Starting phenix.real_space_refine on Wed Jan 15 01:25:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b79_44304/01_2025/9b79_44304.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b79_44304/01_2025/9b79_44304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b79_44304/01_2025/9b79_44304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b79_44304/01_2025/9b79_44304.map" model { file = "/net/cci-nas-00/data/ceres_data/9b79_44304/01_2025/9b79_44304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b79_44304/01_2025/9b79_44304.cif" } resolution = 2.71 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= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 4960 2.51 5 N 1412 2.21 5 O 1476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 7876 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1969 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "B" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1969 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "C" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1969 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "D" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1969 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Time building chain proxies: 5.24, per 1000 atoms: 0.67 Number of scatterers: 7876 At special positions: 0 Unit cell: (104.076, 82.6, 103.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 1476 8.00 N 1412 7.00 C 4960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 1.0 seconds 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1912 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 8 sheets defined 47.3% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 20 through 24 Processing helix chain 'A' and resid 39 through 52 Processing helix chain 'A' and resid 53 through 58 removed outlier: 3.686A pdb=" N GLU A 56 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU A 58 " --> pdb=" O SER A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 109 through 124 Processing helix chain 'A' and resid 155 through 167 removed outlier: 3.659A pdb=" N SER A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 213 Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 247 through 260 Processing helix chain 'B' and resid 20 through 24 Processing helix chain 'B' and resid 39 through 52 Processing helix chain 'B' and resid 53 through 57 removed outlier: 3.650A pdb=" N GLU B 56 " --> pdb=" O GLU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 82 removed outlier: 4.029A pdb=" N TRP B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 109 through 124 Processing helix chain 'B' and resid 155 through 167 removed outlier: 3.774A pdb=" N SER B 167 " --> pdb=" O ALA B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 213 removed outlier: 3.706A pdb=" N PHE B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 removed outlier: 3.715A pdb=" N LEU B 234 " --> pdb=" O THR B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 260 Processing helix chain 'C' and resid 20 through 24 Processing helix chain 'C' and resid 39 through 52 Processing helix chain 'C' and resid 53 through 57 removed outlier: 3.891A pdb=" N GLU C 56 " --> pdb=" O GLU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 82 Processing helix chain 'C' and resid 104 through 108 removed outlier: 3.644A pdb=" N VAL C 108 " --> pdb=" O PRO C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 124 Processing helix chain 'C' and resid 155 through 167 Processing helix chain 'C' and resid 185 through 213 removed outlier: 3.620A pdb=" N PHE C 198 " --> pdb=" O ALA C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 235 Processing helix chain 'C' and resid 247 through 260 Processing helix chain 'D' and resid 20 through 24 Processing helix chain 'D' and resid 39 through 52 Processing helix chain 'D' and resid 53 through 57 removed outlier: 3.705A pdb=" N GLU D 56 " --> pdb=" O GLU D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 removed outlier: 4.076A pdb=" N TRP D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 108 removed outlier: 3.527A pdb=" N VAL D 108 " --> pdb=" O PRO D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 124 Processing helix chain 'D' and resid 155 through 167 removed outlier: 3.648A pdb=" N SER D 167 " --> pdb=" O ALA D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 213 Processing helix chain 'D' and resid 230 through 235 removed outlier: 3.701A pdb=" N LEU D 234 " --> pdb=" O THR D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 261 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 33 removed outlier: 5.533A pdb=" N VAL A 26 " --> pdb=" O SER A 18 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N SER A 18 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN A 28 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR A 61 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ILE A 90 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ALA A 63 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 154 removed outlier: 4.042A pdb=" N GLY A 149 " --> pdb=" O VAL A 140 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA A 126 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL A 225 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE A 128 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR A 227 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL A 130 " --> pdb=" O THR A 227 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 33 removed outlier: 5.382A pdb=" N VAL B 26 " --> pdb=" O SER B 18 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER B 18 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N SER B 65 " --> pdb=" O ILE B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 147 through 154 removed outlier: 4.087A pdb=" N GLY B 149 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N HIS B 243 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE B 224 " --> pdb=" O HIS B 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 25 through 33 removed outlier: 6.901A pdb=" N LEU C 16 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLN C 29 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL C 14 " --> pdb=" O GLN C 29 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ARG C 31 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR C 12 " --> pdb=" O ARG C 31 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 147 through 154 removed outlier: 4.013A pdb=" N GLY C 149 " --> pdb=" O VAL C 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 25 through 33 removed outlier: 5.362A pdb=" N VAL D 26 " --> pdb=" O SER D 18 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N SER D 18 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR D 61 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ILE D 90 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ALA D 63 " --> pdb=" O ILE D 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 147 through 154 removed outlier: 4.060A pdb=" N GLY D 149 " --> pdb=" O VAL D 140 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1326 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2716 1.34 - 1.46: 1054 1.46 - 1.57: 4190 1.57 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 8004 Sorted by residual: bond pdb=" CB ASN A 104 " pdb=" CG ASN A 104 " ideal model delta sigma weight residual 1.516 1.548 -0.032 2.50e-02 1.60e+03 1.60e+00 bond pdb=" CB ASN C 104 " pdb=" CG ASN C 104 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.50e+00 bond pdb=" CB ASN D 104 " pdb=" CG ASN D 104 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.49e+00 bond pdb=" CA VAL C 102 " pdb=" CB VAL C 102 " ideal model delta sigma weight residual 1.546 1.565 -0.019 1.69e-02 3.50e+03 1.24e+00 bond pdb=" CB VAL D 114 " pdb=" CG1 VAL D 114 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.15e+00 ... (remaining 7999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 10651 1.62 - 3.25: 197 3.25 - 4.87: 29 4.87 - 6.49: 9 6.49 - 8.11: 6 Bond angle restraints: 10892 Sorted by residual: angle pdb=" C ASN A 104 " pdb=" CA ASN A 104 " pdb=" CB ASN A 104 " ideal model delta sigma weight residual 111.20 116.50 -5.30 1.81e+00 3.05e-01 8.57e+00 angle pdb=" C ASN B 104 " pdb=" CA ASN B 104 " pdb=" CB ASN B 104 " ideal model delta sigma weight residual 111.20 116.48 -5.28 1.81e+00 3.05e-01 8.50e+00 angle pdb=" C ASN C 104 " pdb=" CA ASN C 104 " pdb=" CB ASN C 104 " ideal model delta sigma weight residual 111.29 116.39 -5.10 1.92e+00 2.71e-01 7.06e+00 angle pdb=" C ASN D 104 " pdb=" CA ASN D 104 " pdb=" CB ASN D 104 " ideal model delta sigma weight residual 111.29 116.26 -4.97 1.92e+00 2.71e-01 6.69e+00 angle pdb=" CA ASN A 104 " pdb=" CB ASN A 104 " pdb=" CG ASN A 104 " ideal model delta sigma weight residual 112.60 115.07 -2.47 1.00e+00 1.00e+00 6.11e+00 ... (remaining 10887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.74: 4437 16.74 - 33.49: 293 33.49 - 