Starting phenix.real_space_refine on Thu Mar 6 06:05:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x1b_37989/03_2025/8x1b_37989.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x1b_37989/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8x1b_37989/03_2025/8x1b_37989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x1b_37989/03_2025/8x1b_37989.map" model { file = "/net/cci-nas-00/data/ceres_data/8x1b_37989/03_2025/8x1b_37989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x1b_37989/03_2025/8x1b_37989.cif" } resolution = 2.59 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= 0.022 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.88, per 1000 atoms: 1.35 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: 1.36 Conformation dependent library (CDL) restraints added in 661.9 milliseconds 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: 0.57 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: 1.99 Time building geometry restraints manager: 1.61 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: 17.310 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 23.510 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:18.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.100 ------------------------------------------------------------------------------- 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 5240 Z= 0.178 Angle : 0.496 7.835 7141 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (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 TRP 0.022 0.001 TRP A 323 HIS 0.003 0.001 HIS A 96 PHE 0.006 0.001 PHE A 202 TYR 0.018 0.001 TYR A 406 ARG 0.001 0.000 ARG A 52 *********************** 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 : 0.801 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 144 average time/residue: 1.2974 time to fit residues: 195.7876 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 : 2.181 ------------------------------------------------------------------------------- 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 54 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.117636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.110258 restraints weight = 7124.372| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.61 r_work: 0.3438 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5240 Z= 0.299 Angle : 0.537 5.945 7141 Z= 0.293 Chirality : 0.047 0.158 754 Planarity : 0.005 0.049 940 Dihedral : 4.941 44.884 730 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.32), residues: 656 helix: 1.31 (0.45), residues: 137 sheet: 0.84 (0.38), residues: 189 loop : -0.66 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 323 HIS 0.004 0.001 HIS A 96 PHE 0.008 0.001 PHE A 606 TYR 0.017 0.002 TYR A 406 ARG 0.004 0.000 ARG A 128 *********************** 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 174 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.620 Fit side-chains REVERT: A 248 ASP cc_start: 0.7281 (p0) cc_final: 0.7059 (p0) REVERT: A 334 GLU cc_start: 0.7843 (mp0) cc_final: 0.7639 (mp0) outliers start: 26 outliers final: 14 residues processed: 154 average time/residue: 1.6834 time to fit residues: 268.0169 Evaluate side-chains 157 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 185 MET 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 506 VAL 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 36 optimal weight: 0.4980 chunk 19 optimal weight: 0.0030 chunk 58 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 A 600 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.117942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.110938 restraints weight = 7163.757| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.54 r_work: 0.3462 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5240 Z= 0.201 Angle : 0.503 5.650 7141 Z= 0.274 Chirality : 0.046 0.142 754 Planarity : 0.004 0.045 940 Dihedral : 4.719 50.887 725 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.24 % Allowed : 20.30 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.32), residues: 656 helix: 1.66 (0.46), residues: 131 sheet: 0.88 (0.38), residues: 189 loop : -0.62 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 323 HIS 0.003 0.001 HIS A 96 PHE 0.009 0.001 PHE A 681 TYR 0.017 0.001 TYR A 406 ARG 0.003 0.000 ARG A 128 *********************** 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 167 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.589 Fit side-chains REVERT: A 239 VAL cc_start: 0.8037 (OUTLIER) cc_final: 0.7688 (p) REVERT: A 248 ASP cc_start: 0.7281 (p0) cc_final: 0.7030 (p0) REVERT: A 600 GLN cc_start: 0.8255 (mm110) cc_final: 0.8027 (mm-40) REVERT: A 663 ASP cc_start: 0.6957 (t70) cc_final: 0.6738 (p0) outliers start: 23 outliers final: 10 residues processed: 151 average time/residue: 1.1936 time to fit residues: 187.7535 Evaluate side-chains 153 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR 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 322 ASN Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 656 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 43 optimal weight: 0.3980 chunk 25 optimal weight: 0.2980 chunk 6 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.117969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.110865 restraints weight = 7239.785| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.56 r_work: 0.3461 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5240 Z= 0.208 Angle : 0.495 5.419 7141 Z= 0.269 Chirality : 0.046 0.145 754 Planarity : 0.004 0.047 940 Dihedral : 4.635 45.685 725 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.43 % Allowed : 21.03 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.32), residues: 