Starting phenix.real_space_refine on Wed Jul 30 03:07:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vwj_21418/07_2025/6vwj_21418.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vwj_21418/07_2025/6vwj_21418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vwj_21418/07_2025/6vwj_21418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vwj_21418/07_2025/6vwj_21418.map" model { file = "/net/cci-nas-00/data/ceres_data/6vwj_21418/07_2025/6vwj_21418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vwj_21418/07_2025/6vwj_21418.cif" } resolution = 4.21 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= 0.021 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 42 5.16 5 C 3802 2.51 5 N 1044 2.21 5 O 1122 1.98 5 H 5789 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11799 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 3865 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 20, 'TRANS': 219} Chain breaks: 2 Chain: "B" Number of atoms: 7934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7934 Classifications: {'peptide': 507} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 471} Chain breaks: 4 Time building chain proxies: 7.19, per 1000 atoms: 0.61 Number of scatterers: 11799 At special positions: 0 Unit cell: (92.22, 113.42, 103.88, 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 42 16.00 O 1122 8.00 N 1044 7.00 C 3802 6.00 H 5789 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 849 " distance=2.03 Simple disulfide: pdb=" SG CYS A 776 " - pdb=" SG CYS A 785 " distance=2.03 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 218 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B 294 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 633 " - pdb=" SG CYS B 849 " 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: 2.94 Conformation dependent library (CDL) restraints added in 875.3 milliseconds 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 18 sheets defined 12.0% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 624 through 629 Processing helix chain 'A' and resid 686 through 700 removed outlier: 4.725A pdb=" N PHE A 692 " --> pdb=" O TYR A 688 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE A 695 " --> pdb=" O VAL A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 784 Processing helix chain 'A' and resid 852 through 859 Processing helix chain 'B' and resid 15 through 22 removed outlier: 4.349A pdb=" N ASN B 21 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 126 through 131 removed outlier: 3.749A 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 253 Processing helix chain 'B' and resid 625 through 630 removed outlier: 4.346A pdb=" N ARG B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N HIS B 630 " --> pdb=" O TYR B 626 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 625 through 630' Processing helix chain 'B' and resid 779 through 784 Processing helix chain 'B' and resid 852 through 859 Processing sheet with id=AA1, first strand: chain 'A' and resid 585 through 593 removed outlier: 4.999A pdb=" N ASP A 586 " --> pdb=" O ASN A 602 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN A 602 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN A 592 " --> pdb=" O GLN A 596 " (cutoff:3.500A) removed outlier: 7.222A 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: 3.800A pdb=" N TYR A 614 " --> pdb=" O VAL A 752 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 809 through 813 Processing sheet with id=AA4, first strand: chain 'A' and resid 846 through 851 removed outlier: 3.745A pdb=" N MET A 834 " --> pdb=" O THR A 878 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ILE A 875 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TRP A 886 " --> pdb=" O ILE A 875 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ALA A 877 " --> pdb=" O GLY A 884 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 846 through 851 removed outlier: 3.745A pdb=" N MET A 834 " --> pdb=" O THR A 878 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2 through 3 removed outlier: 3.691A pdb=" N ILE B 76 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 7 through 10 removed outlier: 6.840A pdb=" N LEU B 29 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N PHE B 58 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE B 31 " --> pdb=" O PHE B 58 