50.23: 48 50.23 - 66.98: 18 66.98 - 83.72: 4 Dihedral angle restraints: 4800 sinusoidal: 1836 harmonic: 2964 Sorted by residual: dihedral pdb=" CA GLN B 80 " pdb=" C GLN B 80 " pdb=" N TYR B 81 " pdb=" CA TYR B 81 " ideal model delta harmonic sigma weight residual -180.00 -162.82 -17.18 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA ASP A 131 " pdb=" CB ASP A 131 " pdb=" CG ASP A 131 " pdb=" OD1 ASP A 131 " ideal model delta sinusoidal sigma weight residual -30.00 -87.65 57.65 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA GLN D 80 " pdb=" C GLN D 80 " pdb=" N TYR D 81 " pdb=" CA TYR D 81 " ideal model delta harmonic sigma weight residual -180.00 -163.64 -16.36 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 4797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 888 0.042 - 0.085: 296 0.085 - 0.127: 110 0.127 - 0.170: 20 0.170 - 0.212: 6 Chirality restraints: 1320 Sorted by residual: chirality pdb=" CA VAL C 102 " pdb=" N VAL C 102 " pdb=" C VAL C 102 " pdb=" CB VAL C 102 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ASN B 104 " pdb=" N ASN B 104 " pdb=" C ASN B 104 " pdb=" CB ASN B 104 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ASN A 104 " pdb=" N ASN A 104 " pdb=" C ASN A 104 " pdb=" CB ASN A 104 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.20 2.00e-01 2.50e+01 9.54e-01 ... (remaining 1317 not shown) Planarity restraints: 1412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 194 " -0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C ALA D 194 " 0.061 2.00e-02 2.50e+03 pdb=" O ALA D 194 " -0.023 2.00e-02 2.50e+03 pdb=" N VAL D 195 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 193 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C GLY B 193 " -0.033 2.00e-02 2.50e+03 pdb=" O GLY B 193 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA B 194 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 193 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.74e+00 pdb=" C GLY C 193 " 0.029 2.00e-02 2.50e+03 pdb=" O GLY C 193 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA C 194 " -0.010 2.00e-02 2.50e+03 ... (remaining 1409 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1114 2.76 - 3.30: 7260 3.30 - 3.83: 13112 3.83 - 4.37: 15211 4.37 - 4.90: 27160 Nonbonded interactions: 63857 Sorted by model distance: nonbonded pdb=" NH2 ARG C 8 " pdb=" OD2 ASP C 131 " model vdw 2.229 3.120 nonbonded pdb=" ND2 ASN D 115 " pdb=" OD2 ASP D 131 " model vdw 2.261 3.120 nonbonded pdb=" NH2 ARG A 75 " pdb=" OE2 GLU A 91 " model vdw 2.280 3.120 nonbonded pdb=" O GLU C 237 " pdb=" NH2 ARG D 208 " model vdw 2.320 3.120 nonbonded pdb=" O GLY C 155 " pdb=" OG SER C 159 " model vdw 2.324 3.040 ... (remaining 63852 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.990 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:13.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8004 Z= 0.206 Angle : 0.596 8.113 10892 Z= 0.315 Chirality : 0.050 0.212 1320 Planarity : 0.005 0.038 1412 Dihedral : 12.077 83.724 2888 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.26), residues: 1036 helix: 1.36 (0.25), residues: 408 sheet: 0.93 (0.35), residues: 228 loop : -0.25 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 30 HIS 0.003 0.001 HIS A 72 PHE 0.019 0.001 PHE B 147 TYR 0.008 0.001 TYR D 120 ARG 0.007 0.001 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.802 Fit side-chains REVERT: A 25 LYS cc_start: 0.7560 (pttt) cc_final: 0.7278 (tptt) REVERT: A 75 ARG cc_start: 0.6081 (mtt180) cc_final: 0.5831 (tpp-160) REVERT: A 246 GLN cc_start: 0.6610 (pt0) cc_final: 0.6126 (tt0) REVERT: B 20 MET cc_start: 0.6680 (pmm) cc_final: 0.6233 (pmm) REVERT: B 25 LYS cc_start: 0.7267 (pttt) cc_final: 0.6611 (ptmt) REVERT: B 48 ASP cc_start: 0.6119 (t0) cc_final: 0.5889 (m-30) REVERT: B 142 SER cc_start: 0.8149 (m) cc_final: 0.7755 (p) REVERT: D 1 MET cc_start: 0.4395 (mmp) cc_final: 0.3701 (ttt) REVERT: D 18 SER cc_start: 0.7385 (t) cc_final: 0.7152 (m) REVERT: D 20 MET cc_start: 0.4723 (pmm) cc_final: 0.4394 (pmm) REVERT: D 25 LYS cc_start: 0.7564 (pttt) cc_final: 0.7217 (ptmt) REVERT: D 29 GLN cc_start: 0.5952 (tt0) cc_final: 0.5569 (tm-30) REVERT: D 106 LYS cc_start: 0.7301 (mttt) cc_final: 0.6355 (mppt) REVERT: D 208 ARG cc_start: 0.7561 (mtt90) cc_final: 0.7286 (mtt-85) REVERT: D 246 GLN cc_start: 0.7598 (pt0) cc_final: 0.7175 (tt0) REVERT: D 258 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6578 (tt0) outliers start: 0 outliers final: 1 residues processed: 175 average time/residue: 1.4046 time to fit residues: 258.4000 Evaluate side-chains 117 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 0.0870 chunk 26 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 0.0040 chunk 49 optimal weight: 0.4980 chunk 60 optimal weight: 0.0040 chunk 94 optimal weight: 20.