Starting phenix.real_space_refine on Wed Feb 12 05:10:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tzp_41765/02_2025/8tzp_41765.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tzp_41765/02_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_41765/02_2025/8tzp_41765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tzp_41765/02_2025/8tzp_41765.map" model { file = "/net/cci-nas-00/data/ceres_data/8tzp_41765/02_2025/8tzp_41765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tzp_41765/02_2025/8tzp_41765.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.61, per 1000 atoms: 0.67 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: 1.83 Conformation dependent library (CDL) restraints added in 986.2 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: 0.73 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: 1.77 Time building geometry restraints manager: 2.11 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: 1.600 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: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.240 Find NCS groups from input model: 0.050 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.030 ------------------------------------------------------------------------------- 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 7097 Z= 0.298 Angle : 0.732 11.763 9585 Z= 0.377 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.001 TRP B 481 HIS 0.005 0.001 HIS B 322 PHE 0.016 0.001 PHE B 432 TYR 0.011 0.001 TYR B 308 ARG 0.003 0.000 ARG A 170 *********************** 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 : 0.797 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 99 average time/residue: 0.1749 time to fit residues: 24.0343 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 : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4197 r_free = 0.4197 target = 0.183117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.140604 restraints weight = 8181.233| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.18 r_work: 0.3520 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.0763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7097 Z= 0.219 Angle : 0.548 8.675 9585 Z= 0.285 Chirality : 0.041 0.164 1029 Planarity : 0.005 0.090 1206 Dihedral : 8.210 88.703 968 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.96 % Allowed : 11.84 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.28), residues: 851 helix: 2.24 (0.25), residues: 394 sheet: 0.07 (0.51), residues: 109 loop : -0.63 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 481 HIS 0.004 0.001 HIS B 322 PHE 0.012 0.001 PHE B 432 TYR 0.012 0.001 TYR B 484 ARG 0.002 0.000 ARG B 127 *********************** 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 116 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.801 Fit side-chains REVERT: A 313 TYR cc_start: 0.7681 (p90) cc_final: 0.7455 (p90) REVERT: B 423 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8191 (mm) outliers start: 22 outliers final: 12 residues processed: 106 average time/residue: 0.1818 time to fit residues: 26.1484 Evaluate side-chains 102 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 25 optimal weight: 0.0370 chunk 62 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 GLN B 470 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.178453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.135737 restraints weight = 8330.808| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.23 r_work: 0.3521 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7097 Z= 0.199 Angle : 0.523 6.587 9585 Z= 0.272 Chirality : 0.041 0.221 1029 Planarity : 0.005 0.070 1206 Dihedral : 7.717 88.721 968 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.23 % Allowed : 12.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.28), residues: 851 helix: 2.21 (0.25), residues: 403 sheet: -0.03 (0.51), residues: 109 loop : -0.68 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 481 HIS 0.004 0.001 HIS B 322 PHE 0.011 0.001 PHE B 432 TYR 0.015 0.001 TYR A 318 ARG 0.004 0.000 ARG A 242 *********************** 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: 24 poor density : 90 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: A 313 TYR cc_start: 0.7762 (p90) cc_final: 0.7502 (p90) REVERT: A 346 TYR cc_start: 0.6793 (OUTLIER) cc_final: 0.6502 (m-10) REVERT: B 423 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8166 (mm) REVERT: C 261 TRP cc_start: 0.8309 (m100) cc_final: 0.8070 (m-90) outliers start: 24 outliers final: 15 residues processed: 105 average time/residue: 0.1871 time to fit residues: 26.9308 Evaluate side-chains 102 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 46 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 13 optimal weight: 7.9990 chunk 55 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4182 r_free = 0.4182 target = 0.181346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.139737 restraints weight = 8277.269| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.15 r_work: 0.3523 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7097 Z= 0.206 Angle : 0.517 6.869 9585 Z= 0.268 Chirality : 0.041 0.166 1029 Planarity : 0.004 0.061 1206 Dihedral : 7.514 86.623 968 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.50 % Allowed : 11.