Starting phenix.real_space_refine on Fri Oct 10 12:36:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x1b_37989/10_2025/8x1b_37989.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x1b_37989/10_2025/8x1b_37989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x1b_37989/10_2025/8x1b_37989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x1b_37989/10_2025/8x1b_37989.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x1b_37989/10_2025/8x1b_37989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x1b_37989/10_2025/8x1b_37989.map" } resolution = 2.59 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= 0.022 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: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 3224 2.51 5 N 837 2.21 5 O 1021 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5106 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5106 Classifications: {'peptide': 658} Link IDs: {'PTRANS': 34, 'TRANS': 623} Time building chain proxies: 1.22, per 1000 atoms: 0.24 Number of scatterers: 5106 At special positions: 0 Unit cell: (62.9, 82.45, 94.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1021 8.00 N 837 7.00 C 3224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 513 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 198.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1182 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 9 sheets defined 23.9% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 280 through 293 removed outlier: 3.723A pdb=" N GLY A 284 " --> pdb=" O ASP A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 301 through 305 removed outlier: 4.006A pdb=" N ILE A 305 " --> pdb=" O PRO A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 331 through 339 removed outlier: 3.735A pdb=" N LEU A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 380 removed outlier: 3.725A pdb=" N ALA A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 404 through 407 removed outlier: 3.507A pdb=" N PHE A 407 " --> pdb=" O PRO A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 407' Processing helix chain 'A' and resid 437 through 454 removed outlier: 3.801A pdb=" N ILE A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 removed outlier: 4.011A pdb=" N SER A 484 " --> pdb=" O PRO A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 503 removed outlier: 4.126A pdb=" N ILE A 491 " --> pdb=" O LYS A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 525 removed outlier: 3.535A pdb=" N SER A 521 " --> pdb=" O ASP A 518 " (cutoff:3.500A) Proline residue: A 523 - end of helix Processing helix chain 'A' and resid 535 through 551 Processing helix chain 'A' and resid 564 through 571 Processing helix chain 'A' and resid 583 through 600 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46 removed outlier: 3.588A pdb=" N ARG A 52 " --> pdb=" O TYR A 65 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 61 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 3.588A pdb=" N ARG A 52 " --> pdb=" O TYR A 65 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 61 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 77 removed outlier: 4.830A pdb=" N GLU A 166 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TRP A 159 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 77 removed outlier: 4.830A pdb=" N GLU A 166 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL A 164 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL A 252 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU A 166 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA A 250 " --> pdb=" O GLU A 166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 94 through 107 removed outlier: 5.648A pdb=" N HIS A 96 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLN A 120 " --> pdb=" O HIS A 96 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 98 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER A 104 " --> pdb=" O GLY A 112 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLY A 112 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER A 106 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLY A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 126 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER A 135 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL A 141 " --> pdb=" O SER A 135 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR A 146 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLY A 270 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TYR A 148 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLU A 268 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ALA A 150 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL A 266 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.689A