Starting phenix.real_space_refine on Thu Feb 13 01:43:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vwh_21416/02_2025/6vwh_21416.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vwh_21416/02_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_21416/02_2025/6vwh_21416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vwh_21416/02_2025/6vwh_21416.map" model { file = "/net/cci-nas-00/data/ceres_data/6vwh_21416/02_2025/6vwh_21416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vwh_21416/02_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-5592/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: 4.44, per 1000 atoms: 0.52 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: 2.14 Conformation dependent library (CDL) restraints added in 684.3 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: 0.90 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: 3.08 Time building geometry restraints manager: 2.58 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: 3.340 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: 0.170 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.070 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.510 ------------------------------------------------------------------------------- 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 : 0.702 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: 0.3966 time to fit residues: 43.1453 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 : 0.644 ------------------------------------------------------------------------------- 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 = 0.109990 restraints weight = 58814.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.113835 restraints weight = 30572.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.116433 restraints weight = 19073.687| |-----------------------------------------------------------------------------| r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5923 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 : 0.681 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: 0.8292 (t) cc_final: 0.8079 (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: 0.5985 (p90) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.3076 time to fit residues: 27.8061 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 : 0.731 ------------------------------------------------------------------------------- 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: 0.5980 chunk 35 optimal weight: 0.1980 chunk 31 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4508 r_free = 0.4508 target = 0.124846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.108831 restraints weight = 58726.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.112845 restraints weight = 29789.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.115482 restraints weight = 18225.679| |-----------------------------------------------------------------------------| r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5962 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4429 Z= 0.175 Angle : 0.587 4.395 6010 Z= 0.320 Chirality : 0.046 0.145 640 Planarity : 0.005 0.037 787 Dihedral : 6.073 25.452 597 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.50 % Favored : 93.12 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: -1.23 (0.36), residues: 523 helix: -1.92 (0.73), residues: 28 sheet: -0.99 (0.44), residues: 124 loop : -0.65 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 618 HIS 0.007 0.001 HIS A 774 PHE 0.012 0.001 PHE A 747 TYR 0.016 0.002 TYR B 628 ARG 0.002 0.000 ARG B 59 *********************** 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 61 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.638 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 582 SER cc_start: 0.8431 (t) cc_final: 0.8211 (m) REVERT: A 598 ILE cc_start: 0.7868 (pt) cc_final: 0.7607 (mp) REVERT: B 136 ASN cc_start: 0.8505 (t0) cc_final: 0.8246 (t0) REVERT: B 242 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8256 (mm-30) REVERT: B 244 TRP cc_start: 0.6666 (p-90) cc_final: 0.6362 (p-90) REVERT: B 601 TRP cc_start: 0.6970 (p90) cc_final: 0.5920 (p90) REVERT: B 773 ILE cc_start: 0.7838 (mt) cc_final: 0.7486 (mp) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.3105 time to fit residues: 24.6502 Evaluate side-chains 46 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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: 0.7980 chunk 12 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 51 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4491 r_free = 0.4491 target = 0.124546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.108970 restraints weight = 58778.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.112838 restraints weight = 29648.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.115413 restraints weight = 18023.666| |-----------------------------------------------------------------------------| r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5981 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4429 Z= 0.165 Angle : 0.558 3.910 6010 Z= 0.303 Chirality : 0.045 0.137 640 Planarity : 0.004 0.036 787 Dihedral : 5.778 25.631 597 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.07 % Favored : 92.54 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: -1.30 (0.36), residues: 523 helix: -1.46 (0.76), residues: 28 sheet: -1.14 (0.44), residues: 124 loop : -0.70 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 618 HIS 0.006 0.001 HIS A 774 PHE 0.014 0.001 PHE B 792 TYR 0.021 0.002 TYR B 626 ARG 0.002 0.000 ARG B 112 *********************** 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 62 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.674 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: A 582 SER cc_start: 0.8470 (t) cc_final: 0.8254 (m) REVERT: A 598 ILE cc_start: 0.7892 (pt) cc_final: 0.7674 (mp) REVERT: B 136 ASN cc_start: 0.8494 (t0) cc_final: 0.8236 (t0) REVERT: B 244 TRP cc_start: 0.6921 (p-90) cc_final: 0.6522 (p-90) REVERT: B 601 TRP cc_start: 0.6953 (p90) cc_final: 0.5897 (p90) REVERT: B 773 ILE cc_start: 0.7938 (mt) cc_final: 0.7535 (mp) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.3281 time to fit residues: 26.2369 Evaluate side-chains 51 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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: 2.