Starting phenix.real_space_refine on Thu Mar 13 03:23:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vwh_21416/03_2025/6vwh_21416.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vwh_21416/03_2025/6vwh_21416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vwh_21416/03_2025/6vwh_21416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vwh_21416/03_2025/6vwh_21416.map" model { file = "/net/cci-nas-00/data/ceres_data/6vwh_21416/03_2025/6vwh_21416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vwh_21416/03_2025/6vwh_21416.cif" } resolution = 4.26 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: 5 Type Number sf(0) Gaussians S 38 5.16 5 C 2726 2.51 5 N 750 2.21 5 O 808 1.98 5 H 4139 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8461 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2196 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 10, 'TRANS': 125} Chain breaks: 2 Chain: "B" Number of atoms: 6265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 6265 Classifications: {'peptide': 403} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 377} Chain breaks: 4 Time building chain proxies: 5.67, per 1000 atoms: 0.67 Number of scatterers: 8461 At special positions: 0 Unit cell: (97.52, 119.78, 79.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 O 808 8.00 N 750 7.00 C 2726 6.00 H 4139 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 776 " - pdb=" SG CYS A 785 " distance=2.04 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 22 " distance=2.04 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 181 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 200 " distance=2.04 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 209 " distance=2.02 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 218 " distance=2.02 Simple disulfide: pdb=" SG CYS B 221 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 252 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 294 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 776 " - pdb=" SG CYS B 785 " 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: 2.23 Conformation dependent library (CDL) restraints added in 675.5 milliseconds 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1026 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 13 sheets defined 11.3% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 684 through 697 removed outlier: 3.717A pdb=" N TYR A 688 " --> pdb=" O GLU A 684 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 692 " --> pdb=" O TYR A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 784 Processing helix chain 'B' and resid 12 through 17 removed outlier: 3.529A pdb=" N LEU B 16 " --> pdb=" O ASP B 12 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 17 " --> pdb=" O TYR B 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 12 through 17' Processing helix chain 'B' and resid 18 through 22 removed outlier: 4.334A pdb=" N ASN B 21 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 131 removed outlier: 3.965A pdb=" N ILE B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 144 through 149 Processing helix chain 'B' and resid 249 through 255 Processing helix chain 'B' and resid 779 through 784 Processing sheet with id=AA1, first strand: chain 'A' and resid 585 through 593 removed outlier: 4.919A pdb=" N ASP A 586 " --> pdb=" O ASN A 602 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN A 602 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASN A 592 " --> pdb=" O GLN A 596 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN A 596 " --> pdb=" O ASN A 592 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 747 through 752 removed outlier: 3.536A pdb=" N TYR A 614 " --> pdb=" O VAL A 752 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR A 769 " --> pdb=" O ALA A 793 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA A 793 " --> pdb=" O TYR A 769 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 3 removed outlier: 3.609A pdb=" N ILE B 25 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 7 through 10 removed outlier: 6.735A pdb=" N ILE B 7 " --> pdb=" O HIS B 30 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N LEU B 32 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE B 9 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU B 29 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N PHE B 58 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE B 31 " --> pdb=" O PHE B 58 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU B 55 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N PHE B 90 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU B 57 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ARG B 112 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL B 88 