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N TYR B 85 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ARG B 112 " --> pdb=" O TYR B 85 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU B 87 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N GLU B 114 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE B 89 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 164 through 165 Processing sheet with id=AA9, first strand: chain 'B' and resid 175 through 177 Processing sheet with id=AB1, first strand: chain 'B' and resid 205 through 209 removed outlier: 4.097A pdb=" N ALA B 220 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N SER B 208 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N CYS B 218 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AB3, first strand: chain 'B' and resid 245 through 248 removed outlier: 8.084A pdb=" N CYS B 273 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG B 240 " --> pdb=" O CYS B 273 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 281 through 283 Processing sheet with id=AB5, first strand: chain 'B' and resid 585 through 590 removed outlier: 5.145A pdb=" N ASP B 586 " --> pdb=" O ASN B 602 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASN B 602 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 747 through 751 Processing sheet with id=AB7, first strand: chain 'B' and resid 809 through 813 Processing sheet with id=AB8, first strand: chain 'B' and resid 846 through 851 removed outlier: 3.700A pdb=" N MET B 834 " --> pdb=" O THR B 878 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 846 through 851 removed outlier: 3.700A pdb=" N MET B 834 " --> pdb=" O THR B 878 " (cutoff:3.500A) 209 hydrogen bonds defined for protein. 528 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: 4.71 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 5789 1.03 - 1.23: 471 1.23 - 1.44: 2236 1.44 - 1.64: 3410 1.64 - 1.84: 50 Bond restraints: 11956 Sorted by residual: bond pdb=" N VAL A 580 " pdb=" CA VAL A 580 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.77e+00 bond pdb=" CB CYS B 205 " pdb=" SG CYS B 205 " ideal model delta sigma weight residual 1.808 1.758 0.050 3.30e-02 9.18e+02 2.30e+00 bond pdb=" N VAL A 580 " pdb=" H VAL A 580 " ideal model delta sigma weight residual 0.860 0.889 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" CB LYS A 897 " pdb=" CG LYS A 897 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.60e+00 bond pdb=" CB CYS A 785 " pdb=" SG CYS A 785 " ideal model delta sigma weight residual 1.808 1.767 0.041 3.30e-02 9.18e+02 1.57e+00 ... (remaining 11951 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 20600 1.70 - 3.40: 842 3.40 - 5.10: 89 5.10 - 6.80: 21 6.80 - 8.50: 1 Bond angle restraints: 21553 Sorted by residual: angle pdb=" N ASN B 11 " pdb=" CA ASN B 11 " pdb=" C ASN B 11 " ideal model delta sigma weight residual 110.80 119.30 -8.50 2.13e+00 2.20e-01 1.59e+01 angle pdb=" CA LYS B 600 " pdb=" CB LYS B 600 " pdb=" CG LYS B 600 " ideal model delta sigma weight residual 114.10 107.58 6.52 2.00e+00 2.50e-01 1.06e+01 angle pdb=" N ASP B 12 " pdb=" CA ASP B 12 " pdb=" C ASP B 12 " ideal model delta sigma weight residual 109.06 114.51 -5.45 1.70e+00 3.46e-01 1.03e+01 angle pdb=" CA TYR A 628 " pdb=" CB TYR A 628 " pdb=" CG TYR A 628 " ideal model delta sigma weight residual 113.90 119.60 -5.70 1.80e+00 3.09e-01 1.00e+01 angle pdb=" CA LYS A 862 " pdb=" CB LYS A 862 " pdb=" CG LYS A 862 " ideal model delta sigma weight residual 114.10 107.84 6.26 2.00e+00 2.50e-01 9.80e+00 ... (remaining 21548 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 5204 17.48 - 34.96: 344 34.96 - 52.45: 111 52.45 - 69.93: 84 69.93 - 87.41: 7 Dihedral angle restraints: 5750 sinusoidal: 3133 harmonic: 2617 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 -145.73 59.73 1 1.00e+01 1.00e-02 4.76e+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 180.00 151.14 28.86 0 5.00e+00 4.00e-02 3.33e+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 180.00 151.30 28.70 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 5747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 456 0.035 - 0.070: 245 0.070 - 0.105: 110 0.105 - 0.140: 52 0.140 - 0.175: 11 Chirality restraints: 874 Sorted by residual: chirality pdb=" CA GLN B 14 " pdb=" N GLN B 14 " pdb=" C GLN B 14 " pdb=" CB GLN B 14 