Starting phenix.real_space_refine on Tue Aug 4 22:49:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8tzp_41765/08_2026/8tzp_41765.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tzp_41765/08_2026/8tzp_41765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tzp_41765/08_2026/8tzp_41765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tzp_41765/08_2026/8tzp_41765.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8tzp_41765/08_2026/8tzp_41765.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8tzp_41765/08_2026/8tzp_41765.cif" model { file = "/net/cci-nas-00/data/ceres_data/8tzp_41765/08_2026/8tzp_41765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tzp_41765/08_2026/8tzp_41765.cif" } resolution = 3.23 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= 0.002 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 75 5.16 5 C 4470 2.51 5 N 1170 2.21 5 O 1204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6920 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2342 Classifications: {'peptide': 301} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 289} Chain breaks: 1 Chain: "B" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 4037 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 21, 'TRANS': 474} Chain: "C" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 484 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PAM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PAM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Time building chain proxies: 1.17, per 1000 atoms: 0.17 Number of scatterers: 6920 At special positions: 0 Unit cell: (87.98, 92.96, 129.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 P 1 15.00 O 1204 8.00 N 1170 7.00 C 4470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 38 " - pdb=" SG CYS A 52 " distance=2.03 Simple disulfide: pdb=" SG CYS A 73 " - pdb=" SG CYS A 84 " distance=2.03 Simple disulfide: pdb=" SG CYS A 123 " - pdb=" SG CYS A 131 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 202 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 309 " distance=2.04 Simple disulfide: pdb=" SG CYS A 294 " - pdb=" SG CYS A 304 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 336 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 332 " distance=2.03 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 71 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 216 " - pdb=" SG CYS C 263 " distance=2.03 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 229 " distance=2.03 Simple disulfide: pdb=" SG CYS C 225 " - pdb=" SG CYS C 250 " distance=2.04 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: 0.43 Conformation dependent library (CDL) restraints added in 268.2 milliseconds 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1598 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 6 sheets defined 52.7% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 37 through 41 removed outlier: 4.293A pdb=" N LYS A 40 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 55 through 77 removed outlier: 3.637A pdb=" N ILE A 59 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 125 Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 154 through 170 removed outlier: 4.000A pdb=" N TYR A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 195 Processing helix chain 'A' and resid 220 through 233 removed outlier: 3.583A pdb=" N LEU A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 308 Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 10 through 35 removed outlier: 3.835A pdb=" N GLY B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 81 Processing helix chain 'B' and resid 121 through 125 removed outlier: 4.142A pdb=" N GLN B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 227 through 258 Proline residue: B 243 - end of helix Processing helix chain 'B' and resid 264 through 282 Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 295 through 322 removed outlier: 3.584A pdb=" N ILE B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 334 Processing helix chain 'B' and resid 335 through 357 Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 358 through 362 Processing helix chain 'B' and resid 367 through 370 Processing helix chain 'B' and