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N GLU B 114 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE B 90 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 164 through 165 Processing sheet with id=AA6, first strand: chain 'B' and resid 175 through 177 Processing sheet with id=AA7, first strand: chain 'B' and resid 194 through 195 Processing sheet with id=AA8, first strand: chain 'B' and resid 205 through 209 removed outlier: 8.147A pdb=" N SER B 208 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N CYS B 218 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AB1, first strand: chain 'B' and resid 245 through 248 removed outlier: 3.664A pdb=" N ARG B 245 " --> pdb=" O PHE B 241 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N CYS B 273 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ARG B 240 " --> pdb=" O CYS B 273 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 281 through 283 Processing sheet with id=AB3, first strand: chain 'B' and resid 585 through 590 removed outlier: 4.801A pdb=" N ASP B 586 " --> pdb=" O ASN B 602 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN B 602 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 747 through 751 removed outlier: 4.145A pdb=" N TYR B 613 " --> pdb=" O CYS B 776 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N CYS B 776 " --> pdb=" O TYR B 613 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 791 " --> pdb=" O ILE B 771 " (cutoff:3.500A) 94 hydrogen bonds defined for protein. 249 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: 2.84 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.04: 4137 1.04 - 1.24: 526 1.24 - 1.44: 1429 1.44 - 1.64: 2432 1.64 - 1.84: 44 Bond restraints: 8568 Sorted by residual: bond pdb=" CB CYS B 205 " pdb=" SG CYS B 205 " ideal model delta sigma weight residual 1.808 1.737 0.071 3.30e-02 9.18e+02 4.57e+00 bond pdb=" CB CYS B 218 " pdb=" SG CYS B 218 " ideal model delta sigma weight residual 1.808 1.752 0.056 3.30e-02 9.18e+02 2.89e+00 bond pdb=" N ASN A 577 " pdb=" H ASN A 577 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.31e+00 bond pdb=" N GLU A 682 " pdb=" CA GLU A 682 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.90e-02 2.77e+03 2.09e+00 bond pdb=" C ARG B 620 " pdb=" N GLN B 621 " ideal model delta sigma weight residual 1.340 1.260 0.080 5.87e-02 2.90e+02 1.87e+00 ... (remaining 8563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 14251 1.55 - 3.09: 1015 3.09 - 4.64: 125 4.64 - 6.18: 17 6.18 - 7.73: 5 Bond angle restraints: 15413 Sorted by residual: angle pdb=" N ASN B 94 " pdb=" CA ASN B 94 " pdb=" C ASN B 94 " ideal model delta sigma weight residual 113.28 120.89 -7.61 1.57e+00 4.06e-01 2.35e+01 angle pdb=" N ASN B 94 " pdb=" CA ASN B 94 " pdb=" CB ASN B 94 " ideal model delta sigma weight residual 114.17 108.88 5.29 1.14e+00 7.69e-01 2.16e+01 angle pdb=" N LEU B 256 " pdb=" CA LEU B 256 " pdb=" C LEU B 256 " ideal model delta sigma weight residual 110.20 103.33 6.87 1.58e+00 4.01e-01 1.89e+01 angle pdb=" N ASN B 602 " pdb=" CA ASN B 602 " pdb=" C ASN B 602 " ideal model delta sigma weight residual 110.10 115.17 -5.07 1.53e+00 4.27e-01 1.10e+01 angle pdb=" CA TYR B 628 " pdb=" CB TYR B 628 " pdb=" CG TYR B 628 " ideal model delta sigma weight residual 113.90 119.31 -5.41 1.80e+00 3.09e-01 9.04e+00 ... (remaining 15408 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 3757 17.84 - 35.68: 258 35.68 - 53.52: 80 53.52 - 71.36: 38 71.36 - 89.20: 5 Dihedral angle restraints: 4138 sinusoidal: 2235 harmonic: 1903 Sorted by residual: dihedral pdb=" CB CYS B 205 " pdb=" SG CYS B 205 " pdb=" SG CYS B 218 " pdb=" CB CYS B 218 " ideal model delta sinusoidal sigma weight residual -86.00 -141.70 55.70 1 1.00e+01 1.00e-02 4.19e+01 dihedral pdb=" CA SER A 788 " pdb=" C SER A 788 " pdb=" N ASN A 789 " pdb=" CA ASN A 789 " ideal model delta harmonic sigma weight residual 180.00 150.77 29.23 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA SER B 788 " pdb=" C SER B 788 " pdb=" N ASN B 789 " pdb=" CA ASN B 789 " ideal model delta harmonic sigma weight residual 180.00 151.22 28.78 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 4135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 362 0.045 - 0.089: 194 0.089 - 0.134: 68 0.134 - 0.179: 13 0.179 - 0.223: 3 Chirality restraints: 640 Sorted by residual: chirality pdb=" CA PHE B 766 " pdb=" N PHE B 766 " pdb=" C PHE B 766 " pdb=" CB PHE B 766 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ASN B 94 " pdb=" N ASN B 94 " pdb=" C ASN B 94 " pdb=" CB ASN B 94 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.79e-01 chirality pdb=" CB ILE B 615 " pdb=" CA ILE B 615 " pdb=" CG1 ILE B 615 " pdb=" CG2 ILE B 615 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.36e-01 ... (remaining 