Starting phenix.real_space_refine on Fri Aug 22 19:32:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tzp_41765/08_2025/8tzp_41765.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tzp_41765/08_2025/8tzp_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_2025/8tzp_41765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tzp_41765/08_2025/8tzp_41765.map" model { file = "/net/cci-nas-00/data/ceres_data/8tzp_41765/08_2025/8tzp_41765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tzp_41765/08_2025/8tzp_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-2.0-5787/lib/python3.9/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: 2.08, per 1000 atoms: 0.30 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: 0.60 Conformation dependent library (CDL) restraints added in 468.6 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.24 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: 1.15 Time building geometry restraints manager: 0.83 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: 355 36.04 - 54.05: 83 54.05 - 72.07: 21 72.07 - 90.09: 9 Dihedral angle restraints: 4254 sinusoidal: 1775 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 4251 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: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.140 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 15.231 90.091 2605 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 aren 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 covalent geometry : bond 0.00443 ( 7097) covalent geometry : angle 0.73176 ( 9585) SS BOND : bond 0.00286 ( 17) SS BOND : angle 1.16007 ( 34) hydrogen bonds : bond 0.13130 ( 375) hydrogen bonds : angle 5.53280 ( 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 : 0.277 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 99 average time/residue: 0.0803 time to fit residues: 11.2276 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 : 0.334 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4182 r_free = 0.4182 target = 0.181596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.138129 restraints weight = 8318.165| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.29 r_work: 0.3501 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7114 Z= 0.152 Angle : 0.555 8.428 9619 Z= 0.288 Chirality : 0.041 0.165 1029 Planarity : 0.005 0.090 1206 Dihedral : 8.220 87.911 968 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.96 % Allowed : 11.57 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.28), residues: 851 helix: 2.22 (0.25), residues: 394 sheet: 0.06 (0.51), residues: 109 loop : -0.64 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 127 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 covalent geometry : bond 0.00350 ( 7097) covalent geometry : angle 0.55101 ( 9585) SS BOND : bond 0.00365 ( 17) SS BOND : angle 1.23013 ( 34) hydrogen bonds : bond 0.04157 ( 375) hydrogen bonds : angle 4.38979 ( 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 : 0.297 Fit side-chains REVERT: A 313 TYR cc_start: 0.7686 (p90) cc_final: 0.7456 (p90) REVERT: B 423 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8229 (mm) outliers start: 22 outliers final: 12 residues processed: 105 average time/residue: 0.0846 time to fit residues: 12.2452 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 : 0.269 ------------------------------------------------------------------------------- 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: 0.7980 chunk 78 optimal weight: 0.5980 chunk 79 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 71 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 GLN B 198 ASN B 470 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.182017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.140322 restraints weight = 8219.806| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.18 r_work: 0.3527 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1004 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= 0.129 Angle : 0.522 6.522 9619 Z= 0.271 Chirality : 0.041 0.219 1029 Planarity : 0.005 0.070 1206 Dihedral : 7.710 88.775 968 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.36 % Allowed : 12.11 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.28), residues: 851 helix: 2.20 (0.25), residues: 403 sheet: 0.00 (0.51), residues: 109 loop : -0.68 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 242 TYR 0.013 0.001 TYR A 318 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 covalent geometry : bond 0.00294 ( 7097) covalent geometry : angle 0.51851 ( 9585) SS BOND : bond 0.00307 ( 17) SS BOND : angle 1.07965 ( 34) hydrogen bonds : bond 0.03806 ( 375) hydrogen bonds : angle 4.12797 ( 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 114 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.272 Fit side-chains REVERT: A 313 TYR cc_start: 0.7753 (p90) cc_final: 0.7510 (p90) REVERT: A 346 TYR cc_start: 0.6838 (OUTLIER) cc_final: 0.6544 (m-10) REVERT: B 423 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8169 (mm) REVERT: C 261 TRP cc_start: 