resid 371 through 414 removed outlier: 3.820A pdb=" N SER B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER B 413 " --> pdb=" O GLY B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 456 Processing helix chain 'B' and resid 469 through 492 Processing helix chain 'C' and resid 210 through 219 removed outlier: 4.797A pdb=" N TYR C 215 " --> pdb=" O ASP C 212 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N CYS C 217 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 236 Processing helix chain 'C' and resid 238 through 250 Processing helix chain 'C' and resid 258 through 270 removed outlier: 3.823A pdb=" N GLN C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER C 270 " --> pdb=" O GLU C 266 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 202 Processing sheet with id=AA2, first strand: chain 'A' and resid 252 through 254 removed outlier: 5.852A pdb=" N VAL A 236 " --> pdb=" O TYR A 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 293 through 294 removed outlier: 4.193A pdb=" N TYR A 346 " --> pdb=" O CYS A 294 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 40 through 46 removed outlier: 6.870A pdb=" N ASP B 117 " --> pdb=" O LYS B 217 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE B 219 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLN B 115 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU B 221 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE B 113 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLY B 223 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU B 111 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU B 114 " --> pdb=" O PRO B 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.504A pdb=" N ALA B 152 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR B 140 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLU B 150 " --> pdb=" O TYR B 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 459 through 462 removed outlier: 3.619A pdb=" N VAL B 465 " --> pdb=" O TRP B 462 " (cutoff:3.500A) 375 hydrogen bonds defined for protein. 1050 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.96 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1085 1.31 - 1.44: 1983 1.44 - 1.57: 3918 1.57 - 1.69: 3 1.69 - 1.82: 108 Bond restraints: 7097 Sorted by residual: bond pdb=" C31 POV B 601 " pdb=" O31 POV B 601 " ideal model delta sigma weight residual 1.327 1.418 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C21 POV B 601 " pdb=" O21 POV B 601 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb="C210 POV B 601 " pdb="C211 POV B 601 " ideal model delta sigma weight residual 1.497 1.558 -0.061 2.00e-02 2.50e+03 9.42e+00 bond pdb=" N POV B 601 " pdb=" C14 POV B 601 " ideal model delta sigma weight residual 1.490 1.436 0.054 2.00e-02 2.50e+03 7.23e+00 bond pdb=" C28 POV B 601 " pdb=" C29 POV B 601 " ideal model delta sigma weight residual 1.497 1.548 -0.051 2.00e-02 2.50e+03 6.44e+00 ... (remaining 7092 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 9420 2.35 - 4.71: 128 4.71 - 7.06: 26 7.06 - 9.41: 9 9.41 - 11.76: 2 Bond angle restraints: 9585 Sorted by residual: angle pdb=" CA PRO A 56 " pdb=" N PRO A 56 " pdb=" CD PRO A 56 " ideal model delta sigma weight residual 112.00 103.61 8.39 1.40e+00 5.10e-01 3.60e+01 angle pdb=" C THR A 297 " pdb=" N ALA A 298 " pdb=" CA ALA A 298 " ideal model delta sigma weight residual 120.09 125.66 -5.57 1.25e+00 6.40e-01 1.99e+01 angle pdb=" O13 POV B 601 " pdb=" P POV B 601 " pdb=" O14 POV B 601 " ideal model delta sigma weight residual 121.11 109.35 11.76 3.00e+00 1.11e-01 1.54e+01 angle pdb=" O11 POV B 601 " pdb=" P POV B 601 " pdb=" O12 POV B 601 " ideal model delta sigma weight residual 97.67 109.26 -11.59 3.00e+00 1.11e-01 1.49e+01 angle pdb=" CA LYS B 208 " pdb=" CB LYS B 208 " pdb=" CG LYS B 208 " ideal model delta sigma weight residual 114.10 121.79 -7.69 2.00e+00 2.50e-01 1.48e+01 ... (remaining 9580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 3786 18.02 - 36.04: 353 36.04 - 54.05: 81 54.05 - 72.07: 19 72.07 - 90.09: 9 Dihedral angle restraints: 4248 sinusoidal: 1769 harmonic: 2479 Sorted by residual: dihedral pdb=" CB CYS C 217 " pdb=" SG CYS C 217 " pdb=" SG CYS C 229 " pdb=" CB CYS C 229 " ideal