637 not shown) Planarity restraints: 1283 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 770 " -0.095 9.50e-02 1.11e+02 4.64e-02 2.69e+01 pdb=" NE ARG A 770 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 770 " -0.067 2.00e-02 2.50e+03 pdb=" NH1 ARG A 770 " 0.058 2.00e-02 2.50e+03 pdb=" NH2 ARG A 770 " 0.039 2.00e-02 2.50e+03 pdb="HH11 ARG A 770 " -0.014 2.00e-02 2.50e+03 pdb="HH12 ARG A 770 " -0.011 2.00e-02 2.50e+03 pdb="HH21 ARG A 770 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 770 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 283 " 0.060 9.50e-02 1.11e+02 3.92e-02 2.60e+01 pdb=" NE ARG B 283 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG B 283 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 283 " -0.067 2.00e-02 2.50e+03 pdb=" NH2 ARG B 283 " -0.049 2.00e-02 2.50e+03 pdb="HH11 ARG B 283 " 0.009 2.00e-02 2.50e+03 pdb="HH12 ARG B 283 " 0.038 2.00e-02 2.50e+03 pdb="HH21 ARG B 283 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 283 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 689 " 0.034 9.50e-02 1.11e+02 3.42e-02 2.36e+01 pdb=" NE ARG A 689 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 689 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 689 " -0.074 2.00e-02 2.50e+03 pdb=" NH2 ARG A 689 " 0.011 2.00e-02 2.50e+03 pdb="HH11 ARG A 689 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 689 " 0.057 2.00e-02 2.50e+03 pdb="HH21 ARG A 689 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 689 " -0.019 2.00e-02 2.50e+03 ... (remaining 1280 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 273 2.10 - 2.72: 14639 2.72 - 3.35: 23897 3.35 - 3.97: 29803 3.97 - 4.60: 46113 Nonbonded interactions: 114725 Sorted by model distance: nonbonded pdb=" O TYR B 614 " pdb=" H VAL B 752 " model vdw 1.470 2.450 nonbonded pdb=" O TYR A 626 " pdb=" H TYR A 628 " model vdw 1.485 2.450 nonbonded pdb=" HG SER B 257 " pdb=" O GLU B 264 " model vdw 1.490 2.450 nonbonded pdb=" O ARG A 764 " pdb=" HG1 THR A 767 " model vdw 1.517 2.450 nonbonded pdb=" O TYR B 626 " pdb=" H TYR B 628 " model vdw 1.517 2.450 ... (remaining 114720 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.800 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: 0.130 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.130 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5785 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 : 0.006 0.080 4429 Z= 0.362 Angle : 1.063 7.731 6010 Z= 0.612 Chirality : 0.058 0.223 640 Planarity : 0.005 0.053 787 Dihedral : 13.745 89.202 1642 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.76 % Allowed : 6.69 % Favored : 92.54 % Rotamer: Outliers : 0.82 % Allowed : 5.97 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.34), residues: 523 helix: -3.57 (0.58), residues: 40 sheet: -0.34 (0.46), residues: 131 loop : -1.21 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.006 TRP B 618 HIS 0.012 0.003 HIS B 774 PHE 0.018 0.003 PHE B 90 TYR 0.042 0.006 TYR B 769 ARG 0.079 0.007 ARG A 770 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 ILE cc_start: 0.8430 (mt) cc_final: 0.8204 (mm) REVERT: B 184 MET cc_start: 0.7692 (mtp) cc_final: 0.7432 (mtt) REVERT: B 242 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7453 (mm-30) REVERT: B 270 ASP cc_start: 0.6463 (t0) cc_final: 0.6110 (t0) REVERT: B 601 TRP cc_start: 0.6939 (p90) cc_final: 0.6050 (p90) REVERT: B 613 TYR cc_start: 0.4841 (p90) cc_final: 0.4202 (p90) outliers start: 4 outliers final: 1 residues processed: 89 average time/residue: 0.3969 time to fit residues: 43.1007 Evaluate side-chains 56 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 GLN A 697 HIS B 14 GLN B 72 ASN B 94 ASN B 102 ASN B 136 ASN B 198 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.125470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.109989 restraints weight = 58813.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.113833 restraints weight = 30579.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.116419 restraints weight = 19077.977| |-----------------------------------------------------------------------------| r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5924 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4429 Z= 0.232 Angle : 0.694 5.155 6010 Z= 0.380 Chirality : 0.048 0.162 640 Planarity : 0.005 0.047 787 Dihedral : 6.857 29.167 597 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.12 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.35), residues: 523 helix: -2.70 (0.67), residues: 36 sheet: -0.80 (0.43), residues: 130 loop : -0.72 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 618 HIS 0.010 0.002 HIS A 774 PHE 0.010 0.001 PHE B 90 TYR 0.019 0.002 TYR B 626 ARG 0.004 0.001 ARG B 620 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 SER cc_start: 0.8294 (t) cc_final: 0.8080 (m) REVERT: A 598 ILE cc_start: 0.7747 (pt) cc_final: 0.7498 (mp) REVERT: B 601 TRP cc_start: 0.6996 (p90) cc_final: 0.5984 (p90) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.3011 time to fit residues: 27.3414 Evaluate side-chains 50 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 6 optimal weight: 0.3980 chunk 35 optimal weight: 0.0970 chunk 31 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 0.2980 chunk 28 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.125362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.109496 restraints weight = 58876.