0.8316 (m100) cc_final: 0.8084 (m-90) outliers start: 25 outliers final: 15 residues processed: 105 average time/residue: 0.0833 time to fit residues: 12.1501 Evaluate side-chains 103 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 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 110 MET Chi-restraints excluded: chain B residue 163 THR 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 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: 0.9990 chunk 27 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 9 optimal weight: 0.0270 chunk 11 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.184444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.142094 restraints weight = 8385.702| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.18 r_work: 0.3550 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7114 Z= 0.121 Angle : 0.509 6.549 9619 Z= 0.264 Chirality : 0.040 0.167 1029 Planarity : 0.004 0.061 1206 Dihedral : 7.433 86.222 968 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.44 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 aren not related in a simple way. whole: 1.33 (0.29), residues: 851 helix: 2.27 (0.24), residues: 406 sheet: 0.05 (0.52), residues: 109 loop : -0.55 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 55 TYR 0.021 0.001 TYR A 318 PHE 0.016 0.001 PHE B 240 TRP 0.013 0.001 TRP B 481 HIS 0.005 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 7097) covalent geometry : angle 0.50565 ( 9585) SS BOND : bond 0.00265 ( 17) SS BOND : angle 1.10802 ( 34) hydrogen bonds : bond 0.03635 ( 375) hydrogen bonds : angle 3.99208 ( 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 108 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.264 Fit side-chains REVERT: A 313 TYR cc_start: 0.7755 (p90) cc_final: 0.7506 (p90) REVERT: A 346 TYR cc_start: 0.6835 (OUTLIER) cc_final: 0.6573 (m-10) REVERT: B 103 MET cc_start: 0.8295 (mtt) cc_final: 0.8042 (mtt) REVERT: B 423 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8142 (mm) REVERT: C 261 TRP cc_start: 0.8289 (m100) cc_final: 0.8079 (m-90) outliers start: 21 outliers final: 16 residues processed: 100 average time/residue: 0.0761 time to fit residues: 10.8552 Evaluate side-chains 102 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 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 91 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 187 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 66 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 6 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.181334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.139134 restraints weight = 8470.865| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.18 r_work: 0.3509 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7114 Z= 0.153 Angle : 0.532 7.046 9619 Z= 0.273 Chirality : 0.041 0.165 1029 Planarity : 0.004 0.053 1206 Dihedral : 7.436 87.398 968 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.77 % Allowed : 11.98 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.29), residues: 851 helix: 2.42 (0.24), residues: 392 sheet: 0.00 (0.52), residues: 109 loop : -0.54 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 342 TYR 0.024 0.001 TYR A 318 PHE 0.011 0.001 PHE A 166 TRP 0.013 0.001 TRP B 481 HIS 0.003 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7097) covalent geometry : angle 0.52914 ( 9585) SS BOND : bond 0.00299 ( 17) SS BOND : angle 1.06390 ( 34) hydrogen bonds : bond 0.03777 ( 375) hydrogen bonds : angle 4.00380 ( 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 120 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.287 Fit side-chains REVERT: A 313 TYR cc_start: 0.7817 (p90) cc_final: 0.7544 (p90) REVERT: A 346 TYR cc_start: 0.6862 (OUTLIER) cc_final: 0.6572 (m-10) REVERT: B 103 MET cc_start: 0.8305 (mtt) cc_final: 0.8057 (mtt) REVERT: B 377 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7109 (mp) REVERT: C 261 TRP cc_start: 0.8315 (m100) cc_final: 0.8100 (m-90) outliers start: 28 outliers final: 21 residues processed: 108 average time/residue: 0.0841 time to fit residues: 12.5207 Evaluate side-chains 111 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 110 MET 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 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: 7.9990 chunk 33 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.177551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.135360 restraints weight = 8499.285| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.15 r_work: 0.3456 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 7114 Z= 0.259 Angle : 0.619 8.474 9619 Z= 0.318 Chirality : 0.044 0.177 1029 Planarity : 0.005 0.050 1206 Dihedral : 7.691 89.242 968 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.77 % Allowed : 12.79 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.28), residues: 851 helix: 1.93 (0.24), residues: 403 sheet: -0.08 (0.52), residues: 110 loop : -0.70 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 220 TYR 0.023 0.002 TYR A 318 PHE 