pdb=" N ARG A 313 " --> pdb=" O GLU A 577 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 342 through 345 removed outlier: 7.051A pdb=" N ALA A 384 " --> pdb=" O GLY A 459 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N LYS A 461 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 386 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ASP A 463 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TRP A 388 " --> pdb=" O ASP A 463 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 605 through 607 removed outlier: 3.660A pdb=" N VAL A 622 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 619 " --> pdb=" O TYR A 634 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N MET A 629 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N MET A 658 " --> pdb=" O ILE A 696 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N TYR A 659 " --> pdb=" O THR A 672 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N THR A 672 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE A 661 " --> pdb=" O VAL A 670 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 648 through 649 205 hydrogen bonds defined for protein. 576 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: 0.72 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1687 1.35 - 1.47: 1331 1.47 - 1.59: 2179 1.59 - 1.70: 1 1.70 - 1.82: 42 Bond restraints: 5240 Sorted by residual: bond pdb=" CB PRO A 642 " pdb=" CG PRO A 642 " ideal model delta sigma weight residual 1.492 1.605 -0.113 5.00e-02 4.00e+02 5.10e+00 bond pdb=" CG PRO A 642 " pdb=" CD PRO A 642 " ideal model delta sigma weight residual 1.503 1.565 -0.062 3.40e-02 8.65e+02 3.30e+00 bond pdb=" CB ASP A 248 " pdb=" CG ASP A 248 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.28e+00 bond pdb=" CB PRO A 701 " pdb=" CG PRO A 701 " ideal model delta sigma weight residual 1.492 1.539 -0.047 5.00e-02 4.00e+02 8.97e-01 bond pdb=" CA LYS A 625 " pdb=" CB LYS A 625 " ideal model delta sigma weight residual 1.529 1.515 0.014 1.54e-02 4.22e+03 8.38e-01 ... (remaining 5235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 7008 1.57 - 3.13: 116 3.13 - 4.70: 15 4.70 - 6.27: 0 6.27 - 7.84: 2 Bond angle restraints: 7141 Sorted by residual: angle pdb=" CA PRO A 642 " pdb=" N PRO A 642 " pdb=" CD PRO A 642 " ideal model delta sigma weight residual 112.00 104.16 7.84 1.40e+00 5.10e-01 3.13e+01 angle pdb=" C ASP A 346 " pdb=" N ASP A 347 " pdb=" CA ASP A 347 " ideal model delta sigma weight residual 120.82 125.02 -4.20 1.47e+00 4.63e-01 8.15e+00 angle pdb=" N ASP A 347 " pdb=" CA ASP A 347 " pdb=" C ASP A 347 " ideal model delta sigma weight residual 110.24 113.82 -3.58 1.30e+00 5.92e-01 7.60e+00 angle pdb=" N PRO A 642 " pdb=" CA PRO A 642 " pdb=" CB PRO A 642 " ideal model delta sigma weight residual 103.25 100.40 2.85 1.05e+00 9.07e-01 7.39e+00 angle pdb=" N GLY A 107 " pdb=" CA GLY A 107 " pdb=" C GLY A 107 " ideal model delta sigma weight residual 111.20 114.26 -3.06 1.39e+00 5.18e-01 4.84e+00 ... (remaining 7136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 2653 17.93 - 35.86: 303 35.86 - 53.80: 77 53.80 - 71.73: 16 71.73 - 89.66: 6 Dihedral angle restraints: 3055 sinusoidal: 1173 harmonic: 1882 Sorted by residual: dihedral pdb=" CB CYS A 511 " pdb=" SG CYS A 511 " pdb=" SG CYS A 513 " pdb=" CB CYS A 513 " ideal model delta sinusoidal sigma weight residual 93.00 147.50 -54.50 1 1.00e+01 1.00e-02 4.02e+01 dihedral pdb=" CA ASN A 512 " pdb=" C ASN A 512 " pdb=" N CYS A 513 " pdb=" CA CYS A 513 " ideal model delta harmonic sigma weight residual -180.00 -162.33 -17.67 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA LYS A 578 " pdb=" C LYS A 578 " pdb=" N ARG A 579 " pdb=" CA ARG A 579 " ideal model delta harmonic sigma weight residual 180.00 -163.51 -16.49 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 3052 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 454 0.029 - 0.058: 173 0.058 - 0.087: 62 0.087 - 0.116: 55 0.116 - 0.146: 10 Chirality restraints: 754 Sorted by residual: chirality pdb=" CA ASP A 248 " pdb=" N ASP A 248 " pdb=" C ASP A 248 " pdb=" CB ASP A 248 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA PRO A 390 " pdb=" N PRO A 390 " pdb=" C PRO A 390 " pdb=" CB PRO A 390 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA PRO A 642 " pdb=" N PRO A 642 " pdb=" C PRO A 642 " pdb=" CB PRO A 642 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 751 not shown) Planarity restraints: 940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 403 " -0.046 5.00e-02 4.00e+02 7.03e-02 7.90e+00 pdb=" N PRO A 404 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 404 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 404 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 641 " 0.044 