Starting phenix.real_space_refine on Fri Aug 22 14:06:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c3f_45167/08_2025/9c3f_45167.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c3f_45167/08_2025/9c3f_45167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c3f_45167/08_2025/9c3f_45167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c3f_45167/08_2025/9c3f_45167.map" model { file = "/net/cci-nas-00/data/ceres_data/9c3f_45167/08_2025/9c3f_45167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c3f_45167/08_2025/9c3f_45167.cif" } resolution = 3.78 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= 0.001 sd= 0.041 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 19 5.16 5 C 2535 2.51 5 N 597 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s 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: 3800 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3714 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 17, 'TRANS': 467} Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'LMT': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.07, per 1000 atoms: 0.28 Number of scatterers: 3800 At special positions: 0 Unit cell: (71.98, 76.7, 87.32, 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 19 16.00 P 1 15.00 O 648 8.00 N 597 7.00 C 2535 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 100.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 880 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 86.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 11 through 29 removed outlier: 4.334A pdb=" N ALA A 15 " --> pdb=" O GLN A 11 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 16 " --> pdb=" O PRO A 12 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) Proline residue: A 27 - end of helix Processing helix chain 'A' and resid 32 through 40 removed outlier: 4.046A pdb=" N GLN A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 37 " --> pdb=" O GLY A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 61 removed outlier: 4.901A pdb=" N LEU A 54 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VAL A 55 " --> pdb=" O PHE A 51 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY A 56 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N TYR A 59 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 66 through 72 removed outlier: 4.025A pdb=" N ASP A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A 71 " --> pdb=" O PRO A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 88 removed outlier: 4.349A pdb=" N TRP A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LEU A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU A 85 " --> pdb=" O ARG A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 101 removed outlier: 3.695A pdb=" N ALA A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 136 removed outlier: 3.515A pdb=" N VAL A 135 " --> pdb=" O TRP A 131 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 170 removed outlier: 4.104A pdb=" N LEU A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 183 Processing helix chain 'A' and resid 184 through 193 Processing helix chain 'A' and resid 206 through 220 Proline residue: A 214 - end of helix Processing helix chain 'A' and resid 224 through 234 Processing helix chain 'A' and resid 235 through 252 removed outlier: 4.216A pdb=" N ALA A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU A 244 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N THR A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 284 removed outlier: 4.708A pdb=" N LEU A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 303 removed outlier: 4.374A pdb=" N ASN A 303 " --> pdb=" O GLN A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 312 removed outlier: 3.744A pdb=" N TRP A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 311 " --> pdb=" O TRP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 345 removed outlier: 3.968A pdb=" N SER A 335 " --> pdb=" O GLY A 331 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA A 336 " --> pdb=" O MET A 332 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N CYS A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 363 removed outlier: 3.566A pdb=" N GLN A 353 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 357 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 391 removed outlier: 4.500A pdb=" N TYR A 367 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 368 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY A 369 " --> pdb=" O ARG A 365 " (cutoff:3.500A) Proline residue: A 370 - end of helix removed outlier: 3.614A pdb=" N VAL A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A 377 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N TRP A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) removed outlier: 9.629A pdb=" N SER A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR A 383 " --> pdb=" O HIS A 379 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR A 385 " --> pdb=" O TRP A 381 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 402 removed outlier: 3.516A pdb=" N LEU