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.123697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.108525 restraints weight = 59151.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.112189 restraints weight = 30106.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.114676 restraints weight = 18533.454| |-----------------------------------------------------------------------------| r_work (final): 0.4351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6007 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4429 Z= 0.192 Angle : 0.568 5.605 6010 Z= 0.307 Chirality : 0.046 0.179 640 Planarity : 0.004 0.035 787 Dihedral : 5.602 24.595 597 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.41 % Favored : 91.20 % 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: -1.40 (0.36), residues: 523 helix: -1.23 (0.78), residues: 28 sheet: -1.28 (0.43), residues: 130 loop : -0.75 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 618 HIS 0.005 0.001 HIS A 774 PHE 0.013 0.001 PHE A 695 TYR 0.015 0.002 TYR B 628 ARG 0.005 0.000 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 60 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.649 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: 0.7954 (pt) cc_final: 0.7728 (mp) REVERT: B 136 ASN cc_start: 0.8462 (t0) cc_final: 0.8163 (t0) REVERT: B 242 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8033 (mm-30) REVERT: B 244 TRP cc_start: 0.7236 (p-90) cc_final: 0.6459 (p-90) REVERT: B 601 TRP cc_start: 0.6915 (p90) cc_final: 0.5840 (p90) REVERT: B 773 ILE cc_start: 0.7939 (mt) cc_final: 0.7574 (mp) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.2995 time to fit residues: 23.5780 Evaluate side-chains 45 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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: 0.9980 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 ASN ** B 72 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 = 0.4463 r_free = 0.4463 target = 0.122022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.106409 restraints weight = 58608.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.110168 restraints weight = 29576.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.112787 restraints weight = 18207.640| |-----------------------------------------------------------------------------| r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6113 moved from start: 0.5995 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= 0.237 Angle : 0.592 4.570 6010 Z= 0.321 Chirality : 0.045 0.150 640 Planarity : 0.005 0.036 787 Dihedral : 5.692 24.844 597 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.94 % Favored : 89.67 % Rotamer: Outliers : 0.21 % Allowed : 1.65 % 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: -1.79 (0.36), residues: 523 helix: -1.42 (0.80), residues: 28 sheet: -1.67 (0.41), residues: 135 loop : -0.96 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 618 HIS 0.004 0.001 HIS A 774 PHE 0.009 0.001 PHE A 747 TYR 0.015 0.002 TYR B 745 ARG 0.005 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 58 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.892 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: 0.8119 (pt) cc_final: 0.7819 (mp) REVERT: B 136 ASN cc_start: 0.8662 (t0) cc_final: 0.8439 (t0) REVERT: B 274 MET cc_start: 0.7532 (mpp) cc_final: 0.7173 (mpp) REVERT: B 601 TRP cc_start: 0.7122 (p90) cc_final: 0.5976 (p90) REVERT: B 773 ILE cc_start: 0.7943 (mt) cc_final: 0.7716 (mp) outliers start: 1 outliers final: 0 residues processed: 58 average time/residue: 0.3009 time to fit residues: 23.4756 Evaluate side-chains 43 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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: 0.0980 chunk 52 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.122459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.107362 restraints weight = 59454.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.111119 restraints weight = 30812.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.113684 restraints weight = 18834.949| |-----------------------------------------------------------------------------| r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 0.6191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4429 Z= 0.168 Angle : 0.545 4.242 6010 Z= 0.294 Chirality : 0.045 0.142 640 Planarity : 0.004 0.034 787 Dihedral : 5.437 23.011 597 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.18 % Favored : 90.44 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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: -1.85 (0.36), residues: 523 helix: -1.49 (0.77), residues: 28 sheet: -1.62 (0.41), residues: 136 loop : -1.05 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 618 HIS 0.006 0.001 HIS A 774 PHE 0.007 0.001 PHE A 747 TYR 0.017 0.002 TYR B 626 ARG 0.008 0.000 ARG B 112 *********************** 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 53 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.706 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: 0.7969 (pt) cc_final: 0.7702 (mp) REVERT: B 136 ASN cc_start: 0.8572 (t0) cc_final: 0.8210 (t0) REVERT: B 274 MET cc_start: 0.7635 (mpp) cc_final: 0.7317 (mpp) REVERT: B 601 TRP cc_start: 0.6876 (p90) cc_final: 0.5868 (p90) REVERT: B 773 ILE cc_start: 0.7929 (mt) cc_final: 0.7577 (mp) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2809 time to fit residues: 20.4958 Evaluate side-chains 44 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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: 1.9990 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 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 = 0.4459 r_free = 0.4459 target = 0.121610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.106047 restraints weight = 58575.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.109841 restraints weight = 30224.