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO A 642 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 642 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 642 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 426 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO A 427 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 427 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 427 " 0.019 5.00e-02 4.00e+02 ... (remaining 937 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 895 2.77 - 3.30: 4378 3.30 - 3.83: 8474 3.83 - 4.37: 9810 4.37 - 4.90: 17834 Nonbonded interactions: 41391 Sorted by model distance: nonbonded pdb=" O LEU A 510 " pdb=" NE2 GLN A 517 " model vdw 2.236 3.120 nonbonded pdb=" O PRO A 469 " pdb=" OG SER A 484 " model vdw 2.306 3.040 nonbonded pdb=" NH1 ARG A 286 " pdb=" O ALA A 548 " model vdw 2.332 3.120 nonbonded pdb=" O ALA A 262 " pdb=" OG SER A 265 " model vdw 2.354 3.040 nonbonded pdb=" OG SER A 233 " pdb=" O THR A 235 " model vdw 2.359 3.040 ... (remaining 41386 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.150 Find NCS groups from input model: 0.020 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:7.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 : 0.003 0.113 5241 Z= 0.116 Angle : 0.497 7.835 7143 Z= 0.274 Chirality : 0.044 0.146 754 Planarity : 0.005 0.070 940 Dihedral : 16.586 89.660 1870 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.48 % Allowed : 24.35 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.33), residues: 656 helix: 1.47 (0.46), residues: 135 sheet: 0.96 (0.38), residues: 195 loop : -0.50 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 52 TYR 0.018 0.001 TYR A 406 PHE 0.006 0.001 PHE A 202 TRP 0.022 0.001 TRP A 323 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 5240) covalent geometry : angle 0.49635 ( 7141) SS BOND : bond 0.00517 ( 1) SS BOND : angle 1.25560 ( 2) hydrogen bonds : bond 0.20375 ( 198) hydrogen bonds : angle 7.48264 ( 576) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.150 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 144 average time/residue: 0.3799 time to fit residues: 57.8059 Evaluate side-chains 143 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 138 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 464 TYR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 672 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 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 113 GLN A 352 ASN A 477 ASN A 600 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.117541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.109904 restraints weight = 7242.993| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.68 r_work: 0.3436 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5241 Z= 0.158 Angle : 0.518 5.541 7143 Z= 0.283 Chirality : 0.046 0.150 754 Planarity : 0.004 0.048 940 Dihedral : 4.848 45.913 730 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.80 % Allowed : 18.82 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.32), residues: 656 helix: 1.41 (0.46), residues: 137 sheet: 0.86 (0.38), residues: 189 loop : -0.63 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 128 TYR 0.016 0.001 TYR A 406 PHE 0.008 0.001 PHE A 681 TRP 0.018 0.002 TRP A 323 HIS 0.004 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 5240) covalent geometry : angle 0.51710 ( 7141) SS BOND : bond 0.00691 ( 1) SS BOND : angle 1.57403 ( 2) hydrogen bonds : bond 0.04947 ( 198) hydrogen bonds : angle 5.39023 ( 576) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.145 Fit side-chains REVERT: A 248 ASP cc_start: 0.7268 (p0) cc_final: 0.7046 (p0) REVERT: A 334 GLU cc_start: 0.7864 (mp0) cc_final: 0.7653 (mp0) REVERT: A 600 GLN cc_start: 0.8261 (mm110) cc_final: 0.8027 (mm-40) outliers start: 26 outliers final: 12 residues processed: 157 average time/residue: 0.4048 time to fit residues: 66.8711 Evaluate side-chains 154 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 317 TRP Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 658 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 11 optimal weight: 2.9990 chunk 19 optimal weight: 0.0010 chunk 47 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 39 optimal weight: 0.0010 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.119026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.111642 restraints weight = 7095.749| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.63 r_work: 0.3465 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5241 Z= 0.113 Angle : 0.488 5.322 7143 Z= 0.265 Chirality : 0.045 0.135 754 Planarity : 0.004 0.044 940 Dihedral : 4.470 40.622 725 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.87 % Allowed : 20.11 