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.113490 restraints weight = 29850.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.116195 restraints weight = 18284.174| |-----------------------------------------------------------------------------| r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5930 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4429 Z= 0.164 Angle : 0.582 4.301 6010 Z= 0.318 Chirality : 0.046 0.140 640 Planarity : 0.004 0.038 787 Dihedral : 6.108 25.844 597 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.31 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.36), residues: 523 helix: -1.89 (0.74), residues: 28 sheet: -1.07 (0.43), residues: 128 loop : -0.61 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 618 HIS 0.007 0.001 HIS A 774 PHE 0.011 0.001 PHE A 747 TYR 0.016 0.001 TYR B 628 ARG 0.002 0.000 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 SER cc_start: 0.8391 (t) cc_final: 0.8170 (m) REVERT: A 598 ILE cc_start: 0.7887 (pt) cc_final: 0.7639 (mp) REVERT: B 136 ASN cc_start: 0.8461 (t0) cc_final: 0.8211 (t0) REVERT: B 242 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8245 (mm-30) REVERT: B 244 TRP cc_start: 0.6621 (p-90) cc_final: 0.6399 (p-90) REVERT: B 601 TRP cc_start: 0.6948 (p90) cc_final: 0.5902 (p90) REVERT: B 773 ILE cc_start: 0.7816 (mt) cc_final: 0.7440 (mp) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.3086 time to fit residues: 25.0007 Evaluate side-chains 49 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.124274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.108755 restraints weight = 58944.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.112616 restraints weight = 29886.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.115160 restraints weight = 18350.562| |-----------------------------------------------------------------------------| r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6008 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4429 Z= 0.200 Angle : 0.584 4.966 6010 Z= 0.318 Chirality : 0.046 0.152 640 Planarity : 0.004 0.036 787 Dihedral : 5.836 26.696 597 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.18 % Favored : 90.44 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.36), residues: 523 helix: -1.55 (0.74), residues: 28 sheet: -1.35 (0.43), residues: 127 loop : -0.73 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 618 HIS 0.006 0.001 HIS A 774 PHE 0.009 0.001 PHE B 82 TYR 0.016 0.002 TYR B 628 ARG 0.005 0.001 ARG B 770 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 598 ILE cc_start: 0.7938 (pt) cc_final: 0.7695 (mp) REVERT: B 136 ASN cc_start: 0.8482 (t0) cc_final: 0.8197 (t0) REVERT: B 244 TRP cc_start: 0.7060 (p-90) cc_final: 0.6549 (p-90) REVERT: B 601 TRP cc_start: 0.7079 (p90) cc_final: 0.5949 (p90) REVERT: B 773 ILE cc_start: 0.7937 (mt) cc_final: 0.7556 (mp) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.3362 time to fit residues: 26.3404 Evaluate side-chains 48 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.123092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.107346 restraints weight = 58522.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.111144 restraints weight = 29888.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.113741 restraints weight = 18257.954| |-----------------------------------------------------------------------------| r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6045 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4429 Z= 0.205 Angle : 0.571 3.974 6010 Z= 0.309 Chirality : 0.045 0.155 640 Planarity : 0.004 0.036 787 Dihedral : 5.671 24.517 597 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.03 % Favored : 91.59 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.36), residues: 523 helix: -1.53 (0.74), residues: 28 sheet: -1.46 (0.42), residues: 125 loop : -0.77 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 618 HIS 0.005 0.001 HIS A 774 PHE 0.010 0.001 PHE A 747 TYR 0.017 0.002 TYR B 626 ARG 0.004 0.001 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 598 ILE cc_start: 0.8035 (pt) cc_final: 0.7768 (mp) REVERT: B 136 ASN cc_start: 0.8509 (t0) cc_final: 0.8221 (t0) REVERT: B 244 TRP cc_start: 0.7208 (p-90) cc_final: 0.6401 (p-90) REVERT: B 274 MET cc_start: 0.7534 (mpp) cc_final: 0.6994 (mpp) REVERT: B 587 VAL cc_start: 0.7171 (t) cc_final: 0.6961 (p) REVERT: B 601 TRP cc_start: 0.7004 (p90) cc_final: 0.5893 (p90) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.2958 time to fit residues: 22.5506 Evaluate side-chains 49 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.125701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.112920 restraints weight = 65511.