model delta sinusoidal sigma weight residual -86.00 -163.07 77.07 1 1.00e+01 1.00e-02 7.45e+01 dihedral pdb=" CB CYS A 324 " pdb=" SG CYS A 324 " pdb=" SG CYS A 339 " pdb=" CB CYS A 339 " ideal model delta sinusoidal sigma weight residual 93.00 155.26 -62.26 1 1.00e+01 1.00e-02 5.13e+01 dihedral pdb=" CB CYS A 38 " pdb=" SG CYS A 38 " pdb=" SG CYS A 52 " pdb=" CB CYS A 52 " ideal model delta sinusoidal sigma weight residual -86.00 -146.52 60.52 1 1.00e+01 1.00e-02 4.87e+01 ... (remaining 4245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 599 0.029 - 0.058: 283 0.058 - 0.087: 99 0.087 - 0.116: 38 0.116 - 0.146: 10 Chirality restraints: 1029 Sorted by residual: chirality pdb=" CA CYS C 250 " pdb=" N CYS C 250 " pdb=" C CYS C 250 " pdb=" CB CYS C 250 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CB THR A 343 " pdb=" CA THR A 343 " pdb=" OG1 THR A 343 " pdb=" CG2 THR A 343 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA ILE A 41 " pdb=" N ILE A 41 " pdb=" C ILE A 41 " pdb=" CB ILE A 41 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 1026 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 55 " 0.100 5.00e-02 4.00e+02 1.46e-01 3.42e+01 pdb=" N PRO A 56 " -0.253 5.00e-02 4.00e+02 pdb=" CA PRO A 56 " 0.077 5.00e-02 4.00e+02 pdb=" CD PRO A 56 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 67 " 0.063 5.00e-02 4.00e+02 9.46e-02 1.43e+01 pdb=" N PRO B 68 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO B 68 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 68 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 208 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.10e+00 pdb=" C LYS B 208 " 0.035 2.00e-02 2.50e+03 pdb=" O LYS B 208 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE B 209 " -0.012 2.00e-02 2.50e+03 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 2 2.05 - 2.76: 1128 2.76 - 3.48: 9683 3.48 - 4.19: 15535 4.19 - 4.90: 28735 Nonbonded interactions: 55083 Sorted by model distance: nonbonded pdb=" OG SER A 206 " pdb=" O1 PAM A 601 " model vdw 1.341 3.040 nonbonded pdb=" OG SER A 206 " pdb=" C1 PAM A 601 " model vdw 1.375 3.270 nonbonded pdb=" O ASN A 181 " pdb=" ND2 ASN A 185 " model vdw 2.169 3.120 nonbonded pdb=" O LEU B 312 " pdb=" OH TYR B 392 " model vdw 2.273 3.040 nonbonded pdb=" O ARG C 231 " pdb=" OG SER C 235 " model vdw 2.314 3.040 ... (remaining 55078 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: 2.750 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: 0.010 Set scattering table: 0.010 Process input model: 5.950 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 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 0.099 7114 Z= 0.203 Angle : 0.734 11.763 9619 Z= 0.378 Chirality : 0.041 0.146 1029 Planarity : 0.006 0.146 1206 Dihedral : 15.091 90.091 2599 Min Nonbonded Distance : 1.341 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.27 % Allowed : 12.52 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.28), residues: 851 helix: 2.20 (0.25), residues: 387 sheet: 0.14 (0.53), residues: 92 loop : -0.60 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 170 TYR 0.011 0.001 TYR B 308 PHE 0.016 0.001 PHE B 432 TRP 0.014 0.001 TRP B 481 HIS 0.005 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 ( 7097) covalent geometry : angle 0.73176 / 0.38 ( 9585) SS BOND : bond 0.00286 / 0.15 ( 17) SS BOND : angle 1.16007 / 0.75 ( 34) hydrogen bonds : bond 0.13130 / 9.19 ( 375) hydrogen bonds : angle 5.53280 / 4.16 ( 1050) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.249 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 99 average time/residue: 0.0585 time to fit residues: 8.2005 Evaluate side-chains 88 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.182809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.138987 restraints weight = 8341.563| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.30 r_work: 0.3506 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7114 Z= 0.147 Angle : 0.555 8.537 9619 Z= 0.288 Chirality : 0.041 0.164 1029 Planarity : 0.005 0.090 1206 Dihedral : 7.859 86.398 962 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.96 % Allowed : 11.98 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.28), residues: 851 