A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 413 removed outlier: 3.892A pdb=" N LEU A 406 " --> pdb=" O CYS A 402 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 411 " --> pdb=" O GLU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 450 removed outlier: 3.684A pdb=" N ALA A 428 " --> pdb=" O GLY A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 487 removed outlier: 3.913A pdb=" N LEU A 462 " --> pdb=" O PHE A 458 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 463 " --> pdb=" O LEU A 459 " (cutoff:3.500A) 257 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.40 Time building geometry restraints manager: 0.40 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: 567 1.31 - 1.43: 1076 1.43 - 1.56: 2215 1.56 - 1.69: 3 1.69 - 1.81: 33 Bond restraints: 3894 Sorted by residual: bond pdb=" C18 PEE A 602 " pdb=" C19 PEE A 602 " ideal model delta sigma weight residual 1.523 1.307 0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C38 PEE A 602 " pdb=" C39 PEE A 602 " ideal model delta sigma weight residual 1.523 1.309 0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C LEU A 26 " pdb=" O LEU A 26 " ideal model delta sigma weight residual 1.244 1.182 0.061 9.80e-03 1.04e+04 3.94e+01 bond pdb=" CA PHE A 22 " pdb=" C PHE A 22 " ideal model delta sigma weight residual 1.523 1.470 0.053 1.35e-02 5.49e+03 1.53e+01 bond pdb=" C PHE A 22 " pdb=" N ALA A 23 " ideal model delta sigma weight residual 1.335 1.388 -0.053 1.35e-02 5.49e+03 1.52e+01 ... (remaining 3889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.32: 5123 3.32 - 6.64: 148 6.64 - 9.96: 17 9.96 - 13.28: 5 13.28 - 16.60: 5 Bond angle restraints: 5298 Sorted by residual: angle pdb=" CA PHE A 22 " pdb=" CB PHE A 22 " pdb=" CG PHE A 22 " ideal model delta sigma weight residual 113.80 128.32 -14.52 1.00e+00 1.00e+00 2.11e+02 angle pdb=" C ARG A 71 " pdb=" CA ARG A 71 " pdb=" CB ARG A 71 " ideal model delta sigma weight residual 110.85 94.25 16.60 1.70e+00 3.46e-01 9.54e+01 angle pdb=" N LEU A 91 " pdb=" CA LEU A 91 " pdb=" C LEU A 91 " ideal model delta sigma weight residual 111.28 102.11 9.17 1.09e+00 8.42e-01 7.07e+01 angle pdb=" CA THR A 31 " pdb=" CB THR A 31 " pdb=" OG1 THR A 31 " ideal model delta sigma weight residual 109.60 97.42 12.18 1.50e+00 4.44e-01 6.60e+01 angle pdb=" N LEU A 85 " pdb=" CA LEU A 85 " pdb=" CB LEU A 85 " ideal model delta sigma weight residual 110.12 121.16 -11.04 1.47e+00 4.63e-01 5.64e+01 ... (remaining 5293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.76: 2100 30.76 - 61.52: 165 61.52 - 92.28: 10 92.28 - 123.05: 4 123.05 - 153.81: 4 Dihedral angle restraints: 2283 sinusoidal: 904 harmonic: 1379 Sorted by residual: dihedral pdb=" CD ARG A 71 " pdb=" NE ARG A 71 " pdb=" CZ ARG A 71 " pdb=" NH1 ARG A 71 " ideal model delta sinusoidal sigma weight residual 0.00 75.82 -75.82 1 1.00e+01 1.00e-02 7.25e+01 dihedral pdb=" CD ARG A 80 " pdb=" NE ARG A 80 " pdb=" CZ ARG A 80 " pdb=" NH1 ARG A 80 " ideal model delta sinusoidal sigma weight residual 0.00 -69.02 69.02 1 1.00e+01 1.00e-02 6.16e+01 dihedral pdb=" C ARG A 71 " pdb=" N ARG A 71 " pdb=" CA ARG A 71 " pdb=" CB ARG A 71 " ideal model delta harmonic sigma weight residual -122.60 -105.10 -17.50 0 2.50e+00 1.60e-01 4.90e+01 ... (remaining 2280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 559 0.080 - 0.159: 51 0.159 - 0.239: 11 0.239 - 0.318: 6 0.318 - 0.398: 1 Chirality restraints: 628 Sorted by residual: chirality pdb=" CA PRO A 27 " pdb=" N PRO A 27 " pdb=" C PRO A 27 " pdb=" CB PRO A 27 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" CA ALA A 86 " pdb=" N ALA A 86 " pdb=" C ALA A 86 " pdb=" CB ALA A 86 " both_signs ideal model delta sigma weight residual False 2.48 2.18 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA LEU A 85 " pdb=" N LEU A 85 " pdb=" C LEU A 85 " pdb=" CB LEU A 85 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 625 not shown) Planarity restraints: 634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 71 " -1.086 9.50e-02 1.11e+02 4.87e-01 1.43e+02 pdb=" NE ARG A 71 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG A 71 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 71 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 71 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 80 " -1.055 9.50e-02 1.11e+02 4.73e-01 1.35e+02 pdb=" NE ARG A 80 " 0.061 2.00e-02 2.50e+03 pdb=" CZ ARG A 80 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG A 80 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 80 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 81 " -0.640 9.50e-02 1.11e+02 2.87e-01 5.02e+01 pdb=" NE ARG A 81 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG A 81 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 81 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 81 " -0.022 2.00e-02 2.50e+03 ... (remaining 631 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 981 2.80 - 3.33: 3684 3.33 - 3.85: 6051 3.85 - 4.38: 6132 4.38 - 4.90: 10953 Nonbonded interactions: 27801 Sorted by model distance: nonbonded pdb=" O ALA A 97 " pdb=" N PHE A 100 " model vdw 