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 HIS B 9 ASN B 28 GLN C 247 HIS D 9 ASN D 247 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.221237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.183823 restraints weight = 8207.691| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 2.00 r_work: 0.4095 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3969 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8004 Z= 0.216 Angle : 0.557 6.068 10892 Z= 0.291 Chirality : 0.046 0.143 1320 Planarity : 0.004 0.033 1412 Dihedral : 4.105 21.442 1126 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.54 % Allowed : 14.50 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.26), residues: 1036 helix: 1.76 (0.25), residues: 416 sheet: 1.06 (0.35), residues: 228 loop : 0.06 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 30 HIS 0.003 0.001 HIS D 72 PHE 0.009 0.001 PHE C 132 TYR 0.008 0.001 TYR D 120 ARG 0.007 0.001 ARG C 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.795 Fit side-chains REVERT: A 56 GLU cc_start: 0.7317 (mp0) cc_final: 0.6893 (mp0) REVERT: A 89 LEU cc_start: 0.5137 (OUTLIER) cc_final: 0.4910 (tp) REVERT: A 90 ILE cc_start: 0.7062 (OUTLIER) cc_final: 0.6438 (pp) REVERT: A 124 ARG cc_start: 0.6066 (mmt180) cc_final: 0.5781 (mpt-90) REVERT: A 246 GLN cc_start: 0.6552 (pt0) cc_final: 0.6079 (tt0) REVERT: B 20 MET cc_start: 0.6934 (pmm) cc_final: 0.6476 (pmm) REVERT: B 25 LYS cc_start: 0.7969 (pttt) cc_final: 0.7495 (pttt) REVERT: D 1 MET cc_start: 0.5230 (mmp) cc_final: 0.4529 (ttm) REVERT: D 29 GLN cc_start: 0.6079 (tt0) cc_final: 0.5875 (tm-30) REVERT: D 106 LYS cc_start: 0.7995 (mttt) cc_final: 0.7481 (mppt) REVERT: D 246 GLN cc_start: 0.7864 (pt0) cc_final: 0.7421 (tt0) REVERT: D 258 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7185 (tt0) outliers start: 30 outliers final: 13 residues processed: 134 average time/residue: 1.3795 time to fit residues: 194.8758 Evaluate side-chains 122 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 218 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 21 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 9 ASN D 185 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.222161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.184221 restraints weight = 8276.341| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 2.06 r_work: 0.4089 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3959 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8004 Z= 0.184 Angle : 0.528 6.023 10892 Z= 0.273 Chirality : 0.045 0.136 1320 Planarity : 0.004 0.039 1412 Dihedral : 3.932 20.704 1126 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.13 % Allowed : 16.51 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.27), residues: 1036 helix: 2.04 (0.25), residues: 416 sheet: 0.65 (0.35), residues: 244 loop : 0.32 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 30 HIS 0.008 0.001 HIS A 87 PHE 0.009 0.001 PHE A 198 TYR 0.008 0.001 TYR D 120 ARG 0.008 0.000 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7430 (mp0) cc_final: 0.7024 (mp0) REVERT: A 75 ARG cc_start: 0.6698 (tpp-160) cc_final: 0.6451 (tpm170) REVERT: A 124 ARG cc_start: 0.6114 (mmt180) cc_final: 0.5786 (mpt-90) REVERT: A 246 GLN cc_start: 0.6586 (pt0) cc_final: 0.6099 (tt0) REVERT: B 20 MET cc_start: 0.6940 (pmm) cc_final: 0.6466 (pmm) REVERT: B 25 LYS cc_start: 0.7979 (pttt) cc_final: 0.7485 (pttt) REVERT: B 121 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7193 (m-30) REVERT: B 175 LEU cc_start: 0.6987 (tp) cc_final: 0.6716 (mm) REVERT: B 237 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7234 (mm-30) REVERT: D 1 MET cc_start: 0.5422 (mmp) cc_final: 0.4695 (ttm) REVERT: D 29 GLN cc_start: 0.6064 (tt0) cc_final: 0.5828 (tm-30) REVERT: D 106 LYS cc_start: 0.8098 (mttt) cc_final: 0.7621 (mppt) REVERT: D 246 GLN cc_start: 0.7919 (pt0) cc_final: 0.7494 (tt0) REVERT: D 258 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7239 (tt0) outliers start: 35 outliers final: 17 residues processed: 137 average time/residue: 1.4552 time to fit