0.014 0.002 PHE B 318 TRP 0.016 0.002 TRP A 147 HIS 0.005 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00630 ( 7097) covalent geometry : angle 0.61684 ( 9585) SS BOND : bond 0.00348 ( 17) SS BOND : angle 1.14047 ( 34) hydrogen bonds : bond 0.04316 ( 375) hydrogen bonds : angle 4.18293 ( 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 122 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 290 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7619 (pp30) REVERT: A 313 TYR cc_start: 0.7922 (p90) cc_final: 0.7708 (p90) REVERT: B 377 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7104 (mp) outliers start: 28 outliers final: 20 residues processed: 113 average time/residue: 0.0804 time to fit residues: 12.7603 Evaluate side-chains 109 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 B residue 26 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 187 ILE 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: 0.7980 chunk 65 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 0.3980 chunk 39 optimal weight: 0.0570 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 323 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.181979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.140904 restraints weight = 8206.990| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.14 r_work: 0.3529 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7114 Z= 0.130 Angle : 0.532 6.921 9619 Z= 0.276 Chirality : 0.040 0.162 1029 Planarity : 0.004 0.048 1206 Dihedral : 7.345 88.418 968 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.69 % Allowed : 14.54 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.29), residues: 851 helix: 2.16 (0.24), residues: 404 sheet: -0.42 (0.51), residues: 117 loop : -0.52 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 220 TYR 0.022 0.001 TYR A 318 PHE 0.012 0.001 PHE A 166 TRP 0.014 0.001 TRP B 481 HIS 0.004 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7097) covalent geometry : angle 0.52891 ( 9585) SS BOND : bond 0.00295 ( 17) SS BOND : angle 1.06488 ( 34) hydrogen bonds : bond 0.03748 ( 375) hydrogen bonds : angle 3.95545 ( 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: 20 poor density : 89 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 290 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7646 (pp30) REVERT: A 313 TYR cc_start: 0.7886 (p90) cc_final: 0.7616 (p90) REVERT: A 346 TYR cc_start: 0.6915 (OUTLIER) cc_final: 0.6653 (m-10) REVERT: C 261 TRP cc_start: 0.8286 (m100) cc_final: 0.8066 (m-90) outliers start: 20 outliers final: 14 residues processed: 101 average time/residue: 0.0826 time to fit residues: 11.7273 Evaluate side-chains 104 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 187 ILE 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: 0.8980 chunk 38 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 12 optimal weight: 0.0050 chunk 13 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.183080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.141482 restraints weight = 8444.383| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.17 r_work: 0.3583 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7114 Z= 0.127 Angle : 0.526 7.037 9619 Z= 0.271 Chirality : 0.040 0.150 1029 Planarity : 0.004 0.047 1206 Dihedral : 7.070 89.173 968 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.56 % Allowed : 14.94 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.29), residues: 851 helix: 2.34 (0.24), residues: 402 sheet: -0.50 (0.48), residues: 127 loop : -0.43 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 220 TYR 0.022 0.001 TYR A 318 PHE 0.012 0.001 PHE B 432 TRP 0.013 0.001 TRP B 481 HIS 0.003 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7097) covalent geometry : angle 0.52343 ( 9585) SS BOND : bond 0.00260 ( 17) SS BOND : angle 0.95269 ( 34) hydrogen bonds : bond 0.03606 ( 375) hydrogen bonds : angle 3.86561 ( 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 107 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 290 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7655 (pp30) REVERT: A 313 TYR cc_start: 0.7897 (p90) cc_final: 0.7601 (p90) REVERT: A 346 TYR cc_start: 0.6941 (OUTLIER) cc_final: 0.6694 (m-10) REVERT: B 220 ARG cc_start: 0.8292 (ttm110) cc_final: 0.7905 (mtm-85) REVERT: C 261 TRP cc_start: 0.8253 (m100) cc_final: 0.7899 (m-90) outliers start: 19 outliers final: 15 residues processed: 101 average time/residue: 0.0894 time to fit residues: 12.3288 Evaluate side-chains 101 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 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 187 ILE 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: 0.4980 chunk 21 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.179417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.137862 restraints weight = 8307.601| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.14 r_work: 0.3577 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1854 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= 0.132 Angle : 0.529 6.792 9619 