2.277 3.120 nonbonded pdb=" NZ LYS A 235 " pdb=" OE1 GLN A 299 " model vdw 2.325 3.120 nonbonded pdb=" OH TYR A 408 " pdb=" OD1 ASN A 412 " model vdw 2.339 3.040 nonbonded pdb=" NH1 ARG A 141 " pdb=" OG1 THR A 343 " model vdw 2.359 3.120 nonbonded pdb=" O LEU A 35 " pdb=" N TRP A 38 " model vdw 2.402 3.120 ... (remaining 27796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue 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: 0.950 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 4.670 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 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 : 0.009 0.216 3894 Z= 0.540 Angle : 1.270 16.602 5298 Z= 0.849 Chirality : 0.058 0.398 628 Planarity : 0.031 0.487 634 Dihedral : 21.433 153.807 1403 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.47 % Allowed : 30.53 % Favored : 65.00 % Cbeta Deviations : 0.45 % 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: 1.59 (0.40), residues: 483 helix: 1.97 (0.29), residues: 364 sheet: None (None), residues: 0 loop : -1.96 (0.48), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 80 TYR 0.008 0.001 TYR A 177 PHE 0.049 0.002 PHE A 22 TRP 0.024 0.001 TRP A 65 HIS 0.001 0.000 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00876 ( 3894) covalent geometry : angle 1.27041 ( 5298) hydrogen bonds : bond 0.13808 ( 257) hydrogen bonds : angle 4.97532 ( 762) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 37 time to evaluate : 0.105 Fit side-chains REVERT: A 80 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7615 (mpp80) outliers start: 17 outliers final: 10 residues processed: 50 average time/residue: 0.0595 time to fit residues: 3.6906 Evaluate side-chains 49 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 93 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4215 r_free = 0.4215 target = 0.202928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.168299 restraints weight = 4679.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.171847 restraints weight = 3231.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.174437 restraints weight = 2518.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.175712 restraints weight = 2131.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.177078 restraints weight = 1931.498| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3894 Z= 0.159 Angle : 0.589 6.015 5298 Z= 0.306 Chirality : 0.039 0.156 628 Planarity : 0.004 0.043 634 Dihedral : 15.777 159.874 647 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 5.53 % Allowed : 32.89 % Favored : 61.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.40), residues: 483 helix: 1.94 (0.28), residues: 378 sheet: None (None), residues: 0 loop : -2.29 (0.50), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 80 TYR 0.008 0.001 TYR A 385 PHE 0.032 0.002 PHE A 295 TRP 0.015 0.001 TRP A 65 HIS 0.002 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 3894) covalent geometry : angle 0.58884 ( 5298) hydrogen bonds : bond 0.05080 ( 257) hydrogen bonds : angle 3.97214 ( 762) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 39 time to evaluate : 0.079 Fit side-chains REVERT: A 183 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6687 (tp) outliers start: 21 outliers final: 13 residues processed: 52 average time/residue: 0.0423 time to fit residues: 3.0101 Evaluate side-chains 53 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 41 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 18 optimal weight: 0.0370 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 27 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- 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 = 0.4263 r_free = 0.4263 target = 0.210475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.175344 restraints weight = 4628.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.178842 restraints weight = 3233.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.181660 restraints weight = 2545.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.183298 restraints weight = 2159.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.184626 restraints weight = 1934.302| |-----------------------------------------------------------------------------| r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3894 Z= 0.116 Angle : 0.521 7.786 5298 Z= 0.263 Chirality : 0.038 0.215 628 Planarity : 0.004 0.038 634 Dihedral : 13.908 178.243 632 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.21 % Allowed : 34.21 % Favored : 61.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.40), residues: 483 helix: 2.23 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -1.93 (0.50), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 71 TYR 0.007 0.001 TYR A 385 PHE 0.027 0.001 PHE A 295 TRP 0.016 0.001 TRP A 65 HIS 0.001 0.000 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 3894) covalent geometry : angle 0.52103 ( 5298) hydrogen bonds : bond 0.04233 ( 257) hydrogen bonds : angle 3.72132 ( 762) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.095 Fit side-chains REVERT: A 208 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6378 (tm-30) REVERT: A 303 ASN cc_start: 0.8630 (p0) cc_final: 0.8252 (p0) outliers start: 16 outliers final: 7 residues processed: 55 average time/residue: 0.0403 time to fit residues: 3.0123 Evaluate side-chains 50 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 211 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 7 optimal weight: 0.0980 chunk 26 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.208122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.173447 restraints weight = 4680.