helix: 2.22 (0.25), residues: 394 sheet: 0.06 (0.51), residues: 109 loop : -0.63 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 170 TYR 0.012 0.001 TYR B 484 PHE 0.012 0.001 PHE B 432 TRP 0.012 0.001 TRP B 481 HIS 0.004 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 7097) covalent geometry : angle 0.55100 / 0.29 ( 9585) SS BOND : bond 0.00373 / 0.23 ( 17) SS BOND : angle 1.22816 / 0.78 ( 34) hydrogen bonds : bond 0.04095 / 2.80 ( 375) hydrogen bonds : angle 4.35954 / 3.27 ( 1050) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.174 Fit side-chains REVERT: A 313 TYR cc_start: 0.7710 (p90) cc_final: 0.7484 (p90) REVERT: B 423 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8192 (mm) outliers start: 22 outliers final: 12 residues processed: 105 average time/residue: 0.0599 time to fit residues: 8.7349 Evaluate side-chains 101 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 437 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 68 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 38 optimal weight: 0.0270 chunk 67 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN B 25 GLN B 470 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.179607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.137712 restraints weight = 8264.890| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.18 r_work: 0.3552 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7114 Z= 0.119 Angle : 0.513 6.221 9619 Z= 0.267 Chirality : 0.040 0.214 1029 Planarity : 0.005 0.070 1206 Dihedral : 7.407 89.676 962 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.10 % Allowed : 12.52 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.29), residues: 851 helix: 2.23 (0.25), residues: 406 sheet: 0.01 (0.51), residues: 109 loop : -0.62 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 320 TYR 0.015 0.001 TYR A 318 PHE 0.012 0.001 PHE B 432 TRP 0.012 0.001 TRP B 481 HIS 0.005 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 7097) covalent geometry : angle 0.51035 / 0.27 ( 9585) SS BOND : bond 0.00308 / 0.19 ( 17) SS BOND : angle 1.05077 / 0.67 ( 34) hydrogen bonds : bond 0.03712 / 2.54 ( 375) hydrogen bonds : angle 4.07160 / 3.05 ( 1050) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 313 TYR cc_start: 0.7756 (p90) cc_final: 0.7517 (p90) REVERT: A 346 TYR cc_start: 0.6833 (OUTLIER) cc_final: 0.6542 (m-10) REVERT: B 423 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8157 (mm) REVERT: C 261 TRP cc_start: 0.8299 (m100) cc_final: 0.8069 (m-90) outliers start: 23 outliers final: 13 residues processed: 106 average time/residue: 0.0636 time to fit residues: 9.4546 Evaluate side-chains 99 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 488 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 65 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN B 198 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.178684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.136317 restraints weight = 8331.938| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.21 r_work: 0.3520 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7114 Z= 0.138 Angle : 0.518 6.817 9619 Z= 0.268 Chirality : 0.040 0.161 1029 Planarity : 0.004 0.060 1206 Dihedral : 7.218 88.504 962 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.83 % Allowed : 12.38 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.29), residues: 851 helix: 2.21 (0.24), residues: 406 sheet: 0.08 (0.52), residues: 109 loop : -0.55 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 55 TYR 0.021 0.001 TYR A 318 PHE 0.014 0.001 PHE B 240 TRP 0.013 0.001 TRP B 481 HIS 0.004 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 7097) covalent geometry : angle 0.51490 / 0.27 ( 9585) SS BOND : bond 0.00280 / 0.17 ( 17) SS BOND : angle 1.07670 / 0.69 ( 34) hydrogen bonds : bond 0.03721 / 2.53 ( 375) hydrogen bonds : angle 4.02186 / 3.00 ( 1050) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.189 Fit side-chains REVERT: A 313 TYR cc_start: 0.7770 (p90) cc_final: 0.7506 (p90) REVERT: A 346 TYR cc_start: 0.6810 (OUTLIER) cc_final: 0.6544 (m-10) REVERT: B 103 MET cc_start: 0.8349 (mtt) cc_final: 0.8120 (mtt) REVERT: C 261 TRP cc_start: 0.8295 (m100) cc_final: 0.8087 (m-90) outliers