656 helix: 1.69 (0.46), residues: 131 sheet: 0.90 (0.39), residues: 189 loop : -0.64 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 323 HIS 0.003 0.001 HIS A 96 PHE 0.009 0.001 PHE A 681 TYR 0.020 0.001 TYR A 406 ARG 0.003 0.000 ARG A 128 *********************** 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 168 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 1.058 Fit side-chains REVERT: A 239 VAL cc_start: 0.8057 (OUTLIER) cc_final: 0.7716 (p) REVERT: A 248 ASP cc_start: 0.7344 (p0) cc_final: 0.7089 (p0) outliers start: 24 outliers final: 13 residues processed: 152 average time/residue: 1.6363 time to fit residues: 259.4158 Evaluate side-chains 152 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 235 THR 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 677 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 0.0270 chunk 56 optimal weight: 0.3980 chunk 58 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 overall best weight: 0.3438 ------------------------------------------------------------------------------- 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 A 517 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.121414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.114158 restraints weight = 7209.093| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.63 r_work: 0.3484 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5240 Z= 0.154 Angle : 0.476 5.161 7141 Z= 0.258 Chirality : 0.045 0.134 754 Planarity : 0.004 0.045 940 Dihedral : 4.395 36.212 725 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.87 % Allowed : 21.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.32), residues: 656 helix: 1.83 (0.46), residues: 131 sheet: 0.88 (0.39), residues: 188 loop : -0.58 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 323 HIS 0.003 0.001 HIS A 96 PHE 0.007 0.001 PHE A 681 TYR 0.017 0.001 TYR A 611 ARG 0.006 0.000 ARG A 414 *********************** 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 170 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.444 Fit side-chains REVERT: A 239 VAL cc_start: 0.8005 (OUTLIER) cc_final: 0.7664 (p) REVERT: A 248 ASP cc_start: 0.7361 (p0) cc_final: 0.7128 (p0) outliers start: 21 outliers final: 13 residues processed: 154 average time/residue: 0.9947 time to fit residues: 160.5543 Evaluate side-chains 159 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 235 THR 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 292 MET 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 49 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 4 optimal weight: 0.0000 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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 = 0.3640 r_free = 0.3640 target = 0.118131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.110842 restraints weight = 7149.309| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.60 r_work: 0.3443 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5240 Z= 0.235 Angle : 0.520 5.553 7141 Z= 0.281 Chirality : 0.046 0.150 754 Planarity : 0.004 0.041 940 Dihedral : 4.781 56.917 725 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.06 % Allowed : 22.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.32), residues: 656 helix: 1.70 (0.46), residues: 131 sheet: 0.91 (0.39), residues: 189 loop : -0.62 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 323 HIS 0.003 0.001 HIS A 96 PHE 0.024 0.002 PHE A 160 TYR 0.023 0.002 TYR A 406 ARG 0.005 0.000 ARG A 414 *********************** 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 165 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.573 Fit side-chains REVERT: A 239 VAL cc_start: 0.8066 (OUTLIER) cc_final: 0.7725 (p) REVERT: A 248 ASP cc_start: 0.7365 (p0) cc_final: 0.7156 (p0) outliers start: 22 outliers final: 12 residues processed: 151 average time/residue: 1.1134 time to fit residues: 176.0958 Evaluate side-chains 152 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 118 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 235 THR 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 344 THR Chi-restraints excluded: chain A residue 379 GLU 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 15 optimal weight: 0.0030 chunk 59 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.4190 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.118727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.111706 restraints weight = 7099.413| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.53 r_work: 0.3474 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5240 Z= 0.178 Angle : 0.495 5.442 7141 Z= 0.267 Chirality : 0.045 0.139 754 Planarity : 0.004 0.043 940 Dihedral : 4.647 52.126 725 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.69 % Allowed : 23.25 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.32), residues: 656 helix: 1.74 (0.46), residues: 131 sheet: 0.89 (0.39), residues: 188 loop : -0.57 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 323 HIS 0.003 0.001 HIS A 96 PHE 0.018 0.001 PHE A 160 TYR 0.024 0.001 TYR A 406 ARG 0.004 0.000 ARG A 414 *********************** 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 158 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.551 Fit side-chains REVERT: A 239 VAL cc_start: 0.8024 (OUTLIER) cc_final: 0.7702 (p) REVERT: A 248 ASP cc_start: 0.7379 (p0) cc_final: 0.7154 (p0) outliers start: 20 outliers final: 15 residues processed: 144 average time/residue: 1.0844 time to fit residues: 164.9772 Evaluate side-chains 157 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 137 ILE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 266 VAL 