Starting phenix.real_space_refine on Fri Dec 27 09:09:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c3f_45167/12_2024/9c3f_45167.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c3f_45167/12_2024/9c3f_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_45167/12_2024/9c3f_45167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c3f_45167/12_2024/9c3f_45167.map" model { file = "/net/cci-nas-00/data/ceres_data/9c3f_45167/12_2024/9c3f_45167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c3f_45167/12_2024/9c3f_45167.cif" } resolution = 3.78 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= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 2.93, per 1000 atoms: 0.77 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: 1.02 Conformation dependent library (CDL) restraints added in 573.2 milliseconds 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: 0.37 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: 1.29 Time building geometry restraints manager: 1.17 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: 0.700 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.870 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.880 ------------------------------------------------------------------------------- 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= 0.523 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 (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: 1.59 (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 TRP 0.024 0.001 TRP A 65 HIS 0.001 0.000 HIS A 379 PHE 0.049 0.002 PHE A 22 TYR 0.008 0.001 TYR A 177 ARG 0.004 0.000 ARG A 80 *********************** 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 : 0.371 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: 0.1725 time to fit residues: 10.7486 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 : 0.399 ------------------------------------------------------------------------------- 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 40 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 0.0770 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3894 Z= 0.165 Angle : 0.547 5.957 5298 Z= 0.285 Chirality : 0.038 0.142 628 Planarity : 0.004 0.041 634 Dihedral : 15.871 161.468 647 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.21 % Allowed : 33.42 % Favored : 62.37 % 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: 1.87 (0.40), residues: 483 helix: 2.14 (0.28), residues: 377 sheet: None (None), residues: 0 loop : -2.25 (0.50), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 65 HIS 0.001 0.000 HIS A 379 PHE 0.030 0.001 PHE A 295 TYR 0.008 0.001 TYR A 385 ARG 0.007 0.001 ARG A 71 *********************** 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 54 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.404 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 47 average time/residue: 0.1282 time to fit residues: 8.1276 Evaluate side-chains 50 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 191 THR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 363 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3894 Z= 0.212 Angle : 0.567 7.651 5298 Z= 0.288 Chirality : 0.039 0.216 628 Planarity : 0.004 0.040 634 Dihedral : 13.947 178.212 632 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.26 % Allowed : 33.42 % 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 (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: 1.91 (0.40), residues: 483 helix: 2.15 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -1.88 (0.49), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 65 HIS 0.001 0.000 HIS A 379 PHE 0.029 0.002 PHE A 295 TYR 0.007 0.001 TYR A 385 ARG 0.004 0.000 ARG A 71 *********************** 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 61 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.394 Fit side-chains REVERT: A 208 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6456 (tm-30) REVERT: A 303 ASN cc_start: 0.8661 (p0) cc_final: 0.8167 (p0) outliers start: 20 outliers final: 10 residues processed: 55 average time/residue: 0.1207 time to fit residues: 8.8670 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 : 0.380 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 430 TRP Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 0.0670 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.7324 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3894 Z= 0.202 Angle : 0.551 6.937 5298 Z= 0.282 Chirality : 0.039 0.340 628 Planarity : 0.004 0.037 634 Dihedral : 12.541 174.913 629 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 6.32 % Allowed : 32.89 % 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 (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: 1.84 (0.40), residues: 483 helix: 2.12 (0.29), residues: 371 sheet: None (None), residues: 0 loop : -2.01 (0.48), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 65 HIS 0.000 0.000 HIS A 379 PHE 0.016 0.001 PHE A 22 TYR 0.006 0.001 TYR A 385 ARG 0.003 0.000 ARG A 71 *********************** 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 68 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 44 time to evaluate : 0.411 Fit side-chains REVERT: A 71 ARG cc_start: 0.8484 (tpt170) cc_final: 0.8239 (tpt170) REVERT: A 303 ASN cc_start: 0.8634 (p0) cc_final: 0.8208 (p0) outliers start: 24 outliers final: 14 residues processed: 63 average time/residue: 0.1323 time to fit residues: 