Z= 0.273 Chirality : 0.040 0.149 1029 Planarity : 0.004 0.047 1206 Dihedral : 6.919 87.977 968 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % 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 aren not related in a simple way. whole: 1.33 (0.29), residues: 851 helix: 2.37 (0.24), residues: 402 sheet: -0.50 (0.48), residues: 127 loop : -0.42 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 220 TYR 0.022 0.001 TYR A 318 PHE 0.012 0.001 PHE B 432 TRP 0.013 0.001 TRP B 481 HIS 0.003 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 7097) covalent geometry : angle 0.52687 ( 9585) SS BOND : bond 0.00258 ( 17) SS BOND : angle 0.92894 ( 34) hydrogen bonds : bond 0.03649 ( 375) hydrogen bonds : angle 3.84759 ( 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 : 0.275 Fit side-chains revert: symmetry clash REVERT: A 290 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7658 (pp30) REVERT: A 313 TYR cc_start: 0.7940 (p90) cc_final: 0.7633 (p90) REVERT: A 346 TYR cc_start: 0.6915 (OUTLIER) cc_final: 0.6702 (m-10) REVERT: B 220 ARG cc_start: 0.8307 (ttm110) cc_final: 0.7911 (mtm-85) REVERT: B 335 TYR cc_start: 0.8226 (m-80) cc_final: 0.7935 (m-80) REVERT: C 261 TRP cc_start: 0.8217 (m100) cc_final: 0.7852 (m-90) outliers start: 19 outliers final: 15 residues processed: 101 average time/residue: 0.0900 time to fit residues: 12.3272 Evaluate side-chains 103 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 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 187 ILE 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: 0.0470 chunk 69 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.185965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.144546 restraints weight = 8261.857| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.22 r_work: 0.3574 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1958 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= 0.123 Angle : 0.541 6.726 9619 Z= 0.281 Chirality : 0.042 0.274 1029 Planarity : 0.004 0.046 1206 Dihedral : 6.852 87.206 968 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.15 % Allowed : 16.15 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.29), residues: 851 helix: 2.43 (0.24), residues: 401 sheet: -0.49 (0.48), residues: 127 loop : -0.43 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 220 TYR 0.022 0.001 TYR A 318 PHE 0.012 0.001 PHE B 432 TRP 0.013 0.001 TRP B 481 HIS 0.004 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7097) covalent geometry : angle 0.53894 ( 9585) SS BOND : bond 0.00246 ( 17) SS BOND : angle 0.89872 ( 34) hydrogen bonds : bond 0.03559 ( 375) hydrogen bonds : angle 3.81511 ( 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: 16 poor density : 92 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 290 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7696 (pp30) REVERT: A 313 TYR cc_start: 0.7975 (p90) cc_final: 0.7665 (p90) REVERT: A 346 TYR cc_start: 0.6915 (OUTLIER) cc_final: 0.6710 (m-10) REVERT: B 220 ARG cc_start: 0.8326 (ttm110) cc_final: 0.7936 (mtm-85) REVERT: B 240 PHE cc_start: 0.8110 (t80) cc_final: 0.7900 (t80) REVERT: B 335 TYR cc_start: 0.8251 (m-80) cc_final: 0.7934 (m-80) REVERT: C 240 MET cc_start: 0.7439 (pmm) cc_final: 0.7175 (pmm) REVERT: C 261 TRP cc_start: 0.8203 (m100) cc_final: 0.7829 (m-90) outliers start: 16 outliers final: 14 residues processed: 103 average time/residue: 0.0910 time to fit residues: 12.7508 Evaluate side-chains 105 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 290 GLN 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 187 ILE 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: 2.9990 chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 51 optimal weight: 0.2980 chunk 63 optimal weight: 2.9990 chunk 21 optimal weight: 0.0670 chunk 79 optimal weight: 8.9990 overall best weight: 1.4724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 322 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.181201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.140093 restraints weight = 8310.449| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.16 r_work: 0.3517 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7114 Z= 0.206 Angle : 0.600 7.588 9619 Z= 0.310 Chirality : 0.043 0.238 1029 Planarity : 0.004 0.046 1206 Dihedral : 7.034 87.109 968 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.96 % Allowed : 15.34 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.29), residues: 851 helix: 2.30 (0.24), residues: 391 sheet: -0.46 (0.49), residues: 118 loop : -0.48 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 220 TYR 0.022 0.002 TYR A 318 PHE 0.011 0.001 PHE B 318 TRP 0.013 0.001 TRP B 481 HIS 0.004 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 7097) covalent geometry : angle 0.59829 ( 9585) SS BOND : bond 0.00316 ( 17) SS BOND : angle 0.98092 ( 34) hydrogen bonds : bond 0.04035 ( 375) hydrogen bonds : angle 3.99584 ( 1050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2278.67 seconds wall clock time: 39 minutes 46.15 seconds (2386.15 seconds total)