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.29), residues: 851 helix: 2.19 (0.25), residues: 406 sheet: 0.06 (0.52), residues: 109 loop : -0.57 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 481 HIS 0.004 0.001 HIS B 322 PHE 0.014 0.001 PHE B 240 TYR 0.021 0.001 TYR A 318 ARG 0.003 0.000 ARG A 55 *********************** 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 117 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.764 Fit side-chains REVERT: A 313 TYR cc_start: 0.7760 (p90) cc_final: 0.7496 (p90) REVERT: A 346 TYR cc_start: 0.6845 (OUTLIER) cc_final: 0.6543 (m-10) REVERT: B 103 MET cc_start: 0.8297 (mtt) cc_final: 0.8025 (mtt) REVERT: B 423 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8167 (mm) REVERT: C 261 TRP cc_start: 0.8316 (m100) cc_final: 0.8107 (m-90) outliers start: 26 outliers final: 19 residues processed: 104 average time/residue: 0.1688 time to fit residues: 24.5948 Evaluate side-chains 110 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 32 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.4132 r_free = 0.4132 target = 0.176325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.133786 restraints weight = 8427.270| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.16 r_work: 0.3436 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 7097 Z= 0.429 Angle : 0.638 8.734 9585 Z= 0.326 Chirality : 0.044 0.157 1029 Planarity : 0.005 0.055 1206 Dihedral : 7.844 88.635 968 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.77 % Allowed : 12.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.28), residues: 851 helix: 1.91 (0.25), residues: 394 sheet: -0.14 (0.52), residues: 109 loop : -0.62 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 147 HIS 0.006 0.001 HIS A 117 PHE 0.015 0.002 PHE B 318 TYR 0.023 0.002 TYR A 318 ARG 0.002 0.000 ARG B 175 *********************** 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 123 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.816 Fit side-chains REVERT: A 290 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7617 (pp30) REVERT: A 313 TYR cc_start: 0.7908 (p90) cc_final: 0.7674 (p90) REVERT: A 346 TYR cc_start: 0.6886 (OUTLIER) cc_final: 0.6613 (m-10) REVERT: B 377 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7069 (mp) outliers start: 28 outliers final: 19 residues processed: 114 average time/residue: 0.1877 time to fit residues: 29.4207 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 : 0.766 ------------------------------------------------------------------------------- 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 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 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 49 optimal weight: 0.5980 chunk 50 optimal weight: 0.0970 chunk 54 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.4183 r_free = 0.4183 target = 0.181766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.139744 restraints weight = 8350.841| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.16 r_work: 0.3528 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7097 Z= 0.178 Angle : 0.522 6.790 9585 Z= 0.273 Chirality : 0.041 0.184 1029 Planarity : 0.004 0.050 1206 Dihedral : 7.439 86.801 968 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.96 % Allowed : 14.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.29), residues: 851 helix: 2.28 (0.25), residues: 395 sheet: -0.05 (0.52), residues: 109 loop : -0.55 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 481 HIS 0.004 0.001 HIS B 322 PHE 0.011 0.001 PHE A 166 TYR 0.022 0.001 TYR A 318 ARG 0.002 0.000 ARG A 342 *********************** 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 113 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.745 Fit side-chains REVERT: A 290 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7641 (pp30) REVERT: A 313 TYR cc_start: 0.7879 (p90) cc_final: 0.7611 (p90) REVERT: A 346 TYR cc_start: 0.6914 (OUTLIER) cc_final: 0.6616 (m-10) REVERT: B 423 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8192 (mm) REVERT: C 261 TRP cc_start: 0.8321 (m100) cc_final: 0.8097 (m-90) outliers start: 22 outliers final: 16 residues processed: 104 average time/residue: 0.1816 time to fit residues: 25.9386 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 : 0.790 ------------------------------------------------------------------------------- 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 275 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 423 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 488 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 81 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.173746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.131745 restraints weight = 8326.336| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.12 r_work: 0.3465 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 7097 Z= 0.372 Angle : 0.603 8.174 9585 Z= 0.310 Chirality : 0.043 0.158 1029 Planarity : 0.004 0.049 1206 Dihedral : 7.604 89.777 968 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.23 % Allowed : 14.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.29), residues: 851 helix: 1.92 (0.24), residues: 403 sheet: -0.51 (0.50), residues: 118 loop : -0.66 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 147 HIS 0.005 0.001 HIS A 117 PHE 0.012 0.002 PHE A 166 TYR 0.022 0.002 TYR A 318 ARG 0.005 0.000 ARG B 220 *********************** 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 112 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.719 Fit side-chains REVERT: A 290 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7647 (pp30) REVERT: A 313 TYR cc_start: 0.7936 (p90) cc_final: 0.7700 (p90) REVERT: A 346 TYR cc_start: 0.6879 (OUTLIER) cc_final: 0.6604 (m-10) REVERT: B 377 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7087 (mp) outliers start: 24 outliers final: 18 residues processed: 104 average time/residue: 0.1702 time to fit residues: 24.6693 Evaluate side-chains 106 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 228 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 15 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.180756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.138964 restraints weight = 8332.065| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.13 r_work: 0.3501 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7097 Z= 0.223 Angle : 0.545 7.280 9585 Z= 0.281 Chirality : 0.041 0.161 1029 Planarity : 0.004 0.048 1206 Dihedral : 7.401 89.651 968 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.36 % Allowed : 14.