10.9926 Evaluate side-chains 58 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 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 188 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 430 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 15 optimal weight: 0.2980 chunk 9 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3894 Z= 0.176 Angle : 0.544 8.249 5298 Z= 0.274 Chirality : 0.038 0.279 628 Planarity : 0.004 0.035 634 Dihedral : 11.952 169.328 629 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 6.05 % Allowed : 32.63 % 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 (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: 1.88 (0.40), residues: 483 helix: 2.17 (0.29), residues: 371 sheet: None (None), residues: 0 loop : -2.08 (0.48), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 65 HIS 0.000 0.000 HIS A 379 PHE 0.013 0.001 PHE A 22 TYR 0.011 0.001 TYR A 385 ARG 0.002 0.000 ARG A 141 *********************** 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 70 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 47 time to evaluate : 0.411 Fit side-chains REVERT: A 71 ARG cc_start: 0.8455 (tpt170) cc_final: 0.7854 (tpt170) REVERT: A 208 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6431 (tm-30) REVERT: A 240 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7678 (t80) REVERT: A 303 ASN cc_start: 0.8540 (p0) cc_final: 0.8321 (p0) outliers start: 23 outliers final: 15 residues processed: 63 average time/residue: 0.1166 time to fit residues: 9.9899 Evaluate side-chains 61 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 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 206 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 430 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3894 Z= 0.212 Angle : 0.555 9.215 5298 Z= 0.281 Chirality : 0.038 0.222 628 Planarity : 0.004 0.036 634 Dihedral : 11.692 165.902 629 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 6.58 % Allowed : 32.37 % Favored : 61.05 % 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: 1.73 (0.40), residues: 483 helix: 2.06 (0.29), residues: 372 sheet: None (None), residues: 0 loop : -2.19 (0.48), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 65 HIS 0.000 0.000 HIS A 379 PHE 0.014 0.001 PHE A 22 TYR 0.007 0.001 TYR A 385 ARG 0.002 0.000 ARG A 141 *********************** 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 70 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 45 time to evaluate : 0.400 Fit side-chains REVERT: A 71 ARG cc_start: 0.8384 (tpt170) cc_final: 0.7607 (tpt170) REVERT: A 208 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6498 (tm-30) REVERT: A 240 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.7623 (t80) REVERT: A 303 ASN cc_start: 0.8521 (p0) cc_final: 0.8288 (p0) outliers start: 25 outliers final: 18 residues processed: 63 average time/residue: 0.1308 time to fit residues: 10.8873 Evaluate side-chains 63 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 43 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 73 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 206 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 274 VAL Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 430 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 8 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3894 Z= 0.167 Angle : 0.530 7.658 5298 Z= 0.267 Chirality : 0.036 0.196 628 Planarity : 0.004 0.033 634 Dihedral : 11.437 161.122 629 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.53 % Allowed : 33.16 % 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 (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: 1.75 (0.40), residues: 483 helix: 2.08 (0.29), residues: 372 sheet: None (None), residues: 0 loop : -2.20 (0.49), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 65 HIS 0.000 0.000 HIS A 379 PHE 0.012 0.001 PHE A 22 TYR 0.005 0.001 TYR A 385 ARG 0.002 0.000 ARG A 141 *********************** 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 66 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 45 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6477 (tm-30) REVERT: A 240 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7592 (t80) REVERT: A 439 LEU cc_start: 0.5694 (OUTLIER) cc_final: 0.5440 (mp) outliers start: 21 outliers final: 14 residues processed: 59 average time/residue: 0.1419 time to fit residues: 10.8586 Evaluate side-chains 60 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 73 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 206 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 430 TRP 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 29 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 0.0870 chunk 36 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 40 optimal weight: 0.0570 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 18 optimal weight: 0.0570 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2035 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= 0.137 Angle : 0.514 8.141 5298 Z= 0.257 Chirality : 0.036 0.168 628 Planarity : 0.004 0.032 634 Dihedral : 10.942 151.716 629 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.47 % Allowed : 33.42 % 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 (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: 2.12 (0.40), residues: 483 helix: 2.33 (0.29), residues: 365 sheet: None (None), residues: 0 loop : -1.72 (0.52), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 65 HIS 0.000 0.000 HIS A 379 PHE 0.015 0.001 PHE A 76 TYR 0.005 0.001 TYR A 385 ARG 0.002 0.000 ARG A 141 *********************** 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 64 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.392 Fit side-chains REVERT: A 208 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6426 (tm-30) REVERT: A 240 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7606 (t80) REVERT: A 430 TRP cc_start: 0.4783 (OUTLIER) cc_final: 0.3690 (m-90) outliers start: 17 outliers final: 10 residues processed: 58 average time/residue: 0.1040 time to fit residues: 8.3251 Evaluate side-chains 55 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 90 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 430 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 21 optimal weight: 0.0030 chunk 31 optimal weight: 0.0060 chunk 47 optimal weight: 2.9990 overall best weight: 0.4406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.2079 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= 0.154 Angle : 0.517 8.033 5298 Z= 0.258 Chirality : 0.036 0.155 628 Planarity : 0.004 0.032 634 Dihedral : 10.739 149.532 627 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.95 % Allowed : 33.68 % Favored : 62.37 % 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: 2.13 (0.40), residues: 483 helix: 2.35 (0.29), residues: 365 sheet: None (None), residues: 0 loop : -1.78 (0.51), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 65 HIS 0.000 0.000 HIS A 379 PHE 0.016 0.001 PHE A 295 TYR 0.011 0.001 TYR A 385 ARG 0.002 0.000 ARG A 141 *********************** 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 : 0.399 Fit side-chains REVERT: A 208 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6375 (tm-30) REVERT: A 240 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.7569 (t80) REVERT: A 332 MET cc_start: 0.7573 (ttt) cc_final: 0.7305 (ttt) REVERT: A 430 TRP cc_start: 0.4818 (OUTLIER) cc_final: 0.3583 (m-90) outliers start: 15 outliers final: 10 residues processed: 52 average time/residue: 0.1196 time to fit residues: 8.5460 Evaluate side-chains 53 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 90 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 430 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 0.0670 chunk 30 optimal weight: 0.8980 chunk 40 optimal weight: 0.0670 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.2980 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.2203 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= 0.139 Angle : 0.509 7.980 5298 Z= 0.253 Chirality : 0.035 0.142 628 Planarity : 0.003 0.031 634 Dihedral : 10.426 148.129 625 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.21 % Allowed : 33.16 % Favored : 62.63 % 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: 2.17 (0.40), residues: 483 helix: 2.41 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -1.84 (0.49), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 65 HIS 0.000 0.000 HIS A 379 PHE 0.017 0.001 PHE A 295 TYR 0.008 0.001 TYR A 385 ARG 0.003 0.000 ARG A 141 ********************** 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 57 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.383 Fit side-chains REVERT: A 208 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6325 (tm-30) REVERT: A 240 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7564 (t80) REVERT: A 430 TRP cc_start: 0.4918 (OUTLIER) cc_final: 0.3884 (m-90) outliers start: 16 outliers final: 12 residues processed: 53 average time/residue: 0.1148 time to fit residues: 8.3660 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 : 0.384 ------------------------------------------------------------------------------- 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 44 ILE Chi-restraints excluded: chain A residue 68 LEU 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 177 TYR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 430 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 0.0980 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 7 optimal weight: 0.0370 chunk 33 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.4258 ------------------------------------------------------------------------------- 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 = 0.4246 r_free = 0.4246 target = 0.207678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.173686 restraints weight = 4622.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.176986 restraints weight = 3298.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.179287 restraints weight = 2625.574| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.2227 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= 0.150 Angle : 0.511 8.563 5298 Z= 0.254 Chirality : 0.035 0.138 628 Planarity : 0.003 0.031 634 Dihedral : 10.415 148.755 625 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.47 % Allowed : 32.63 % Favored : 62.89 % 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: 2.15 (0.40), residues: 483 helix: 2.41 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -1.91 (0.49), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 65 HIS 0.001 0.000 HIS A 379 PHE 0.016 0.001 PHE A 295 TYR 0.008 0.001 TYR A 385 ARG 0.003 0.000 ARG A 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1029.87 seconds wall clock time: 19 minutes 42.88 seconds (1182.88 seconds total)