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.32), residues: 656 helix: 1.78 (0.46), residues: 131 sheet: 0.91 (0.38), residues: 189 loop : -0.57 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.016 0.001 TYR A 406 PHE 0.017 0.001 PHE A 160 TRP 0.017 0.001 TRP A 323 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 5240) covalent geometry : angle 0.48735 ( 7141) SS BOND : bond 0.00484 ( 1) SS BOND : angle 1.27851 ( 2) hydrogen bonds : bond 0.04151 ( 198) hydrogen bonds : angle 4.99353 ( 576) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.191 Fit side-chains REVERT: A 239 VAL cc_start: 0.8019 (OUTLIER) cc_final: 0.7667 (p) REVERT: A 248 ASP cc_start: 0.7280 (p0) cc_final: 0.7055 (p0) outliers start: 21 outliers final: 11 residues processed: 151 average time/residue: 0.3541 time to fit residues: 56.5510 Evaluate side-chains 154 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 317 TRP Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 464 TYR Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 677 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 57 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.116583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.109533 restraints weight = 7217.477| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.54 r_work: 0.3436 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 5241 Z= 0.211 Angle : 0.545 6.133 7143 Z= 0.298 Chirality : 0.048 0.165 754 Planarity : 0.005 0.047 940 Dihedral : 4.697 36.168 725 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.98 % Allowed : 19.74 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.32), residues: 656 helix: 1.21 (0.45), residues: 137 sheet: 0.91 (0.38), residues: 189 loop : -0.72 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 414 TYR 0.014 0.002 TYR A 611 PHE 0.018 0.002 PHE A 160 TRP 0.020 0.002 TRP A 323 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00503 ( 5240) covalent geometry : angle 0.54469 ( 7141) SS BOND : bond 0.00802 ( 1) SS BOND : angle 1.78376 ( 2) hydrogen bonds : bond 0.05047 ( 198) hydrogen bonds : angle 5.06916 ( 576) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.199 Fit side-chains REVERT: A 248 ASP cc_start: 0.7341 (p0) cc_final: 0.7106 (p0) REVERT: A 662 VAL cc_start: 0.8783 (t) cc_final: 0.8574 (t) outliers start: 27 outliers final: 13 residues processed: 149 average time/residue: 0.4028 time to fit residues: 63.1464 Evaluate side-chains 151 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 317 TRP Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 506 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 59 optimal weight: 0.0050 chunk 45 optimal weight: 0.5980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.117491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.110375 restraints weight = 7239.509| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.56 r_work: 0.3453 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5241 Z= 0.152 Angle : 0.520 5.891 7143 Z= 0.283 Chirality : 0.047 0.148 754 Planarity : 0.004 0.047 940 Dihedral : 4.819 49.950 725 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.06 % Allowed : 21.22 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.32), residues: 656 helix: 1.52 (0.45), residues: 131 sheet: 0.88 (0.38), residues: 189 loop : -0.65 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 414 TYR 0.022 0.002 TYR A 406 PHE 0.016 0.001 PHE A 160 TRP 0.022 0.002 TRP A 323 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 5240) covalent geometry : angle 0.51928 ( 7141) SS BOND : bond 0.00597 ( 1) SS BOND : angle 1.44470 ( 2) hydrogen bonds : bond 0.04460 ( 198) hydrogen bonds : angle 4.91713 ( 576) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.131 Fit side-chains REVERT: A 138 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7246 (mm-30) REVERT: A 248 ASP cc_start: 0.7360 (p0) cc_final: 0.7129 (p0) REVERT: A 517 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7537 (tt0) outliers start: 22 outliers final: 16 residues processed: 150 average time/residue: 0.3796 time to fit residues: 60.1727 Evaluate side-chains 160 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 317 TRP Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 464 TYR Chi-restraints excluded: chain A residue 517 GLN Chi-restraints excluded: chain A residue 559 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 24 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 57 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 0.0870 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 0.0870 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.118356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.111294 restraints weight = 7229.472| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.56 