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.116118 restraints weight = 34992.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.118323 restraints weight = 22124.634| |-----------------------------------------------------------------------------| r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6097 moved from start: 0.6085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4429 Z= 0.223 Angle : 0.593 4.770 6010 Z= 0.322 Chirality : 0.046 0.159 640 Planarity : 0.004 0.036 787 Dihedral : 5.752 24.841 597 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.33 % Favored : 89.29 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.36), residues: 523 helix: -1.63 (0.79), residues: 29 sheet: -1.82 (0.40), residues: 137 loop : -0.99 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 618 HIS 0.004 0.001 HIS A 774 PHE 0.016 0.002 PHE A 695 TYR 0.021 0.002 TYR B 626 ARG 0.004 0.001 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 ASN cc_start: 0.8535 (t0) cc_final: 0.8137 (t0) REVERT: B 601 TRP cc_start: 0.7059 (p90) cc_final: 0.5927 (p90) REVERT: B 773 ILE cc_start: 0.8016 (mt) cc_final: 0.7736 (mp) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.2770 time to fit residues: 23.3600 Evaluate side-chains 49 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 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 577 ASN B 630 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.120954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.106001 restraints weight = 58670.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.109759 restraints weight = 29710.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.112315 restraints weight = 18010.983| |-----------------------------------------------------------------------------| r_work (final): 0.4300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6138 moved from start: 0.6426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4429 Z= 0.216 Angle : 0.587 4.543 6010 Z= 0.316 Chirality : 0.046 0.136 640 Planarity : 0.004 0.036 787 Dihedral : 5.665 24.375 597 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.56 % Favored : 90.06 % Rotamer: Outliers : 0.21 % Allowed : 1.44 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.36), residues: 523 helix: -2.14 (0.72), residues: 34 sheet: -1.87 (0.41), residues: 135 loop : -1.09 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 618 HIS 0.005 0.001 HIS A 774 PHE 0.010 0.001 PHE B 82 TYR 0.017 0.002 TYR B 745 ARG 0.006 0.001 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 598 ILE cc_start: 0.8161 (pt) cc_final: 0.7846 (pt) REVERT: B 25 ILE cc_start: 0.6642 (mp) cc_final: 0.6204 (mt) REVERT: B 136 ASN cc_start: 0.8577 (t0) cc_final: 0.8234 (t0) REVERT: B 274 MET cc_start: 0.7753 (mpp) cc_final: 0.7295 (mpp) REVERT: B 601 TRP cc_start: 0.6992 (p90) cc_final: 0.6002 (p90) REVERT: B 773 ILE cc_start: 0.8112 (mt) cc_final: 0.7839 (mp) outliers start: 1 outliers final: 0 residues processed: 64 average time/residue: 0.2897 time to fit residues: 24.4953 Evaluate side-chains 54 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 2 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.120395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.105318 restraints weight = 58571.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.109000 restraints weight = 29913.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.111532 restraints weight = 18393.339| |-----------------------------------------------------------------------------| r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 0.6711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 4429 Z= 0.235 Angle : 0.597 5.119 6010 Z= 0.323 Chirality : 0.046 0.150 640 Planarity : 0.004 0.036 787 Dihedral : 5.661 25.411 597 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.13 % Favored : 89.48 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.36), residues: 523 helix: -2.54 (0.69), residues: 35 sheet: -2.03 (0.40), residues: 135 loop : -1.17 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 618 HIS 0.006 0.002 HIS B 774 PHE 0.011 0.001 PHE B 82 TYR 0.020 0.002 TYR B 745 ARG 0.008 0.001 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 ASN cc_start: 0.8695 (t0) cc_final: 0.8408 (t0) REVERT: B 274 MET cc_start: 0.7816 (mpp) cc_final: 0.7587 (mpp) REVERT: B 601 TRP cc_start: 0.7130 (p90) cc_final: 0.6079 (p90) REVERT: B 773 ILE cc_start: 0.8091 (mt) cc_final: 0.7491 (pt) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.3202 time to fit residues: 26.8697 Evaluate side-chains 54 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.119720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.104436 restraints weight = 58792.