start: 21 outliers final: 14 residues processed: 102 average time/residue: 0.0623 time to fit residues: 9.1789 Evaluate side-chains 101 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 437 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 66 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.176449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.134419 restraints weight = 8470.705| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.13 r_work: 0.3493 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7114 Z= 0.183 Angle : 0.558 7.534 9619 Z= 0.286 Chirality : 0.042 0.174 1029 Planarity : 0.004 0.054 1206 Dihedral : 7.165 87.200 962 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.90 % Allowed : 12.11 % Favored : 83.98 % 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 are not related in a simple way. whole: 1.28 (0.29), residues: 851 helix: 2.29 (0.24), residues: 392 sheet: -0.02 (0.52), residues: 109 loop : -0.52 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 342 TYR 0.023 0.002 TYR A 318 PHE 0.011 0.001 PHE A 166 TRP 0.013 0.001 TRP B 481 HIS 0.004 0.001 HIS A 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 ( 7097) covalent geometry : angle 0.55527 / 0.28 ( 9585) SS BOND : bond 0.00318 / 0.19 ( 17) SS BOND : angle 1.10118 / 0.71 ( 34) hydrogen bonds : bond 0.03978 / 2.70 ( 375) hydrogen bonds : angle 4.08101 / 3.04 ( 1050) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.188 Fit side-chains REVERT: A 313 TYR cc_start: 0.7882 (p90) cc_final: 0.7587 (p90) REVERT: A 346 TYR cc_start: 0.6873 (OUTLIER) cc_final: 0.6584 (m-10) REVERT: B 377 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7087 (mp) REVERT: C 261 TRP cc_start: 0.8355 (m100) cc_final: 0.8143 (m-90) outliers start: 29 outliers final: 21 residues processed: 107 average time/residue: 0.0607 time to fit residues: 9.2792 Evaluate side-chains 107 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 488 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 6 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.175909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.133816 restraints weight = 8453.426| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.14 r_work: 0.3483 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7114 Z= 0.187 Angle : 0.556 7.781 9619 Z= 0.287 Chirality : 0.042 0.177 1029 Planarity : 0.004 0.050 1206 Dihedral : 7.087 87.436 962 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.63 % Allowed : 12.52 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.29), residues: 851 helix: 2.12 (0.24), residues: 401 sheet: -0.01 (0.53), residues: 109 loop : -0.66 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 342 TYR 0.022 0.002 TYR A 318 PHE 0.011 0.001 PHE A 166 TRP 0.013 0.001 TRP A 147 HIS 0.003 0.001 HIS A 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 ( 7097) covalent geometry : angle 0.55347 / 0.29 ( 9585) SS BOND : bond 0.00325 / 0.19 ( 17) SS BOND : angle 1.09915 / 0.72 ( 34) hydrogen bonds : bond 0.03976 / 2.71 ( 375) hydrogen bonds : angle 4.05932 / 3.02 ( 1050) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 290 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7645 (pp30) REVERT: A 313 TYR cc_start: 0.7903 (p90) cc_final: 0.7626 (p90) REVERT: A 346 TYR cc_start: 0.6862 (OUTLIER) cc_final: 0.6553 (m-10) REVERT: B 377 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7128 (mp) REVERT: C 261 TRP cc_start: 0.8344 (m100) cc_final: 0.8135 (m-90) outliers start: 27 outliers final: 19 residues processed: 108 average time/residue: 0.0711 time to fit residues: 10.7574 Evaluate side-chains 108 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 437 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 51 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 chunk 56 optimal weight: 0.0470 chunk 39 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 40 optimal weight: 0.0570 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.180700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.139560 restraints weight = 8248.011| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.14 r_work: 0.3563 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7114 Z= 0.109 Angle : 0.518 7.103 9619 Z= 0.267 