residues: 210.2081 Evaluate side-chains 122 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 214 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 74 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN B 260 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.217997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.178329 restraints weight = 8212.519| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 2.14 r_work: 0.4009 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3876 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8004 Z= 0.260 Angle : 0.580 7.388 10892 Z= 0.301 Chirality : 0.047 0.148 1320 Planarity : 0.004 0.035 1412 Dihedral : 4.153 19.563 1126 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.25 % Allowed : 18.04 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.26), residues: 1036 helix: 1.90 (0.25), residues: 416 sheet: 0.39 (0.34), residues: 248 loop : 0.24 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 30 HIS 0.005 0.001 HIS D 243 PHE 0.014 0.002 PHE B 198 TYR 0.010 0.002 TYR A 81 ARG 0.009 0.001 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.832 Fit side-chains REVERT: A 56 GLU cc_start: 0.7497 (mp0) cc_final: 0.7125 (mp0) REVERT: A 124 ARG cc_start: 0.6187 (mmt180) cc_final: 0.5836 (mpt-90) REVERT: A 246 GLN cc_start: 0.6556 (pt0) cc_final: 0.6065 (tt0) REVERT: A 260 ASN cc_start: 0.5389 (OUTLIER) cc_final: 0.5066 (m-40) REVERT: B 20 MET cc_start: 0.6935 (pmm) cc_final: 0.6462 (pmm) REVERT: B 25 LYS cc_start: 0.8062 (pttt) cc_final: 0.7534 (pttt) REVERT: B 121 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7427 (t70) REVERT: B 175 LEU cc_start: 0.7058 (tp) cc_final: 0.6790 (mm) REVERT: B 237 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7265 (mm-30) REVERT: C 57 ARG cc_start: 0.6962 (ttp-110) cc_final: 0.6370 (mtm180) REVERT: D 1 MET cc_start: 0.5325 (mmp) cc_final: 0.4571 (ttm) REVERT: D 29 GLN cc_start: 0.6299 (tt0) cc_final: 0.5940 (tm-30) REVERT: D 106 LYS cc_start: 0.8075 (mttt) cc_final: 0.7568 (mppt) REVERT: D 246 GLN cc_start: 0.7894 (pt0) cc_final: 0.7436 (tt0) REVERT: D 258 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7293 (tt0) outliers start: 36 outliers final: 21 residues processed: 131 average time/residue: 1.4162 time to fit residues: 195.4727 Evaluate side-chains 128 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 218 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN ** A 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.218590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.178477 restraints weight = 8153.701| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 2.15 r_work: 0.4039 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3909 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8004 Z= 0.232 Angle : 0.574 10.910 10892 Z= 0.294 Chirality : 0.046 0.138 1320 Planarity : 0.004 0.038 1412 Dihedral : 4.023 16.706 1124 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.95 % Allowed : 18.75 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.27), residues: 1036 helix: 1.94 (0.25), residues: 416 sheet: 0.36 (0.34), residues: 248 loop : 0.28 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 30 HIS 0.004 0.001 HIS A 87 PHE 0.011 0.001 PHE C 132 TYR 0.009 0.001 TYR D 120 ARG 0.011 0.000 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 111 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7569 (mp0) cc_final: 0.7212 (mp0) REVERT: A 124 ARG cc_start: 0.6140 (mmt180) cc_final: 0.5863 (mpt-90) REVERT: A 246 GLN cc_start: 0.6480 (pt0) cc_final: 0.5983 (tt0) REVERT: A 260 ASN cc_start: 0.5312 (OUTLIER) cc_final: 0.4998 (m-40) REVERT: B 20 MET cc_start: 0.6887 (pmm) cc_final: 0.6460 (pmm) REVERT: B 25 LYS cc_start: 0.8025 (pttt) cc_final: 0.7508 (pttt) REVERT: B 121 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7381 (t70) REVERT: B 175 LEU cc_start: 0.7124 (tp) cc_final: 0.6843 (mm) REVERT: B 237 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7226 (mm-30) REVERT: D 1 MET cc_start: 0.5352 (mmp) cc_final: 0.4620 (ttm) REVERT: D 29 GLN cc_start: 0.6255 (tt0) cc_final: 0.5907 (tm-30) REVERT: D 106 LYS cc_start: 0.8081 (mttt) cc_final: 0.7570 (mppt) REVERT: D 246 GLN cc_start: 0.7801 (pt0) cc_final: 0.7369 (tt0) REVERT: D 259 ARG cc_start: 0.6660 (ttm110) cc_final: 0.5924 (ptp90) outliers start: 42 outliers final: 25 residues processed: 137 average time/residue: 1.4153 time to fit residues: 204.1066 Evaluate side-chains 134 