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.108185 restraints weight = 30185.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.110803 restraints weight = 18533.522| |-----------------------------------------------------------------------------| r_work (final): 0.4278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 moved from start: 0.7095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 4429 Z= 0.254 Angle : 0.613 5.531 6010 Z= 0.332 Chirality : 0.046 0.136 640 Planarity : 0.005 0.038 787 Dihedral : 5.806 25.251 597 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.85 % Favored : 87.76 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.36), residues: 523 helix: -2.35 (0.68), residues: 35 sheet: -1.92 (0.41), residues: 130 loop : -1.37 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 618 HIS 0.007 0.002 HIS B 774 PHE 0.011 0.002 PHE A 747 TYR 0.021 0.002 TYR B 745 ARG 0.005 0.001 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 598 ILE cc_start: 0.8407 (pt) cc_final: 0.8114 (pt) REVERT: B 25 ILE cc_start: 0.6596 (mp) cc_final: 0.6145 (mt) REVERT: B 136 ASN cc_start: 0.8735 (t0) cc_final: 0.8468 (t0) REVERT: B 274 MET cc_start: 0.7884 (mpp) cc_final: 0.7675 (mpp) REVERT: B 601 TRP cc_start: 0.7218 (p90) cc_final: 0.6131 (p90) REVERT: B 773 ILE cc_start: 0.8513 (mt) cc_final: 0.7861 (pt) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.3334 time to fit residues: 28.0037 Evaluate side-chains 54 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.120301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.105118 restraints weight = 58164.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.108909 restraints weight = 29505.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.111340 restraints weight = 18097.277| |-----------------------------------------------------------------------------| r_work (final): 0.4283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6192 moved from start: 0.7214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4429 Z= 0.198 Angle : 0.571 4.844 6010 Z= 0.308 Chirality : 0.045 0.138 640 Planarity : 0.004 0.041 787 Dihedral : 5.607 23.719 597 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.75 % Favored : 89.87 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.36), residues: 523 helix: -1.69 (0.80), residues: 29 sheet: -1.96 (0.41), residues: 129 loop : -1.42 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 618 HIS 0.006 0.001 HIS B 774 PHE 0.010 0.001 PHE A 747 TYR 0.015 0.002 TYR B 745 ARG 0.005 0.000 ARG B 112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 619 GLN cc_start: 0.7752 (tt0) cc_final: 0.7358 (tt0) REVERT: B 53 GLU cc_start: 0.7868 (mp0) cc_final: 0.7649 (mp0) REVERT: B 136 ASN cc_start: 0.8783 (t0) cc_final: 0.8571 (t0) REVERT: B 274 MET cc_start: 0.7737 (mpp) cc_final: 0.7442 (mpp) REVERT: B 601 TRP cc_start: 0.7130 (p90) cc_final: 0.6054 (p90) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2910 time to fit residues: 23.8704 Evaluate side-chains 53 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN B 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.120825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.105269 restraints weight = 58754.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.109232 restraints weight = 29623.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.111821 restraints weight = 17953.521| |-----------------------------------------------------------------------------| r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 moved from start: 0.7360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4429 Z= 0.169 Angle : 0.538 4.320 6010 Z= 0.289 Chirality : 0.044 0.137 640 Planarity : 0.004 0.036 787 Dihedral : 5.353 22.719 597 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.56 % Favored : 90.06 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.36), residues: 523 helix: -1.54 (0.82), residues: 29 sheet: -1.76 (0.43), residues: 127 loop : -1.42 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 618 HIS 0.006 0.001 HIS B 774 PHE 0.009 0.001 PHE A 747 TYR 0.017 0.001 TYR B 628 ARG 0.006 0.000 ARG B 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4048.48 seconds wall clock time: 69 minutes 33.21 seconds (4173.21 seconds total)