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.61e-01 chirality pdb=" CA ASN B 11 " pdb=" N ASN B 11 " pdb=" C ASN B 11 " pdb=" CB ASN B 11 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA ILE A 832 " pdb=" N ILE A 832 " pdb=" C ILE A 832 " pdb=" CB ILE A 832 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 871 not shown) Planarity restraints: 1785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 112 " -0.099 9.50e-02 1.11e+02 4.89e-02 3.05e+01 pdb=" NE ARG B 112 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG B 112 " -0.079 2.00e-02 2.50e+03 pdb=" NH1 ARG B 112 " 0.051 2.00e-02 2.50e+03 pdb=" NH2 ARG B 112 " 0.039 2.00e-02 2.50e+03 pdb="HH11 ARG B 112 " -0.016 2.00e-02 2.50e+03 pdb="HH12 ARG B 112 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG B 112 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 112 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 865 " 0.032 9.50e-02 1.11e+02 3.24e-02 2.12e+01 pdb=" NE ARG A 865 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG A 865 " 0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG A 865 " -0.041 2.00e-02 2.50e+03 pdb=" NH2 ARG A 865 " 0.041 2.00e-02 2.50e+03 pdb="HH11 ARG A 865 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 865 " 0.027 2.00e-02 2.50e+03 pdb="HH21 ARG A 865 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 865 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 269 " -0.001 2.00e-02 2.50e+03 2.84e-02 1.81e+01 pdb=" CG HIS B 269 " 0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS B 269 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS B 269 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 HIS B 269 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS B 269 " -0.051 2.00e-02 2.50e+03 pdb=" HD2 HIS B 269 " 0.014 2.00e-02 2.50e+03 pdb=" HE1 HIS B 269 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 HIS B 269 " 0.041 2.00e-02 2.50e+03 ... (remaining 1782 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 335 2.09 - 2.72: 20056 2.72 - 3.35: 33407 3.35 - 3.97: 41862 3.97 - 4.60: 65099 Nonbonded interactions: 160759 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 635 " pdb=" OE2 GLU B 836 " model vdw 1.463 2.450 nonbonded pdb=" HH TYR B 171 " pdb=" O LEU B 880 " model vdw 1.471 2.450 nonbonded pdb="HH11 ARG B 874 " pdb=" O THR B 887 " model vdw 1.484 2.450 nonbonded pdb=" O ASN A 610 " pdb=" H HIS A 778 " model vdw 1.507 2.450 nonbonded pdb=" OD2 ASP A 586 " pdb="HD21 ASN A 602 " model vdw 1.527 2.450 ... (remaining 160754 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: 4.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.190 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 30.080 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 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 : 0.005 0.050 6184 Z= 0.223 Angle : 0.996 8.496 8404 Z= 0.564 Chirality : 0.055 0.175 874 Planarity : 0.006 0.060 1101 Dihedral : 13.450 80.669 2316 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.79 % Favored : 94.80 % Rotamer: Outliers : 1.20 % Allowed : 4.19 % Favored : 94.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -1.20 (0.29), residues: 731 helix: -3.55 (0.43), residues: 65 sheet: 0.23 (0.36), residues: 212 loop : -0.87 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP B 176 HIS 0.017 0.003 HIS B 269 PHE 0.020 0.003 PHE B 90 TYR 0.025 0.006 TYR A 628 ARG 0.089 0.009 ARG B 112 Details of bonding type rmsd hydrogen bonds : bond 0.27436 ( 183) hydrogen bonds : angle 10.13624 ( 528) SS BOND : bond 0.00421 ( 17) SS BOND : angle 2.04624 ( 34) covalent geometry : bond 0.00509 ( 6167) covalent geometry : angle 0.98936 ( 8370) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 1.008 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 870 ASN cc_start: 0.4986 (m-40) cc_final: 0.4719 (m-40) REVERT: B 131 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7257 (pp) REVERT: B 878 THR cc_start: 0.8570 (m) cc_final: 0.8307 (p) outliers start: 8 outliers final: 3 residues processed: 107 average time/residue: 0.3911 time to fit residues: 54.9711 Evaluate side-chains 68 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.096989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.083714 restraints weight = 104039.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.085954 restraints weight = 56538.