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.112411 restraints weight = 18516.612| |-----------------------------------------------------------------------------| r_work (final): 0.4306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6120 moved from start: 0.6414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 4429 Z= 0.206 Angle : 0.567 6.028 6010 Z= 0.305 Chirality : 0.045 0.139 640 Planarity : 0.004 0.034 787 Dihedral : 5.437 23.045 597 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.75 % Favored : 89.87 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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: -1.97 (0.36), residues: 523 helix: -1.34 (0.80), residues: 28 sheet: -1.83 (0.41), residues: 132 loop : -1.11 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 618 HIS 0.005 0.001 HIS A 774 PHE 0.008 0.001 PHE B 82 TYR 0.015 0.002 TYR B 745 ARG 0.003 0.000 ARG B 180 *********************** 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 58 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.652 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: A 598 ILE cc_start: 0.8080 (pt) cc_final: 0.7793 (mp) REVERT: B 136 ASN cc_start: 0.8647 (t0) cc_final: 0.8308 (t0) REVERT: B 287 GLN cc_start: 0.7022 (mt0) cc_final: 0.6486 (pm20) REVERT: B 601 TRP cc_start: 0.6998 (p90) cc_final: 0.6034 (p90) REVERT: B 773 ILE cc_start: 0.7942 (mt) cc_final: 0.7680 (mp) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.3074 time to fit residues: 23.4926 Evaluate side-chains 51 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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: 0.9990 chunk 4 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 41 optimal weight: 0.0770 chunk 51 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.4539 r_free = 0.4539 target = 0.126302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.113973 restraints weight = 66697.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.117126 restraints weight = 35760.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.119333 restraints weight = 22403.666| |-----------------------------------------------------------------------------| r_work (final): 0.4347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6055 moved from start: 0.6591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4429 Z= 0.164 Angle : 0.532 4.636 6010 Z= 0.286 Chirality : 0.045 0.140 640 Planarity : 0.004 0.034 787 Dihedral : 5.253 22.105 597 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.80 % Favored : 90.82 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: -1.93 (0.36), residues: 523 helix: -1.40 (0.81), residues: 28 sheet: -1.66 (0.41), residues: 134 loop : -1.13 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 618 HIS 0.007 0.001 HIS B 774 PHE 0.007 0.001 PHE B 90 TYR 0.015 0.001 TYR B 628 ARG 0.002 0.000 ARG B 180 *********************** 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 60 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.633 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: 0.8011 (pt) cc_final: 0.7742 (mp) REVERT: B 136 ASN cc_start: 0.8633 (t0) cc_final: 0.8275 (t0) REVERT: B 274 MET cc_start: 0.7502 (mpp) cc_final: 0.6810 (mpp) REVERT: B 287 GLN cc_start: 0.6944 (mt0) cc_final: 0.6421 (pm20) REVERT: B 586 ASP cc_start: 0.7037 (t0) cc_final: 0.6726 (t0) REVERT: B 601 TRP cc_start: 0.6863 (p90) cc_final: 0.5919 (p90) REVERT: B 773 ILE cc_start: 0.7910 (mt) cc_final: 0.7624 (mp) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.3334 time to fit residues: 26.4414 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 : 0.680 ------------------------------------------------------------------------------- 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: 0.9980 chunk 40 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4518 r_free = 0.4518 target = 0.124578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.112093 restraints weight = 66290.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.115192 restraints weight = 35832.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.117198 restraints weight = 22535.922| |-----------------------------------------------------------------------------| r_work (final): 0.4321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6135 moved from start: 0.6873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 4429 Z= 0.214 Angle : 0.558 4.306 6010 Z= 0.300 Chirality : 0.044 0.135 640 Planarity : 0.004 0.036 787 Dihedral : 5.362 23.058 597 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.56 % Favored : 90.06 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: -2.00 (0.36), residues: 523 helix: -1.35 (0.83), residues: 28 sheet: -1.77 (0.42), residues: 133 loop : -1.16 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 618 HIS 0.006 0.001 HIS B 774 PHE 0.013 0.001 PHE B 82 TYR 0.030 0.002 TYR B 85 ARG 0.007 0.001 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 60 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.717 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: B 136 ASN cc_start: 0.8748 (t0) cc_final: 0.8397 (t0) REVERT: B 274 MET cc_start: 0.7580 (mpp) cc_final: 0.6968 (mpp) REVERT: B 287 GLN cc_start: 0.7002 (mt0) cc_final: 0.6498 (pm20) REVERT: B 586 ASP cc_start: 0.6941 (t0) cc_final: 0.6700 (t0) REVERT: B 601 TRP cc_start: 0.7022 (p90) cc_final: 0.6128 (p90) REVERT: B 602 ASN cc_start: 0.7733 (m110) cc_final: 0.7303 (m110) REVERT: B 773 ILE cc_start: 0.7940 (mt) cc_final: 0.7724 (mp) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.3113 time to fit residues: 24.5068 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 : 0.689 ------------------------------------------------------------------------------- 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: 0.6980 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4534 r_free = 0.4534 target = 0.125362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.112683 restraints weight = 66933.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.115924 restraints weight = 36005.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.118093 restraints weight = 22645.371| |-----------------------------------------------------------------------------| r_work (final): 0.4332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6086 moved from start: 0.7042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4429 Z= 0.170 Angle : 0.534 4.024 6010 Z= 0.286 Chirality : 0.044 0.137 640 Planarity : 0.004 0.035 787 Dihedral : 5.196 21.919 597 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.60 % Favored : 91.01 % 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: -2.00 (0.36), residues: 523 helix: -1.23 (0.83), residues: 28 sheet: -1.69 (0.42), residues: 134 loop : -1.21 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 618 HIS 0.007 0.001 HIS B 774 PHE 0.008 0.001 PHE A 747 TYR 0.017 0.001 TYR B 85 ARG 0.002 0.000 ARG B 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3934.48 seconds wall clock time: 70 minutes 6.18 seconds (4206.18 seconds total)