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.176884 restraints weight = 3309.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.179564 restraints weight = 2624.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.181038 restraints weight = 2236.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.182300 restraints weight = 2016.585| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3894 Z= 0.132 Angle : 0.540 6.700 5298 Z= 0.276 Chirality : 0.039 0.340 628 Planarity : 0.004 0.037 634 Dihedral : 12.433 173.902 629 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 5.53 % Allowed : 33.68 % Favored : 60.79 % 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: 1.89 (0.40), residues: 483 helix: 2.16 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -2.02 (0.48), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 141 TYR 0.006 0.001 TYR A 385 PHE 0.013 0.001 PHE A 22 TRP 0.011 0.001 TRP A 65 HIS 0.001 0.000 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 3894) covalent geometry : angle 0.54038 ( 5298) hydrogen bonds : bond 0.04434 ( 257) hydrogen bonds : angle 3.78538 ( 762) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 45 time to evaluate : 0.131 Fit side-chains REVERT: A 303 ASN cc_start: 0.8602 (p0) cc_final: 0.8193 (p0) outliers start: 21 outliers final: 12 residues processed: 59 average time/residue: 0.0438 time to fit residues: 3.5429 Evaluate side-chains 57 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 319 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 18 optimal weight: 0.0040 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 17 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.206543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.172118 restraints weight = 4567.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.175816 restraints weight = 3134.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.178221 restraints weight = 2445.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.180121 restraints weight = 2062.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.181165 restraints weight = 1836.445| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 3894 Z= 0.116 Angle : 0.527 7.160 5298 Z= 0.266 Chirality : 0.038 0.283 628 Planarity : 0.004 0.034 634 Dihedral : 11.829 167.510 629 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 5.26 % Allowed : 33.16 % Favored : 61.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.40), residues: 483 helix: 2.27 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -2.05 (0.48), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 141 TYR 0.013 0.001 TYR A 385 PHE 0.013 0.001 PHE A 22 TRP 0.012 0.001 TRP A 65 HIS 0.000 0.000 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 3894) covalent geometry : angle 0.52737 ( 5298) hydrogen bonds : bond 0.04024 ( 257) hydrogen bonds : angle 3.69230 ( 762) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 48 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6387 (tm-30) REVERT: A 240 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7575 (t80) REVERT: A 439 LEU cc_start: 0.5593 (OUTLIER) cc_final: 0.5364 (mp) outliers start: 20 outliers final: 12 residues processed: 61 average time/residue: 0.0443 time to fit residues: 3.8036 Evaluate side-chains 59 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 439 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.0980 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.204611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.170393 restraints weight = 4646.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.173938 restraints weight = 3197.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.176463 restraints weight = 2496.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.178009 restraints weight = 2113.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.179319 restraints weight = 1888.123| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3894 Z= 0.122 Angle : 0.528 8.067 5298 Z= 0.266 Chirality : 0.037 0.226 628 Planarity : 0.004 0.034 634 Dihedral : 11.474 162.352 629 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.74 % Allowed : 33.68 % Favored : 61.