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.087499 restraints weight = 37483.571| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6184 Z= 0.171 Angle : 0.707 5.943 8404 Z= 0.384 Chirality : 0.048 0.162 874 Planarity : 0.005 0.046 1101 Dihedral : 6.861 30.359 831 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.38 % Favored : 95.35 % Rotamer: Outliers : 0.15 % Allowed : 3.44 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.30), residues: 731 helix: -2.12 (0.57), residues: 54 sheet: -0.26 (0.35), residues: 201 loop : -0.45 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 618 HIS 0.007 0.002 HIS B 778 PHE 0.017 0.002 PHE B 45 TYR 0.016 0.002 TYR A 858 ARG 0.006 0.001 ARG B 874 Details of bonding type rmsd hydrogen bonds : bond 0.04488 ( 183) hydrogen bonds : angle 7.71622 ( 528) SS BOND : bond 0.00520 ( 17) SS BOND : angle 1.73246 ( 34) covalent geometry : bond 0.00379 ( 6167) covalent geometry : angle 0.70016 ( 8370) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.968 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: symmetry clash REVERT: A 602 ASN cc_start: 0.8936 (m-40) cc_final: 0.8611 (m-40) REVERT: A 870 ASN cc_start: 0.3788 (m-40) cc_final: 0.3527 (m-40) REVERT: B 852 ARG cc_start: 0.6463 (ttt-90) cc_final: 0.6135 (ptm160) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.3935 time to fit residues: 39.6664 Evaluate side-chains 51 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 56 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.095223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.081722 restraints weight = 104412.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.083894 restraints weight = 56306.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.085384 restraints weight = 37286.652| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6184 Z= 0.188 Angle : 0.665 5.780 8404 Z= 0.359 Chirality : 0.048 0.149 874 Planarity : 0.005 0.042 1101 Dihedral : 6.493 32.811 831 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.34 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.14 (0.30), residues: 731 helix: -2.11 (0.59), residues: 63 sheet: -0.74 (0.35), residues: 205 loop : -0.50 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 618 HIS 0.005 0.002 HIS A 774 PHE 0.019 0.002 PHE A 892 TYR 0.016 0.002 TYR B 239 ARG 0.004 0.001 ARG B 617 Details of bonding type rmsd hydrogen bonds : bond 0.04281 ( 183) hydrogen bonds : angle 7.26314 ( 528) SS BOND : bond 0.00538 ( 17) SS BOND : angle 1.51510 ( 34) covalent geometry : bond 0.00413 ( 6167) covalent geometry : angle 0.65942 ( 8370) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.963 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: symmetry clash REVERT: A 610 ASN cc_start: 0.8461 (m110) cc_final: 0.8016 (m110) REVERT: A 693 GLU cc_start: 0.7361 (tm-30) cc_final: 0.6960 (tm-30) REVERT: B 602 ASN cc_start: 0.8922 (t0) cc_final: 0.8586 (t0) REVERT: B 810 TRP cc_start: 0.5376 (p-90) cc_final: 0.5078 (p-90) REVERT: B 833 LEU cc_start: 0.9002 (mm) cc_final: 0.8311 (tp) REVERT: B 852 ARG cc_start: 0.6424 (ttt-90) cc_final: 0.6132 (ptm160) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.3515 time to fit residues: 30.8708 Evaluate side-chains 54 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 8 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 608 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.095190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.081754 restraints weight = 105324.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.083992 restraints weight = 57380.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.085519 restraints weight = 37897.233| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6184 Z= 0.141 Angle : 0.602 6.069 8404 Z= 0.324 Chirality : 0.046 0.150 874 Planarity : 0.005 0.044 1101 Dihedral : 6.037 33.345 831 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.20 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.22 (0.30), residues: 731 helix: -2.21 (0.60), residues: 63 sheet: -0.92 (0.34), residues: 213 loop : -0.46 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 618 HIS 0.006 0.001 HIS A 774 PHE 0.012 0.001 PHE B 45 TYR 0.017 0.001 TYR B 13 ARG 0.003 0.000 ARG B 617 Details of bonding type rmsd hydrogen bonds : bond 0.03511 ( 183) hydrogen bonds : angle 6.80759 ( 528) SS BOND : bond 0.00270 ( 17) SS BOND : angle 