r_work: 0.3469 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5241 Z= 0.119 Angle : 0.490 5.305 7143 Z= 0.266 Chirality : 0.045 0.139 754 Planarity : 0.004 0.045 940 Dihedral : 4.595 43.277 725 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.06 % Allowed : 21.59 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.32), residues: 656 helix: 1.68 (0.46), residues: 131 sheet: 0.87 (0.38), residues: 188 loop : -0.60 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 414 TYR 0.018 0.001 TYR A 406 PHE 0.014 0.001 PHE A 160 TRP 0.025 0.001 TRP A 323 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 5240) covalent geometry : angle 0.48983 ( 7141) SS BOND : bond 0.00476 ( 1) SS BOND : angle 1.26403 ( 2) hydrogen bonds : bond 0.03971 ( 198) hydrogen bonds : angle 4.75396 ( 576) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.172 Fit side-chains REVERT: A 239 VAL cc_start: 0.8021 (OUTLIER) cc_final: 0.7685 (p) REVERT: A 248 ASP cc_start: 0.7352 (p0) cc_final: 0.7144 (p0) REVERT: A 517 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7512 (tt0) outliers start: 22 outliers final: 9 residues processed: 154 average time/residue: 0.3689 time to fit residues: 60.0422 Evaluate side-chains 155 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 317 TRP Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 464 TYR Chi-restraints excluded: chain A residue 517 GLN Chi-restraints excluded: chain A residue 677 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.117404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.110143 restraints weight = 7216.511| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.58 r_work: 0.3449 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5241 Z= 0.170 Angle : 0.533 5.730 7143 Z= 0.289 Chirality : 0.047 0.153 754 Planarity : 0.004 0.041 940 Dihedral : 4.660 39.407 725 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.69 % Allowed : 21.96 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.32), residues: 656 helix: 1.51 (0.46), residues: 131 sheet: 0.90 (0.39), residues: 189 loop : -0.65 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 414 TYR 0.019 0.002 TYR A 406 PHE 0.015 0.002 PHE A 160 TRP 0.029 0.002 TRP A 323 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 5240) covalent geometry : angle 0.53250 ( 7141) SS BOND : bond 0.00661 ( 1) SS BOND : angle 1.54764 ( 2) hydrogen bonds : bond 0.04553 ( 198) hydrogen bonds : angle 4.87661 ( 576) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.152 Fit side-chains REVERT: A 248 ASP cc_start: 0.7363 (p0) cc_final: 0.7159 (p0) outliers start: 20 outliers final: 13 residues processed: 153 average time/residue: 0.3846 time to fit residues: 62.1458 Evaluate side-chains 159 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 317 TRP Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 559 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 44 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.0070 chunk 59 optimal weight: 0.0980 chunk 35 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 352 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.119247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.112042 restraints weight = 7206.865| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.57 r_work: 0.3471 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5241 Z= 0.111 Angle : 0.499 5.228 7143 Z= 0.269 Chirality : 0.045 0.134 754 Planarity : 0.004 0.042 940 Dihedral : 4.819 59.867 725 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.58 % Allowed : 23.99 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.32), residues: 656 helix: 1.74 (0.47), residues: 131 sheet: 0.90 (0.39), residues: 188 loop : -0.56 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 414 TYR 0.019 0.001 TYR A 406 PHE 0.013 0.001 PHE A 160 TRP 0.033 0.002 TRP A 323 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 5240) covalent geometry : angle 0.49865 ( 7141) SS BOND : bond 0.00450 ( 1) SS BOND : angle 1.21734 ( 2) hydrogen bonds : bond 0.03826 ( 198) hydrogen bonds : angle 4.70849 ( 576) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.138 Fit side-chains REVERT: A 344 THR cc_start: 0.8251 (OUTLIER) cc_final: 0.7962 (p) outliers start: 14 outliers final: 9 residues processed: 152 average time/residue: 0.3663 time to fit residues: 58.7218 Evaluate side-chains 153 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 317 TRP Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 464 TYR Chi-restraints excluded: chain A residue 677 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 37 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 0.0970 chunk 4 optimal weight: 0.0670 chunk 27 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 352 ASN A 477 