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 218 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 36 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 87 HIS B 29 GLN B 260 ASN D 251 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.216133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.178108 restraints weight = 8182.618| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 2.12 r_work: 0.3984 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3852 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8004 Z= 0.310 Angle : 0.643 11.951 10892 Z= 0.328 Chirality : 0.048 0.141 1320 Planarity : 0.004 0.040 1412 Dihedral : 4.263 16.701 1124 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.95 % Allowed : 19.46 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.26), residues: 1036 helix: 1.72 (0.25), residues: 416 sheet: 0.21 (0.33), residues: 248 loop : 0.23 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 82 HIS 0.006 0.001 HIS D 243 PHE 0.016 0.002 PHE B 198 TYR 0.013 0.002 TYR A 81 ARG 0.012 0.001 ARG C 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 106 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7575 (mp0) cc_final: 0.7197 (mp0) REVERT: A 246 GLN cc_start: 0.6507 (pt0) cc_final: 0.6050 (tt0) REVERT: A 259 ARG cc_start: 0.7871 (mtp85) cc_final: 0.7635 (mtp85) REVERT: A 260 ASN cc_start: 0.5466 (OUTLIER) cc_final: 0.5085 (m-40) REVERT: B 20 MET cc_start: 0.6909 (pmm) cc_final: 0.6206 (pmm) REVERT: B 23 HIS cc_start: 0.6655 (m90) cc_final: 0.6436 (m90) REVERT: B 25 LYS cc_start: 0.8031 (pttt) cc_final: 0.7572 (ptmt) REVERT: B 29 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.7040 (tt0) REVERT: B 175 LEU cc_start: 0.7178 (tp) cc_final: 0.6901 (mm) REVERT: B 237 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7238 (mm-30) REVERT: C 57 ARG cc_start: 0.6967 (ttp-110) cc_final: 0.6368 (mtm180) REVERT: D 1 MET cc_start: 0.5441 (mmp) cc_final: 0.4655 (ttm) REVERT: D 29 GLN cc_start: 0.6356 (tt0) cc_final: 0.5958 (tm-30) REVERT: D 33 ARG cc_start: 0.7912 (mtt-85) cc_final: 0.7561 (mpt180) REVERT: D 106 LYS cc_start: 0.8203 (mttt) cc_final: 0.7712 (mppt) REVERT: D 246 GLN cc_start: 0.7811 (pt0) cc_final: 0.7344 (tt0) REVERT: D 259 ARG cc_start: 0.6717 (ttm110) cc_final: 0.5983 (ptp90) outliers start: 42 outliers final: 30 residues processed: 130 average time/residue: 1.4707 time to fit residues: 201.5615 Evaluate side-chains 143 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain B residue 29 GLN Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 218 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 79 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.215045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.177496 restraints weight = 8271.764| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 2.13 r_work: 0.3977 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3847 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8004 Z= 0.331 Angle : 0.657 12.322 10892 Z= 0.336 Chirality : 0.049 0.160 1320 Planarity : 0.004 0.033 1412 Dihedral : 4.346 16.897 1124 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 5.07 % Allowed : 20.17 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.26), residues: 1036 helix: 1.59 (0.25), residues: 416 sheet: 0.44 (0.34), residues: 232 loop : 0.04 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 82 HIS 0.006 0.001 HIS D 243 PHE 0.016 0.002 PHE B 198 TYR 0.016 0.002 TYR A 81 ARG 0.010 0.001 ARG C 57 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 108 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7545 (mp0) cc_final: 0.7167 (mp0) REVERT: A 246 GLN cc_start: 0.6511 (pt0) cc_final: 0.6046 (tt0) REVERT: A 259 ARG cc_start: 0.7913 (mtp85) cc_final: 0.7676 (mtp85) REVERT: A 260 ASN cc_start: 0.5401 (OUTLIER) cc_final: 0.5029 (m-40) REVERT: B 20 MET cc_start: 0.6878 (pmm) cc_final: 0.6160 (pmm) REVERT: B 23 HIS cc_start: 0.6757 (m90) cc_final: 0.6532 (m90) REVERT: B 25 LYS cc_start: 0.8019 (pttt) cc_final: 0.7565 (ptmt) REVERT: B 175 LEU cc_start: 0.7212 (tp) cc_final: 0.6939 (mm) REVERT: B 237 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7259 (mm-30) REVERT: D 1 MET cc_start: 0.5471 (mmp) cc_final: 0.4672 (ttm) REVERT: D 29 GLN cc_start: 0.6347 (tt0) cc_final: 0.5946 (tm-30) REVERT: D 33 ARG cc_start: 0.7919 (mtt-85) cc_final: 0.7555 (mpt180) REVERT: D 106 LYS cc_start: 0.8286 (mttt) cc_final: 0.7752 (mppt) REVERT: D 224 