1.28854 ( 34) covalent geometry : bond 0.00310 ( 6167) covalent geometry : angle 0.59731 ( 8370) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.886 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: symmetry clash revert: symmetry clash REVERT: A 624 ASP cc_start: 0.7933 (m-30) cc_final: 0.7598 (t0) REVERT: A 693 GLU cc_start: 0.7429 (tm-30) cc_final: 0.7063 (tm-30) REVERT: B 602 ASN cc_start: 0.8975 (t0) cc_final: 0.8551 (t0) REVERT: B 810 TRP cc_start: 0.5379 (p-90) cc_final: 0.5168 (p-90) REVERT: B 833 LEU cc_start: 0.9061 (mm) cc_final: 0.8339 (tp) REVERT: B 852 ARG cc_start: 0.6448 (ttt180) cc_final: 0.5895 (ptm160) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.3505 time to fit residues: 30.8396 Evaluate side-chains 54 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 47 optimal weight: 0.0970 chunk 14 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 876 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.094717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.081100 restraints weight = 104984.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.083300 restraints weight = 57377.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.084830 restraints weight = 38302.424| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6184 Z= 0.149 Angle : 0.602 6.434 8404 Z= 0.324 Chirality : 0.046 0.164 874 Planarity : 0.005 0.045 1101 Dihedral : 5.928 33.155 831 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.70 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.19 (0.31), residues: 731 helix: -1.52 (0.64), residues: 60 sheet: -1.05 (0.33), residues: 222 loop : -0.46 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 244 HIS 0.009 0.002 HIS A 774 PHE 0.011 0.001 PHE B 45 TYR 0.013 0.001 TYR B 13 ARG 0.003 0.000 ARG B 874 Details of bonding type rmsd hydrogen bonds : bond 0.03656 ( 183) hydrogen bonds : angle 6.70733 ( 528) SS BOND : bond 0.00339 ( 17) SS BOND : angle 1.58998 ( 34) covalent geometry : bond 0.00331 ( 6167) covalent geometry : angle 0.59500 ( 8370) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.987 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: symmetry clash REVERT: A 693 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7142 (tm-30) REVERT: B 602 ASN cc_start: 0.8971 (t0) cc_final: 0.8595 (t0) REVERT: B 810 TRP cc_start: 0.5468 (p-90) cc_final: 0.5157 (p-90) REVERT: B 833 LEU cc_start: 0.9140 (mm) cc_final: 0.8458 (tp) REVERT: B 852 ARG cc_start: 0.6460 (ttt180) cc_final: 0.6008 (ptm160) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.3677 time to fit residues: 32.3816 Evaluate side-chains 55 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.095297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.081689 restraints weight = 103949.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.083914 restraints weight = 56263.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.085253 restraints weight = 37210.678| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6184 Z= 0.135 Angle : 0.586 6.681 8404 Z= 0.314 Chirality : 0.046 0.144 874 Planarity : 0.005 0.044 1101 Dihedral : 5.754 32.155 831 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.84 % Favored : 93.02 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.12 (0.31), residues: 731 helix: -1.42 (0.70), residues: 54 sheet: -1.01 (0.33), residues: 222 loop : -0.43 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 127 HIS 0.009 0.002 HIS A 774 PHE 0.010 0.001 PHE B 45 TYR 0.020 0.001 TYR B 13 ARG 0.004 0.001 ARG B 874 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 183) hydrogen bonds : angle 6.59517 ( 528) SS BOND : bond 0.00234 ( 17) SS BOND : angle 1.36301 ( 34) covalent geometry : bond 0.00300 ( 6167) covalent geometry : angle 0.58063 ( 8370) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.044 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: A 624 ASP cc_start: 0.8267 (m-30) cc_final: 0.7585 (t0) REVERT: A 693 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7231 (tm-30) REVERT: B 602 ASN cc_start: 0.8991 (t0) cc_final: 0.8713 (t0) REVERT: B 810 TRP cc_start: 0.5520 (p-90) cc_final: 0.5182 (p-90) REVERT: B 833 LEU cc_start: 0.9172 (mm) cc_final: 0.8509 (tp) REVERT: B 852 ARG cc_start: 0.6482 (ttt180) cc_final: 0.6224 (ptm160) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.3473 time to fit residues: 31.6216 Evaluate side-chains 51 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 11 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 65 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 0.0770 chunk 3 optimal weight: 0.9990 chunk 52 optimal weight: 0.0870 chunk 51 optimal weight: 0.8980 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 ASN B 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.095710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.082167 restraints weight = 104458.