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.29), residues: 851 helix: 2.10 (0.24), residues: 403 sheet: -0.38 (0.50), residues: 116 loop : -0.61 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 481 HIS 0.003 0.001 HIS B 322 PHE 0.012 0.001 PHE B 432 TYR 0.023 0.002 TYR A 318 ARG 0.007 0.000 ARG B 220 *********************** 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 117 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.784 Fit side-chains REVERT: A 290 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7690 (pp30) REVERT: A 313 TYR cc_start: 0.7917 (p90) cc_final: 0.7678 (p90) REVERT: A 346 TYR cc_start: 0.6857 (OUTLIER) cc_final: 0.6618 (m-10) REVERT: B 220 ARG cc_start: 0.8301 (ttm110) cc_final: 0.7964 (mtm-85) REVERT: B 377 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7164 (mp) outliers start: 25 outliers final: 19 residues processed: 108 average time/residue: 0.1821 time to fit residues: 27.0878 Evaluate side-chains 113 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 187 ILE Chi-restraints excluded: chain B residue 209 ILE 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 Chi-restraints excluded: chain B residue 488 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 37 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4181 r_free = 0.4181 target = 0.180829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.139696 restraints weight = 8349.227| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.13 r_work: 0.3512 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7097 Z= 0.216 Angle : 0.537 7.043 9585 Z= 0.277 Chirality : 0.041 0.158 1029 Planarity : 0.004 0.048 1206 Dihedral : 7.097 88.194 968 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.23 % Allowed : 14.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.29), residues: 851 helix: 2.21 (0.24), residues: 402 sheet: -0.55 (0.48), residues: 128 loop : -0.56 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 481 HIS 0.003 0.001 HIS B 322 PHE 0.012 0.001 PHE B 432 TYR 0.022 0.001 TYR A 318 ARG 0.006 0.000 ARG B 220 *********************** 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 117 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.924 Fit side-chains REVERT: A 290 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7719 (pp30) REVERT: A 313 TYR cc_start: 0.7959 (p90) cc_final: 0.7679 (p90) REVERT: A 346 TYR cc_start: 0.6904 (OUTLIER) cc_final: 0.6659 (m-10) REVERT: B 220 ARG cc_start: 0.8314 (ttm110) cc_final: 0.7956 (mtm-85) REVERT: B 249 MET cc_start: 0.8925 (tpp) cc_final: 0.8340 (mmm) outliers start: 24 outliers final: 19 residues processed: 108 average time/residue: 0.1716 time to fit residues: 25.6670 Evaluate side-chains 112 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 187 ILE Chi-restraints excluded: chain B residue 209 ILE 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 414 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 488 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 77 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN B 411 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.175821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.134020 restraints weight = 8406.546| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.16 r_work: 0.3484 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7097 Z= 0.259 Angle : 0.559 7.033 9585 Z= 0.288 Chirality : 0.042 0.156 1029 Planarity : 0.004 0.048 1206 Dihedral : 7.065 86.960 968 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.23 % Allowed : 14.80 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.29), residues: 851 helix: 2.11 (0.24), residues: 402 sheet: -0.64 (0.48), residues: 128 loop : -0.58 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 481 HIS 0.003 0.001 HIS A 117 PHE 0.012 0.001 PHE B 291 TYR 0.023 0.002 TYR A 318 ARG 0.006 0.000 ARG B 220 ********************** 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 114 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 290 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7744 (pp30) REVERT: A 313 TYR cc_start: 0.7956 (p90) cc_final: 0.7688 (p90) REVERT: A 346 TYR cc_start: 0.6948 (OUTLIER) cc_final: 0.6701 (m-10) REVERT: B 220 ARG cc_start: 0.8337 (ttm110) cc_final: 0.7996 (mtm-85) REVERT: B 249 MET cc_start: 0.8919 (tpp) cc_final: 0.8361 (mmm) REVERT: B 377 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7153 (mp) outliers start: 24 outliers final: 19 residues processed: 106 average time/residue: 0.1897 time to fit residues: 27.4117 Evaluate side-chains 111 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 110 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 20.0000 chunk 71 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 9 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4214 r_free = 0.4214 target = 0.182818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.142234 restraints weight = 8262.672| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.13 r_work: 0.3523 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7097 Z= 0.196 Angle : 0.538 6.644 9585 Z= 0.279 Chirality : 0.041 0.151 1029 Planarity : 0.004 0.048 1206 Dihedral : 6.899 86.533 968 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.36 % Allowed : 14.67 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.29), residues: 851 helix: 2.24 (0.25), residues: 402 sheet: -0.60 (0.48), residues: 128 loop : -0.53 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 481 HIS 0.003 0.001 HIS B 322 PHE 0.014 0.001 PHE B 291 TYR 0.023 0.001 TYR A 318 ARG 0.006 0.000 ARG B 220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4262.96 seconds wall clock time: 76 minutes 2.63 seconds (4562.63 seconds total)