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.40), residues: 483 helix: 2.23 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -2.13 (0.48), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 141 TYR 0.008 0.001 TYR A 385 PHE 0.012 0.001 PHE A 22 TRP 0.009 0.001 TRP A 65 HIS 0.000 0.000 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 3894) covalent geometry : angle 0.52757 ( 5298) hydrogen bonds : bond 0.04135 ( 257) hydrogen bonds : angle 3.71819 ( 762) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.129 Fit side-chains REVERT: A 71 ARG cc_start: 0.8499 (tpt170) cc_final: 0.7871 (tpt170) REVERT: A 240 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7648 (t80) outliers start: 18 outliers final: 13 residues processed: 55 average time/residue: 0.0469 time to fit residues: 3.6269 Evaluate side-chains 55 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 319 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.0770 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.4245 r_free = 0.4245 target = 0.208456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.173800 restraints weight = 4781.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.177383 restraints weight = 3391.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.179571 restraints weight = 2700.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.181381 restraints weight = 2321.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.182373 restraints weight = 2082.530| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3894 Z= 0.121 Angle : 0.534 8.660 5298 Z= 0.266 Chirality : 0.037 0.194 628 Planarity : 0.004 0.033 634 Dihedral : 11.232 157.323 629 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 5.26 % Allowed : 32.89 % Favored : 61.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.40), residues: 483 helix: 2.22 (0.29), residues: 371 sheet: None (None), residues: 0 loop : -2.18 (0.48), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 141 TYR 0.009 0.001 TYR A 385 PHE 0.013 0.001 PHE A 76 TRP 0.009 0.001 TRP A 65 HIS 0.000 0.000 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 3894) covalent geometry : angle 0.53441 ( 5298) hydrogen bonds : bond 0.04115 ( 257) hydrogen bonds : angle 3.73742 ( 762) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 42 time to evaluate : 0.122 Fit side-chains REVERT: A 71 ARG cc_start: 0.8490 (tpt170) cc_final: 0.7804 (tpt170) REVERT: A 208 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6421 (tm-30) REVERT: A 240 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7641 (t80) REVERT: A 439 LEU cc_start: 0.5635 (OUTLIER) cc_final: 0.5373 (mp) outliers start: 20 outliers final: 12 residues processed: 53 average time/residue: 0.0427 time to fit residues: 3.1110 Evaluate side-chains 56 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 439 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.0870 chunk 1 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 3 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 30 optimal weight: 0.0000 overall best weight: 0.3762 ------------------------------------------------------------------------------- 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 = 0.4243 r_free = 0.4243 target = 0.207635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.173398 restraints weight = 4643.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.176846 restraints weight = 3194.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.179574 restraints weight = 2492.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.180954 restraints weight = 2101.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.182416 restraints weight = 1891.684| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3894 Z= 0.107 Angle : 0.518 9.411 5298 Z= 0.255 Chirality : 0.036 0.161 628 Planarity : 0.003 0.031 634 Dihedral : 10.763 148.283 628 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.95 % Allowed : 33.95 % Favored : 62.11 % 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: 2.20 (0.40), residues: 483 helix: 2.40 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -1.72 (0.52), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 141 TYR 0.007 0.001 TYR A 385 PHE 0.010 0.001 PHE A 22 TRP 0.010 0.001 TRP A 65 HIS 0.000 0.000 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 3894) covalent geometry : angle 0.51787 ( 5298) hydrogen bonds : bond 0.03709 ( 257) hydrogen bonds : angle 3.66744 ( 762) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.130 Fit side-chains REVERT: A 208 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6325 (tm-30) REVERT: A 240 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7603 (t80) outliers start: 15 outliers final: 9 residues processed: 55 average time/residue: 0.0371 time to fit residues: 2.9721 Evaluate side-chains 51 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 240 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 0 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 40 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4191 r_free = 0.4191 target = 0.201664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.167853 restraints weight = 4716.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.171343 restraints weight = 3278.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.173744 restraints weight = 2571.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.174881 restraints weight = 2190.