Chirality : 0.040 0.160 1029 Planarity : 0.004 0.047 1206 Dihedral : 6.789 86.691 962 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.56 % Allowed : 14.54 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.29), residues: 851 helix: 2.36 (0.24), residues: 403 sheet: -0.06 (0.52), residues: 111 loop : -0.47 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 220 TYR 0.021 0.001 TYR A 318 PHE 0.012 0.001 PHE B 432 TRP 0.013 0.001 TRP B 481 HIS 0.005 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 7097) covalent geometry : angle 0.51526 / 0.27 ( 9585) SS BOND : bond 0.00246 / 0.15 ( 17) SS BOND : angle 0.96331 / 0.63 ( 34) hydrogen bonds : bond 0.03570 / 2.43 ( 375) hydrogen bonds : angle 3.87445 / 2.89 ( 1050) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 183 HIS cc_start: 0.7927 (t-90) cc_final: 0.7571 (t-170) REVERT: A 290 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7636 (pp30) REVERT: A 313 TYR cc_start: 0.7864 (p90) cc_final: 0.7583 (p90) REVERT: A 346 TYR cc_start: 0.6893 (OUTLIER) cc_final: 0.6628 (m-10) REVERT: C 261 TRP cc_start: 0.8277 (m100) cc_final: 0.7899 (m-90) outliers start: 19 outliers final: 13 residues processed: 104 average time/residue: 0.0612 time to fit residues: 9.0336 Evaluate side-chains 101 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 437 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 72 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 0.0670 chunk 13 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.183818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.142273 restraints weight = 8349.993| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.15 r_work: 0.3547 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7114 Z= 0.127 Angle : 0.522 6.818 9619 Z= 0.269 Chirality : 0.040 0.154 1029 Planarity : 0.004 0.046 1206 Dihedral : 6.731 87.868 962 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.69 % Allowed : 14.27 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.29), residues: 851 helix: 2.36 (0.24), residues: 403 sheet: -0.37 (0.50), residues: 117 loop : -0.41 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 220 TYR 0.023 0.001 TYR A 318 PHE 0.020 0.001 PHE B 240 TRP 0.013 0.001 TRP B 481 HIS 0.003 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 7097) covalent geometry : angle 0.52025 / 0.27 ( 9585) SS BOND : bond 0.00258 / 0.16 ( 17) SS BOND : angle 0.93012 / 0.60 ( 34) hydrogen bonds : bond 0.03609 / 2.45 ( 375) hydrogen bonds : angle 3.86655 / 2.88 ( 1050) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 290 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7642 (pp30) REVERT: A 313 TYR cc_start: 0.7880 (p90) cc_final: 0.7613 (p90) REVERT: A 346 TYR cc_start: 0.6928 (OUTLIER) cc_final: 0.6683 (m-10) REVERT: B 220 ARG cc_start: 0.8212 (ttm110) cc_final: 0.7898 (mtm-85) REVERT: B 335 TYR cc_start: 0.8218 (m-80) cc_final: 0.7925 (m-80) REVERT: C 261 TRP cc_start: 0.8272 (m100) cc_final: 0.7913 (m-90) outliers start: 20 outliers final: 13 residues processed: 104 average time/residue: 0.0723 time to fit residues: 10.2538 Evaluate side-chains 99 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 437 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 70 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.0470 chunk 25 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.181884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.138444 restraints weight = 8336.722| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.28 r_work: 0.3531 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7114 Z= 0.156 Angle : 0.561 7.247 9619 Z= 0.289 Chirality : 0.042 0.242 1029 Planarity : 0.004 0.046 1206 Dihedral : 6.820 88.662 962 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.56 % Allowed : 15.21 % Favored : 82.23 % 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 are not related in a simple way. whole: 1.25 (0.29), residues: 851 helix: 2.29 (0.24), residues: 401 sheet: -0.55 (0.48), residues: 127 loop : -0.43 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 220 TYR 0.023 0.001 TYR A 318 PHE 0.013 0.001 PHE B 291 TRP 0.013 0.001 TRP B 481 HIS 0.003 0.001 HIS A 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 7097) covalent