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.084340 restraints weight = 56718.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.085903 restraints weight = 37618.811| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.5359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6184 Z= 0.103 Angle : 0.560 6.901 8404 Z= 0.299 Chirality : 0.046 0.147 874 Planarity : 0.004 0.045 1101 Dihedral : 5.528 30.072 831 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.02 % Favored : 93.84 % Rotamer: Outliers : 0.15 % Allowed : 1.20 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.31), residues: 731 helix: -1.34 (0.70), residues: 54 sheet: -0.90 (0.33), residues: 222 loop : -0.32 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 618 HIS 0.008 0.001 HIS A 774 PHE 0.019 0.001 PHE A 695 TYR 0.010 0.001 TYR B 835 ARG 0.014 0.001 ARG B 10 Details of bonding type rmsd hydrogen bonds : bond 0.03227 ( 183) hydrogen bonds : angle 6.34188 ( 528) SS BOND : bond 0.00212 ( 17) SS BOND : angle 1.04698 ( 34) covalent geometry : bond 0.00235 ( 6167) covalent geometry : angle 0.55754 ( 8370) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.914 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: symmetry clash revert: symmetry clash REVERT: A 624 ASP cc_start: 0.8204 (m-30) cc_final: 0.7592 (t0) REVERT: B 602 ASN cc_start: 0.8944 (t0) cc_final: 0.8708 (t0) REVERT: B 810 TRP cc_start: 0.5426 (p-90) cc_final: 0.5125 (p-90) REVERT: B 833 LEU cc_start: 0.9141 (mm) cc_final: 0.8528 (tp) outliers start: 1 outliers final: 0 residues processed: 66 average time/residue: 0.3389 time to fit residues: 30.8097 Evaluate side-chains 54 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.094742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.081163 restraints weight = 103607.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.083420 restraints weight = 56531.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.084971 restraints weight = 37507.128| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.5552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6184 Z= 0.138 Angle : 0.580 7.148 8404 Z= 0.312 Chirality : 0.046 0.140 874 Planarity : 0.005 0.057 1101 Dihedral : 5.569 29.133 831 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.80 % Favored : 92.07 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -1.14 (0.31), residues: 731 helix: -1.33 (0.72), residues: 54 sheet: -0.98 (0.33), residues: 228 loop : -0.47 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 618 HIS 0.009 0.001 HIS A 774 PHE 0.019 0.001 PHE A 695 TYR 0.013 0.001 TYR B 13 ARG 0.010 0.000 ARG B 10 Details of bonding type rmsd hydrogen bonds : bond 0.03431 ( 183) hydrogen bonds : angle 6.43706 ( 528) SS BOND : bond 0.00255 ( 17) SS BOND : angle 1.25470 ( 34) covalent geometry : bond 0.00314 ( 6167) covalent geometry : angle 0.57588 ( 8370) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.995 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 602 ASN cc_start: 0.8976 (t0) cc_final: 0.8740 (t0) REVERT: B 810 TRP cc_start: 0.5434 (p-90) cc_final: 0.5105 (p-90) REVERT: B 833 LEU cc_start: 0.9126 (mm) cc_final: 0.8658 (tp) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.3315 time to fit residues: 29.3767 Evaluate side-chains 48 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 15 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 0.0770 chunk 69 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 39 optimal weight: 0.2980 chunk 66 optimal weight: 0.1980 chunk 14 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.095449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.082018 restraints weight = 102782.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.084180 restraints weight = 55833.