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.176155 restraints weight = 1996.005| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3894 Z= 0.143 Angle : 0.562 8.493 5298 Z= 0.280 Chirality : 0.038 0.152 628 Planarity : 0.004 0.033 634 Dihedral : 10.638 150.936 625 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.95 % Allowed : 34.74 % Favored : 61.32 % 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: 2.02 (0.41), residues: 483 helix: 2.28 (0.29), residues: 366 sheet: None (None), residues: 0 loop : -1.87 (0.52), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 141 TYR 0.006 0.001 TYR A 385 PHE 0.014 0.001 PHE A 22 TRP 0.008 0.001 TRP A 65 HIS 0.001 0.000 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 3894) covalent geometry : angle 0.56197 ( 5298) hydrogen bonds : bond 0.04451 ( 257) hydrogen bonds : angle 3.80951 ( 762) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.132 Fit side-chains REVERT: A 205 LYS cc_start: 0.4247 (mptt) cc_final: 0.3932 (mptt) REVERT: A 240 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7572 (t80) outliers start: 15 outliers final: 11 residues processed: 51 average time/residue: 0.0469 time to fit residues: 3.2599 Evaluate side-chains 53 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 319 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 10 optimal weight: 0.0010 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 44 optimal weight: 4.9990 chunk 21 optimal weight: 0.3980 chunk 36 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 overall best weight: 0.4586 ------------------------------------------------------------------------------- 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 = 0.4256 r_free = 0.4256 target = 0.210087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.175069 restraints weight = 4851.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.178353 restraints weight = 3452.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.181005 restraints weight = 2754.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.182455 restraints weight = 2352.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.183709 restraints weight = 2126.654| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3894 Z= 0.112 Angle : 0.523 8.695 5298 Z= 0.260 Chirality : 0.036 0.143 628 Planarity : 0.004 0.031 634 Dihedral : 10.520 148.687 625 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.42 % Allowed : 35.00 % Favored : 61.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.40), residues: 483 helix: 2.38 (0.29), residues: 365 sheet: None (None), residues: 0 loop : -1.87 (0.50), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 141 TYR 0.005 0.001 TYR A 385 PHE 0.011 0.001 PHE A 22 TRP 0.012 0.001 TRP A 65 HIS 0.001 0.000 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 3894) covalent geometry : angle 0.52302 ( 5298) hydrogen bonds : bond 0.03923 ( 257) hydrogen bonds : angle 3.68714 ( 762) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.087 Fit side-chains REVERT: A 205 LYS cc_start: 0.4273 (mptt) cc_final: 0.4012 (mptt) REVERT: A 240 PHE cc_start: 0.7856 (OUTLIER) cc_final: 0.7550 (t80) outliers start: 13 outliers final: 11 residues processed: 48 average time/residue: 0.0455 time to fit residues: 2.9361 Evaluate side-chains 52 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 319 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 3 optimal weight: 0.0060 chunk 11 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 0.0010 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 overall best weight: 0.4402 ------------------------------------------------------------------------------- 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 = 0.4234 r_free = 0.4234 target = 0.206756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.172237 restraints weight = 4650.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.175678 restraints weight = 3225.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.178339 restraints weight = 2529.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.179818 restraints weight = 2145.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.180225 restraints weight = 1930.300| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3894 Z= 0.112 Angle : 0.525 8.833 5298 Z= 0.260 Chirality : 0.036 0.149 628 Planarity : 0.003 0.031 634 Dihedral : 10.488 148.271 625 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.68 % Allowed : 35.00 % Favored : 61.32 % 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: 2.11 (0.40), residues: 483 helix: 2.39 (0.29), residues: 365 sheet: None (None), residues: 0 loop : -1.96 (0.49), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 141 TYR 0.012 0.001 TYR A 385 PHE 0.011 0.001 PHE A 22 TRP 0.011 0.001 TRP A 65 HIS 0.001 0.000 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 3894) covalent geometry : angle 0.52493 ( 5298) hydrogen bonds : bond 0.03868 ( 257) hydrogen bonds : angle 3.69262 ( 762) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 695.88 seconds wall clock time: 12 minutes 37.33 seconds (757.33 seconds total)