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.118767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.111386 restraints weight = 7158.152| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.61 r_work: 0.3459 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5241 Z= 0.132 Angle : 0.518 5.298 7143 Z= 0.280 Chirality : 0.046 0.158 754 Planarity : 0.004 0.042 940 Dihedral : 4.822 59.286 725 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.77 % Allowed : 24.91 % Favored : 72.32 % 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: 0.46 (0.32), residues: 656 helix: 1.66 (0.46), residues: 131 sheet: 0.90 (0.39), residues: 188 loop : -0.58 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 414 TYR 0.021 0.001 TYR A 406 PHE 0.013 0.001 PHE A 160 TRP 0.039 0.002 TRP A 323 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 5240) covalent geometry : angle 0.51712 ( 7141) SS BOND : bond 0.00520 ( 1) SS BOND : angle 1.31322 ( 2) hydrogen bonds : bond 0.04022 ( 198) hydrogen bonds : angle 4.70424 ( 576) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.248 Fit side-chains REVERT: A 334 GLU cc_start: 0.7838 (mp0) cc_final: 0.7615 (mp0) outliers start: 15 outliers final: 12 residues processed: 145 average time/residue: 0.4049 time to fit residues: 61.8979 Evaluate side-chains 151 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 317 TRP Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 464 TYR Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 677 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 37 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 6 optimal weight: 0.0070 chunk 34 optimal weight: 0.1980 chunk 61 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 56 optimal weight: 0.0770 chunk 55 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 overall best weight: 0.2556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.122245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.114742 restraints weight = 7284.659| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.69 r_work: 0.3480 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5241 Z= 0.100 Angle : 0.502 5.156 7143 Z= 0.271 Chirality : 0.045 0.157 754 Planarity : 0.004 0.042 940 Dihedral : 4.745 58.957 725 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.03 % Allowed : 25.83 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.32), residues: 656 helix: 1.81 (0.46), residues: 131 sheet: 0.83 (0.39), residues: 188 loop : -0.52 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.018 0.001 TYR A 406 PHE 0.011 0.001 PHE A 160 TRP 0.043 0.002 TRP A 323 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 5240) covalent geometry : angle 0.50128 ( 7141) SS BOND : bond 0.00389 ( 1) SS BOND : angle 1.09136 ( 2) hydrogen bonds : bond 0.03576 ( 198) hydrogen bonds : angle 4.59917 ( 576) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.165 Fit side-chains REVERT: A 334 GLU cc_start: 0.7884 (mp0) cc_final: 0.7619 (mp0) REVERT: A 468 MET cc_start: 0.8427 (tpp) cc_final: 0.8000 (tpp) REVERT: A 482 GLU cc_start: 0.7793 (mp0) cc_final: 0.7431 (mp0) REVERT: A 662 VAL cc_start: 0.8773 (t) cc_final: 0.8558 (t) outliers start: 11 outliers final: 10 residues processed: 148 average time/residue: 0.3736 time to fit residues: 58.4647 Evaluate side-chains 153 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 464 TYR Chi-restraints excluded: chain A residue 677 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 45 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 51 optimal weight: 0.0770 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 32 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.119732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.112330 restraints weight = 7254.957| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.60 r_work: 0.3464 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5241 Z= 0.141 Angle : 0.526 5.365 7143 Z= 0.284 Chirality : 0.046 0.165 754 Planarity : 0.004 0.041 940 Dihedral : 4.827 59.166 725 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.66 % Allowed : 26.57 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.33), residues: 656 helix: 1.71 (0.46), residues: 131 sheet: 0.90 (0.39), residues: 189 loop : -0.57 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 414 TYR 0.019 0.001 TYR A 406 PHE 0.012 0.001 PHE A 160 TRP 0.046 0.002 TRP A 323 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 5240) covalent geometry : angle 0.52600 ( 7141) SS BOND : bond 0.00536 ( 1) SS BOND : angle 1.39441 ( 2) hydrogen bonds : bond 0.04007 ( 198) hydrogen bonds : angle 4.66415 ( 576) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2056.38 seconds wall clock time: 35 minutes 44.67 seconds (2144.67 seconds total)