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.085693 restraints weight = 37263.145| |-----------------------------------------------------------------------------| r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.5743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6184 Z= 0.098 Angle : 0.545 7.041 8404 Z= 0.292 Chirality : 0.046 0.145 874 Planarity : 0.004 0.044 1101 Dihedral : 5.303 25.859 831 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.06 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -1.00 (0.31), residues: 731 helix: -1.14 (0.74), residues: 54 sheet: -0.83 (0.33), residues: 227 loop : -0.42 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 822 HIS 0.008 0.001 HIS A 774 PHE 0.016 0.001 PHE A 695 TYR 0.011 0.001 TYR A 835 ARG 0.008 0.000 ARG B 10 Details of bonding type rmsd hydrogen bonds : bond 0.03121 ( 183) hydrogen bonds : angle 6.24791 ( 528) SS BOND : bond 0.00219 ( 17) SS BOND : angle 1.09389 ( 34) covalent geometry : bond 0.00225 ( 6167) covalent geometry : angle 0.54157 ( 8370) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.865 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: B 602 ASN cc_start: 0.8935 (t0) cc_final: 0.8733 (t0) REVERT: B 810 TRP cc_start: 0.5468 (p-90) cc_final: 0.5131 (p-90) REVERT: B 833 LEU cc_start: 0.9156 (mm) cc_final: 0.8654 (tp) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.3692 time to fit residues: 32.0656 Evaluate side-chains 49 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 61 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.094947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.081514 restraints weight = 102848.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.083751 restraints weight = 56378.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.085285 restraints weight = 37479.551| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.5927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6184 Z= 0.121 Angle : 0.558 7.220 8404 Z= 0.299 Chirality : 0.046 0.139 874 Planarity : 0.005 0.044 1101 Dihedral : 5.330 24.732 831 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.93 % Favored : 91.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.31), residues: 731 helix: -0.64 (0.81), residues: 48 sheet: -0.97 (0.34), residues: 214 loop : -0.37 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 618 HIS 0.008 0.001 HIS A 774 PHE 0.015 0.001 PHE A 695 TYR 0.020 0.001 TYR B 871 ARG 0.007 0.001 ARG B 10 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 183) hydrogen bonds : angle 6.23912 ( 528) SS BOND : bond 0.00222 ( 17) SS BOND : angle 1.05613 ( 34) covalent geometry : bond 0.00277 ( 6167) covalent geometry : angle 0.55492 ( 8370) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.025 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: B 810 TRP cc_start: 0.5455 (p-90) cc_final: 0.5118 (p-90) REVERT: B 833 LEU cc_start: 0.9163 (mm) cc_final: 0.8713 (tp) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.3594 time to fit residues: 29.9147 Evaluate side-chains 49 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 254 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.093406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.080270 restraints weight = 103693.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.082445 restraints weight = 56080.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.083913 restraints weight = 37207.343| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.6238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6184 Z= 0.159 Angle : 0.591 6.923 8404 Z= 0.318 Chirality : 0.046 0.145 874 Planarity : 0.005 0.044 1101 Dihedral : 5.558 22.234 831 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.17 % Favored : 90.70 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -1.20 (0.31), residues: 731 helix: -1.28 (0.75), residues: 53 sheet: -1.12 (0.34), residues: 215 loop : -0.50 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 618 HIS 0.010 0.002 HIS A 774 PHE 0.014 0.001 PHE A 695 TYR 0.016 0.002 TYR B 13 ARG 0.006 0.001 ARG B 10 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 183) hydrogen bonds : angle 6.45347 ( 528) SS BOND : bond 0.00215 ( 17) SS BOND : angle 1.16120 ( 34) covalent geometry : bond 0.00359 ( 6167) covalent geometry : angle 0.58781 ( 8370) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4822.33 seconds wall clock time: 82 minutes 57.45 seconds (4977.45 seconds total)