.004 0.039 9318 Z= 0.190 Angle : 0.636 10.496 12767 Z= 0.296 Chirality : 0.043 0.204 1448 Planarity : 0.004 0.042 1601 Dihedral : 6.887 71.958 2056 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.23 % Allowed : 14.49 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 1.31 (0.26), residues: 1128 helix: 1.84 (0.27), residues: 406 sheet: 0.70 (0.33), residues: 234 loop : 0.23 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 86 TYR 0.011 0.001 TYR B 154 PHE 0.013 0.001 PHE B 396 TRP 0.041 0.001 TRP D 1 HIS 0.005 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 9316) covalent geometry : angle 0.63646 (12767) hydrogen bonds : bond 0.03106 ( 463) hydrogen bonds : angle 4.38150 ( 1293) Misc. bond : bond 0.00331 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6500 (OUTLIER) REVERT: B 108 PHE cc_start: 0.8948 (m-10) cc_final: 0.8566 (m-10) REVERT: B 204 LEU cc_start: 0.9153 (tp) cc_final: 0.8870 (pp) REVERT: B 246 GLN cc_start: 0.9124 (tt0) cc_final: 0.8855 (tt0) REVERT: C 296 MET cc_start: 0.9041 (mtp) cc_final: 0.8805 (mtp) REVERT: C 317 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7729 (tm-30) outliers start: 20 outliers final: 14 residues processed: 77 average time/residue: 0.3472 time to fit residues: 29.5391 Evaluate side-chains 76 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 1 TRP Chi-restraints excluded: chain D residue 6 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 80 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 28 optimal weight: 0.1980 chunk 38 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.097412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.065877 restraints weight = 19444.557| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.29 r_work: 0.2793 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9318 Z= 0.126 Angle : 0.614 10.416 12767 Z= 0.282 Chirality : 0.041 0.201 1448 Planarity : 0.004 0.042 1601 Dihedral : 6.764 71.773 2056 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.56 % Allowed : 14.94 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 1.39 (0.26), residues: 1128 helix: 1.94 (0.27), residues: 407 sheet: 0.75 (0.33), residues: 233 loop : 0.24 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.014 0.001 TYR C 138 PHE 0.012 0.001 PHE B 396 TRP 0.040 0.001 TRP D 1 HIS 0.005 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9316) covalent geometry : angle 0.61447 (12767) hydrogen bonds : bond 0.02758 ( 463) hydrogen bonds : angle 4.28383 ( 1293) Misc. bond : bond 0.00328 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6458 (OUTLIER) REVERT: B 108 PHE cc_start: 0.8920 (m-10) cc_final: 0.8527 (m-10) REVERT: B 204 LEU cc_start: 0.9107 (tp) cc_final: 0.8879 (pp) REVERT: B 246 GLN cc_start: 0.9097 (tt0) cc_final: 0.8843 (tt0) REVERT: C 296 MET cc_start: 0.9033 (mtp) cc_final: 0.8772 (mtp) outliers start: 14 outliers final: 13 residues processed: 78 average time/residue: 0.4127 time to fit residues: 35.2365 Evaluate side-chains 76 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 1 TRP Chi-restraints excluded: chain D residue 6 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 63 optimal weight: 0.0970 chunk 48 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 32 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.096179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.065324 restraints weight = 19286.042| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.27 r_work: 0.2777 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9318 Z= 0.125 Angle : 0.621 9.820 12767 Z= 0.285 Chirality : 0.042 0.197 1448 Planarity : 0.004 0.041 1601 Dihedral : 6.753 71.911 2056 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.78 % Allowed : 14.94 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 1.37 (0.26), residues: 1128 helix: 1.96 (0.27), residues: 406 sheet: 0.75 (0.33), residues: 233 loop : 0.19 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.011 0.001 TYR B 154 PHE 0.012 0.001 PHE B 396 TRP 0.040 0.001 TRP D 1 HIS 0.005 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9316) covalent geometry : angle 0.62056 (12767) hydrogen bonds : bond 0.02753 ( 463) hydrogen bonds : angle 4.25239 ( 1293) Misc. bond : bond 0.00324 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6413 (OUTLIER) REVERT: B 108 PHE cc_start: 0.8909 (m-10) cc_final: 0.8545 (m-10) REVERT: B 204 LEU cc_start: 0.9076 (tp) cc_final: 0.8861 (pp) REVERT: B 246 GLN cc_start: 0.9070 (tt0) cc_final: 0.8790 (tt0) REVERT: C 296 MET cc_start: 0.8994 (mtp) cc_final: 0.8782 (mtp) outliers start: 16 outliers final: 14 residues processed: 76 average time/residue: 0.4197 time to fit residues: 34.9779 Evaluate side-chains 78 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 1 TRP Chi-restraints excluded: chain D residue 6 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 27 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.096328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.065360 restraints weight = 19253.348| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.28 r_work: 0.2775 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9318 Z= 0.128 Angle : 0.624 9.785 12767 Z= 0.288 Chirality : 0.042 0.195 1448 Planarity : 0.004 0.041 1601 Dihedral : 6.750 72.025 2056 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.56 % Allowed : 15.27 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 1.36 (0.26), residues: 1128 helix: 1.97 (0.27), residues: 406 sheet: 0.76 (0.33), residues: 233 loop : 0.15 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.016 0.001 TYR C 138 PHE 0.012 0.001 PHE B 396 TRP 0.040 0.001 TRP D 1 HIS 0.005 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9316) covalent geometry : angle 0.62378 (12767) hydrogen bonds : bond 0.02725 ( 463) hydrogen bonds : angle 4.22752 ( 1293) Misc. bond : bond 0.00321 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2104.02 seconds wall clock time: 36 minutes 46.07 seconds (2206.07 seconds total)