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 654 ASP Chi-restraints excluded: chain A residue 656 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 A 517 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.116815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.109662 restraints weight = 7139.098| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.56 r_work: 0.3442 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5240 Z= 0.297 Angle : 0.540 6.096 7141 Z= 0.292 Chirality : 0.047 0.158 754 Planarity : 0.004 0.041 940 Dihedral : 4.750 46.287 725 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.69 % Allowed : 23.43 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.32), residues: 656 helix: 1.44 (0.45), residues: 131 sheet: 0.95 (0.39), residues: 189 loop : -0.63 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 323 HIS 0.003 0.001 HIS A 96 PHE 0.022 0.002 PHE A 160 TYR 0.024 0.002 TYR A 406 ARG 0.004 0.000 ARG A 414 *********************** 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 157 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.571 Fit side-chains REVERT: A 248 ASP cc_start: 0.7375 (p0) cc_final: 0.7172 (p0) outliers start: 20 outliers final: 12 residues processed: 142 average time/residue: 0.9095 time to fit residues: 136.0776 Evaluate side-chains 145 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 185 MET Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 266 VAL 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 559 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.117051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.109956 restraints weight = 7099.046| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.54 r_work: 0.3445 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5240 Z= 0.289 Angle : 0.549 6.127 7141 Z= 0.297 Chirality : 0.047 0.155 754 Planarity : 0.004 0.042 940 Dihedral : 4.703 36.638 725 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.14 % Allowed : 24.17 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.32), residues: 656 helix: 1.36 (0.45), residues: 131 sheet: 0.88 (0.39), residues: 188 loop : -0.63 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 323 HIS 0.003 0.001 HIS A 96 PHE 0.021 0.002 PHE A 160 TYR 0.023 0.002 TYR A 406 ARG 0.004 0.000 ARG A 414 *********************** 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 155 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.570 Fit side-chains REVERT: A 248 ASP cc_start: 0.7360 (p0) cc_final: 0.7119 (p0) outliers start: 17 outliers final: 11 residues processed: 143 average time/residue: 0.8944 time to fit residues: 134.9248 Evaluate side-chains 149 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 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 243 VAL 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 344 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 559 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 23 optimal weight: 0.0970 chunk 49 optimal weight: 0.5980 chunk 35 optimal weight: 0.0370 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 21 optimal weight: 0.3980 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 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 = 0.3654 r_free = 0.3654 target = 0.119107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.111850 restraints weight = 7107.440| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.60 r_work: 0.3477 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5240 Z= 0.171 Angle : 0.519 5.408 7141 Z= 0.280 Chirality : 0.045 0.134 754 Planarity : 0.004 0.042 940 Dihedral : 4.825 56.356 725 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.85 % Allowed : 26.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.32), residues: 656 helix: 1.64 (0.46), residues: 131 sheet: 0.85 (0.39), residues: 188 loop : -0.55 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 323 HIS 0.003 0.001 HIS A 96 PHE 0.017 0.001 PHE A 160 TYR 0.019 0.001 TYR A 406 ARG 0.004 0.000 ARG A 414 ********************** 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 149 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.534 Fit side-chains REVERT: A 248 ASP cc_start: 0.7350 (p0) cc_final: 0.7138 (p0) outliers start: 10 outliers final: 8 residues processed: 142 average time/residue: 0.8554 time to fit residues: 128.3610 Evaluate side-chains 147 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 243 VAL Chi-restraints excluded: chain A residue 317 TRP Chi-restraints excluded: chain A residue 344 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 chunk 4 optimal weight: 0.0570 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 0.0870 chunk 33 optimal weight: 2.9990 chunk 43 optimal weight: 0.0970 chunk 31 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 overall best weight: 0.3074 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.121905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.114546 restraints weight = 7272.296| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.65 r_work: 0.3484 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5240 Z= 0.163 Angle : 0.512 5.155 7141 Z= 0.276 Chirality : 0.045 0.133 754 Planarity : 0.004 0.041 940 Dihedral : 4.668 51.039 725 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.03 % Allowed : 26.38 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.33), residues: 656 helix: 1.70 (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 TRP 0.042 0.002 TRP A 323 HIS 0.003 0.001 HIS A 96 PHE 0.015 0.001 PHE A 160 TYR 0.018 0.001 TYR A 406 ARG 0.005 0.000 ARG A 414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5028.75 seconds wall clock time: 89 minutes 29.09 seconds (5369.09 seconds total)