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8257 (mm) REVERT: D 246 GLN cc_start: 0.7896 (pt0) cc_final: 0.7472 (tt0) REVERT: D 259 ARG cc_start: 0.6702 (ttm110) cc_final: 0.5963 (ptp90) outliers start: 43 outliers final: 32 residues processed: 134 average time/residue: 1.3989 time to fit residues: 197.4266 Evaluate side-chains 140 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 224 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 44 optimal weight: 0.5980 chunk 47 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 94 optimal weight: 0.0020 chunk 59 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.219932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.181699 restraints weight = 8341.901| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 2.15 r_work: 0.4031 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3900 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8004 Z= 0.194 Angle : 0.600 13.443 10892 Z= 0.301 Chirality : 0.045 0.143 1320 Planarity : 0.004 0.046 1412 Dihedral : 3.932 17.251 1124 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.66 % Allowed : 21.70 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.27), residues: 1036 helix: 2.01 (0.26), residues: 416 sheet: 0.26 (0.34), residues: 248 loop : 0.34 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 30 HIS 0.003 0.000 HIS D 72 PHE 0.008 0.001 PHE A 198 TYR 0.008 0.001 TYR D 120 ARG 0.014 0.000 ARG C 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7516 (mp0) cc_final: 0.7141 (mp0) REVERT: A 121 ASP cc_start: 0.6824 (m-30) cc_final: 0.6445 (t0) REVERT: A 246 GLN cc_start: 0.6467 (pt0) cc_final: 0.5905 (tt0) REVERT: A 260 ASN cc_start: 0.5426 (OUTLIER) cc_final: 0.5042 (m-40) REVERT: B 20 MET cc_start: 0.6875 (pmm) cc_final: 0.6172 (pmm) REVERT: B 23 HIS cc_start: 0.6728 (m90) cc_final: 0.6487 (m90) REVERT: B 25 LYS cc_start: 0.8028 (pttt) cc_final: 0.7580 (ptmt) REVERT: B 102 VAL cc_start: 0.6975 (OUTLIER) cc_final: 0.6523 (m) REVERT: B 175 LEU cc_start: 0.7153 (tp) cc_final: 0.6830 (mm) REVERT: B 237 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7241 (mm-30) REVERT: C 22 GLU cc_start: 0.7344 (tp30) cc_final: 0.7022 (tp30) REVERT: C 57 ARG cc_start: 0.6970 (ttp-110) cc_final: 0.6348 (mtm180) REVERT: D 1 MET cc_start: 0.5443 (mmp) cc_final: 0.4734 (ttm) REVERT: D 29 GLN cc_start: 0.6244 (tt0) cc_final: 0.5926 (tm-30) REVERT: D 106 LYS cc_start: 0.8215 (mttt) cc_final: 0.7732 (mppt) REVERT: D 246 GLN cc_start: 0.7754 (pt0) cc_final: 0.7334 (tt0) REVERT: D 259 ARG cc_start: 0.6627 (ttm110) cc_final: 0.5892 (ptp90) outliers start: 31 outliers final: 20 residues processed: 134 average time/residue: 1.3702 time to fit residues: 193.4876 Evaluate side-chains 129 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 218 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 101 optimal weight: 0.1980 chunk 18 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 74 optimal weight: 0.0570 chunk 84 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN B 185 ASN D 251 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.220919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.182207 restraints weight = 8274.110| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 2.08 r_work: 0.4059 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3927 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8004 Z= 0.182 Angle : 0.591 14.435 10892 Z= 0.294 Chirality : 0.045 0.134 1320 Planarity : 0.004 0.050 1412 Dihedral : 3.804 16.788 1124 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.66 % Allowed : 22.64 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.27), residues: 1036 helix: 2.19 (0.26), residues: 408 sheet: 0.32 (0.34), residues: 248 loop : 0.40 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 30 HIS 0.003 0.000 HIS D 72 PHE 0.010 0.001 PHE B 198 TYR 0.012 0.001 TYR A 81 ARG 0.012 0.000 ARG C 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 121 ASP cc_start: 0.7082 (m-30) cc_final: 0.6526 (t0) REVERT: A 246 GLN cc_start: 0.6465 (pt0) cc_final: 0.5906 (tt0) REVERT: A 260 ASN cc_start: 0.5303 (OUTLIER) cc_final: 0.4952 (m-40) REVERT: B 20 MET cc_start: 0.6852 (pmm) cc_final: 0.6137 (pmm) REVERT: B 23 HIS cc_start: 0.6650 (m90) cc_final: 0.6413 (m90) REVERT: B 25 LYS cc_start: 0.7994 (pttt) cc_final: 0.7485 (pttt) REVERT: B 102 VAL cc_start: 0.6849 (OUTLIER) cc_final: 0.6412 (m) REVERT: B 175 LEU cc_start: 0.7155 (tp) cc_final: 0.6821 (mm) REVERT: B 237 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7233 (mm-30) REVERT: C 25 LYS cc_start: 0.8612 (mtmt) cc_final: 0.8210 (mptp) REVERT: C 57 ARG cc_start: 0.6978 (ttp-110) cc_final: 0.6409 (mtm180) REVERT: C 224 ILE cc_start: 0.8064 (mt) cc_final: 0.7554 (mm) REVERT: D 1 MET cc_start: 0.5422 (mmp) cc_final: 0.4714 (ttm) REVERT: D 29 GLN cc_start: 0.6138 (tt0) cc_final: 0.5843 (tm-30) REVERT: D 53 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6808 (pm20) REVERT: D 106 LYS cc_start: 0.8168 (mttt) cc_final: 0.7684 (mppt) REVERT: D 246 GLN cc_start: 0.7774 (pt0) cc_final: 0.7361 (tt0) REVERT: D 259 ARG cc_start: 0.6586 (ttm110) cc_final: 0.5858 (ptp90) outliers start: 31 outliers final: 17 residues processed: 128 average time/residue: 1.3022 time to fit residues: 176.1269 Evaluate side-chains 127 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 2.9990 chunk 54 optimal weight: 0.2980 chunk 100 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 69 optimal weight: 0.0870 chunk 101 optimal weight: 0.4980 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.219484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.181519 restraints weight = 8193.603| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 2.11 r_work: 0.4034 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3903 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8004 Z= 0.212 Angle : 0.619 14.490 10892 Z= 0.308 Chirality : 0.045 0.138 1320 Planarity : 0.004 0.046 1412 Dihedral : 3.880 16.506 1124 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.18 % Allowed : 23.58 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.27), residues: 1036 helix: 2.14 (0.26), residues: 408 sheet: 0.31 (0.34), residues: 248 loop : 0.39 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 30 HIS 0.003 0.001 HIS D 72 PHE 0.011 0.001 PHE B 198 TYR 0.023 0.002 TYR A 81 ARG 0.012 0.000 ARG C 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7530 (mp0) cc_final: 0.7151 (mp0) REVERT: A 121 ASP cc_start: 0.7094 (m-30) cc_final: 0.6728 (t0) REVERT: A 124 ARG cc_start: 0.6688 (mpt-90) cc_final: 0.6435 (mmm160) REVERT: A 246 GLN cc_start: 0.6483 (pt0) cc_final: 0.5918 (tt0) REVERT: A 260 ASN cc_start: 0.5222 (OUTLIER) cc_final: 0.4879 (m-40) REVERT: B 20 MET cc_start: 0.6886 (pmm) cc_final: 0.6161 (pmm) REVERT: B 23 HIS cc_start: 0.6702 (m90) cc_final: 0.6469 (m90) REVERT: B 25 LYS cc_start: 0.8008 (pttt) cc_final: 0.7569 (ptmt) REVERT: B 102 VAL cc_start: 0.6896 (OUTLIER) cc_final: 0.6463 (m) REVERT: B 175 LEU cc_start: 0.7153 (tp) cc_final: 0.6827 (mm) REVERT: B 237 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7253 (mm-30) REVERT: C 25 LYS cc_start: 0.8539 (mtmt) cc_final: 0.8131 (mptp) REVERT: C 57 ARG cc_start: 0.7152 (ttp-110) cc_final: 0.6440 (mtm180) REVERT: C 224 ILE cc_start: 0.8015 (mt) cc_final: 0.7463 (mm) REVERT: D 1 MET cc_start: 0.5369 (mmp) cc_final: 0.4668 (ttm) REVERT: D 29 GLN cc_start: 0.6188 (tt0) cc_final: 0.5880 (tm-30) REVERT: D 53 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6877 (pm20) REVERT: D 106 LYS cc_start: 0.8195 (mttt) cc_final: 0.7699 (mppt) REVERT: D 246 GLN cc_start: 0.7858 (pt0) cc_final: 0.7463 (tt0) REVERT: D 259 ARG cc_start: 0.6596 (ttm110) cc_final: 0.5869 (ptp90) outliers start: 27 outliers final: 20 residues processed: 121 average time/residue: 1.3810 time to fit residues: 176.1639 Evaluate side-chains 125 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 91 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.214534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.176214 restraints weight = 8316.565| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 2.19 r_work: 0.3978 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3849 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8004 Z= 0.351 Angle : 0.699 14.120 10892 Z= 0.355 Chirality : 0.049 0.183 1320 Planarity : 0.004 0.039 1412 Dihedral : 4.373 16.466 1124 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.54 % Allowed : 23.23 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.26), residues: 1036 helix: 1.68 (0.25), residues: 408 sheet: 0.10 (0.33), residues: 248 loop : 0.25 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 82 HIS 0.006 0.001 HIS D 243 PHE 0.018 0.002 PHE B 198 TYR 0.012 0.002 TYR A 81 ARG 0.012 0.001 ARG C 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6926.28 seconds wall clock time: 123 minutes 46.96 seconds (7426.96 seconds total)