geometry : angle 0.55936 / 0.29 ( 9585) SS BOND : bond 0.00274 / 0.16 ( 17) SS BOND : angle 0.94495 / 0.62 ( 34) hydrogen bonds : bond 0.03727 / 2.53 ( 375) hydrogen bonds : angle 3.91712 / 2.92 ( 1050) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 290 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7686 (pp30) REVERT: A 313 TYR cc_start: 0.7943 (p90) cc_final: 0.7662 (p90) REVERT: A 346 TYR cc_start: 0.6921 (OUTLIER) cc_final: 0.6682 (m-10) REVERT: B 220 ARG cc_start: 0.8267 (ttm110) cc_final: 0.7948 (mtm-85) REVERT: B 335 TYR cc_start: 0.8321 (m-80) cc_final: 0.8064 (m-80) REVERT: C 240 MET cc_start: 0.7376 (pmm) cc_final: 0.7109 (pmm) outliers start: 19 outliers final: 13 residues processed: 101 average time/residue: 0.0671 time to fit residues: 9.3577 Evaluate side-chains 102 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 437 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 36 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 0.0980 chunk 69 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.185430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.143375 restraints weight = 8254.212| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.28 r_work: 0.3580 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7114 Z= 0.122 Angle : 0.535 6.515 9619 Z= 0.277 Chirality : 0.041 0.223 1029 Planarity : 0.004 0.046 1206 Dihedral : 6.673 89.295 962 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.42 % Allowed : 15.75 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.29), residues: 851 helix: 2.40 (0.24), residues: 401 sheet: -0.53 (0.48), residues: 127 loop : -0.38 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 220 TYR 0.022 0.001 TYR A 318 PHE 0.012 0.001 PHE B 291 TRP 0.014 0.001 TRP B 481 HIS 0.004 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 7097) covalent geometry : angle 0.53336 / 0.28 ( 9585) SS BOND : bond 0.00251 / 0.15 ( 17) SS BOND : angle 0.89283 / 0.58 ( 34) hydrogen bonds : bond 0.03531 / 2.40 ( 375) hydrogen bonds : angle 3.84130 / 2.87 ( 1050) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 183 HIS cc_start: 0.7927 (t-90) cc_final: 0.7516 (t-170) REVERT: A 290 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7712 (pp30) REVERT: A 313 TYR cc_start: 0.7950 (p90) cc_final: 0.7647 (p90) REVERT: A 346 TYR cc_start: 0.6923 (OUTLIER) cc_final: 0.6691 (m-10) REVERT: B 134 MET cc_start: 0.8812 (mtm) cc_final: 0.8536 (mtt) REVERT: B 220 ARG cc_start: 0.8272 (ttm110) cc_final: 0.7938 (mtm-85) REVERT: B 240 PHE cc_start: 0.8116 (t80) cc_final: 0.7879 (t80) REVERT: B 335 TYR cc_start: 0.8251 (m-80) cc_final: 0.7935 (m-80) outliers start: 18 outliers final: 13 residues processed: 104 average time/residue: 0.0741 time to fit residues: 10.5933 Evaluate side-chains 102 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 437 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 50 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 79 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 237 HIS A 323 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.178827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.136551 restraints weight = 8160.783| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.23 r_work: 0.3564 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7114 Z= 0.142 Angle : 0.554 6.752 9619 Z= 0.286 Chirality : 0.042 0.199 1029 Planarity : 0.004 0.046 1206 Dihedral : 6.696 89.745 962 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.15 % Allowed : 16.02 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.29), residues: 851 helix: 2.34 (0.25), residues: 401 sheet: -0.53 (0.47), residues: 128 loop : -0.43 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 220 TYR 0.022 0.001 TYR A 318 PHE 0.016 0.001 PHE B 291 TRP 0.013 0.001 TRP B 481 HIS 0.003 0.001 HIS A 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 7097) covalent geometry : angle 0.55252 / 0.29 ( 9585) SS BOND : bond 0.00261 / 0.16 ( 17) SS BOND : angle 0.92652 / 0.61 ( 34) hydrogen bonds : bond 0.03652 / 2.48 ( 375) hydrogen bonds : angle 3.88753 / 2.90 ( 1050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1734.18 seconds wall clock time: 30 minutes 11.22 seconds (1811.22 seconds total)