Starting phenix.real_space_refine on Wed Sep 17 05:51:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xcd_38240/09_2025/8xcd_38240.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xcd_38240/09_2025/8xcd_38240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xcd_38240/09_2025/8xcd_38240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xcd_38240/09_2025/8xcd_38240.map" model { file = "/net/cci-nas-00/data/ceres_data/8xcd_38240/09_2025/8xcd_38240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xcd_38240/09_2025/8xcd_38240.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.035 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 50 5.16 5 C 3629 2.51 5 N 894 2.21 5 O 1053 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5626 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2223 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 15, 'TRANS': 274} Chain: "H" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1693 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 208} Chain: "L" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1640 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 202} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'TCH': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.54, per 1000 atoms: 0.27 Number of scatterers: 5626 At special positions: 0 Unit cell: (72.08, 62.54, 137.8, 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 50 16.00 O 1053 8.00 N 894 7.00 C 3629 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS L 133 " - pdb=" SG CYS L 193 " distance=2.03 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: 0.47 Conformation dependent library (CDL) restraints added in 248.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1350 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 11 sheets defined 39.2% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 21 through 43 Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 59 through 71 Processing helix chain 'A' and resid 71 through 83 Processing helix chain 'A' and resid 86 through 99 Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.962A pdb=" N VAL A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 142 removed outlier: 3.588A pdb=" N ILE A 120 " --> pdb=" O MET A 116 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 155 through 160 removed outlier: 3.504A pdb=" N ILE A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 160' Processing helix chain 'A' and resid 163 through 180 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 186 through 216 removed outlier: 3.838A pdb=" N ILE A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASN A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 245 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 248 through 258 removed outlier: 3.657A pdb=" N ARG A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 removed outlier: 4.200A pdb=" N SER A 267 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.641A pdb=" N ILE A 279 " --> pdb=" O PRO A 275 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 280 " --> pdb=" O PRO A 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 275 through 280' Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 284 through 310 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.041A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 200 Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.917A pdb=" N ALA L 82 " --> pdb=" O ALA L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 127 removed outlier: 3.522A pdb=" N LEU L 124 " --> pdb=" O SER L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 188 removed outlier: 3.683A pdb=" N HIS L 188 " --> pdb=" O GLU L 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.587A pdb=" N THR H 119 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL H 12 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR H 94 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN H 59 " --> pdb=" O GLU H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.587A pdb=" N THR H 119 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL H 12 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR H 94 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP H 102 " --> pdb=" O PHE H 107 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE H 107 " --> pdb=" O ASP H 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 129 through 133 removed outlier: 4.005A pdb=" N SER H 129 " --> pdb=" O LYS H 152 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY H 148 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL H 192 " --> pdb=" O VAL H 145 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS H 149 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER H 188 " --> pdb=" O CYS H 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 129 through 133 removed outlier: 4.005A pdb=" N SER H 129 " --> pdb=" O LYS H 152 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY H 148 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY H 153 " --> pdb=" O TYR H 184 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR H 184 " --> pdb=" O GLY H 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 160 through 161 Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.559A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL L 19 " --> pdb=" O ILE L 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 11 removed outlier: 5.917A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.900A pdb=" N GLN L 89 " --> pdb=" O THR L 96 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR L 96 " --> pdb=" O GLN L 89 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 115 through 117 removed outlier: 3.643A pdb=" N PHE L 117 " --> pdb=" O VAL L 132 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL L 132 " --> pdb=" O PHE L 117 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU L 135 " --> pdb=" O MET L 174 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N TYR L 172 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 152 through 153 284 hydrogen bonds defined for protein. 771 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: 0.95 Time building geometry restraints manager: 0.63 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: 1694 1.34 - 1.46: 1181 1.46 - 1.58: 2812 1.58 - 1.69: 1 1.69 - 1.81: 76 Bond restraints: 5764 Sorted by residual: bond pdb=" CB PRO H 127 " pdb=" CG PRO H 127 " ideal model delta sigma weight residual 1.492 1.662 -0.170 5.00e-02 4.00e+02 1.15e+01 bond pdb=" N PRO H 127 " pdb=" CD PRO H 127 " ideal model delta sigma weight residual 1.473 1.518 -0.045 1.40e-02 5.10e+03 1.04e+01 bond pdb=" CG PRO H 127 " pdb=" CD PRO H 127 " ideal model delta sigma weight residual 1.503 1.405 0.098 3.40e-02 8.65e+02 8.24e+00 bond pdb=" C VAL A 164 " pdb=" N PRO A 165 " ideal model delta sigma weight residual 1.337 1.355 -0.018 9.80e-03 1.04e+04 3.43e+00 bond pdb=" N PRO H 127 " pdb=" CA PRO H 127 " ideal model delta sigma weight residual 1.465 1.431 0.034 2.03e-02 2.43e+03 2.85e+00 ... (remaining 5759 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 7816 3.27 - 6.53: 32 6.53 - 9.80: 2 9.80 - 13.06: 3 13.06 - 16.33: 1 Bond angle restraints: 7854 Sorted by residual: angle pdb=" CA PRO H 127 " pdb=" N PRO H 127 " pdb=" CD PRO H 127 " ideal model delta sigma weight residual 112.00 95.67 16.33 1.40e+00 5.10e-01 1.36e+02 angle pdb=" N PRO H 127 " pdb=" CD PRO H 127 " pdb=" CG PRO H 127 " ideal model delta sigma weight residual 103.20 95.31 7.89 1.50e+00 4.44e-01 2.77e+01 angle pdb=" CA PRO H 127 " pdb=" CB PRO H 127 " pdb=" CG PRO H 127 " ideal model delta sigma weight residual 104.50 96.85 7.65 1.90e+00 2.77e-01 1.62e+01 angle pdb=" CB MET A 34 " pdb=" CG MET A 34 " pdb=" SD MET A 34 " ideal model delta sigma weight residual 112.70 123.46 -10.76 3.00e+00 1.11e-01 1.29e+01 angle pdb=" N ILE A 145 " pdb=" CA ILE A 145 " pdb=" C ILE A 145 " ideal model delta sigma weight residual 112.96 109.71 3.25 1.00e+00 1.00e+00 1.06e+01 ... (remaining 7849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.04: 3223 24.04 - 48.08: 277 48.08 - 72.11: 30 72.11 - 96.15: 19 96.15 - 120.19: 7 Dihedral angle restraints: 3556 sinusoidal: 1449 harmonic: 2107 Sorted by residual: dihedral pdb=" C4 TCH A 401 " pdb=" C5 TCH A 401 " pdb=" C6 TCH A 401 " pdb=" C7 TCH A 401 " ideal model delta sinusoidal sigma weight residual 74.38 -165.43 -120.19 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" CB CYS H 149 " pdb=" SG CYS H 149 " pdb=" SG CYS H 204 " pdb=" CB CYS H 204 " ideal model delta sinusoidal sigma weight residual 93.00 59.47 33.53 1 1.00e+01 1.00e-02 1.60e+01 dihedral pdb=" C10 TCH A 401 " pdb=" C5 TCH A 401 " pdb=" C6 TCH A 401 " pdb=" C7 TCH A 401 " ideal model delta sinusoidal sigma weight residual -53.95 60.40 -114.35 1 3.00e+01 1.11e-03 1.51e+01 ... (remaining 3553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 725 0.046 - 0.092: 150 0.092 - 0.139: 45 0.139 - 0.185: 1 0.185 - 0.231: 1 Chirality restraints: 922 Sorted by residual: chirality pdb=" CA PRO H 127 " pdb=" N PRO H 127 " pdb=" C PRO H 127 " pdb=" CB PRO H 127 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C5 TCH A 401 " pdb=" C10 TCH A 401 " pdb=" C4 TCH A 401 " pdb=" C6 TCH A 401 " both_signs ideal model delta sigma weight residual False -2.45 -2.27 -0.18 2.00e-01 2.50e+01 8.49e-01 chirality pdb=" CA ILE L 47 " pdb=" N ILE L 47 " pdb=" C ILE L 47 " pdb=" CB ILE L 47 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 919 not shown) Planarity restraints: 959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR H 126 " 0.078 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO H 127 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO H 127 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO H 127 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 21 " -0.037 5.00e-02 4.00e+02 5.50e-02 4.85e+00 pdb=" N PRO A 22 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 22 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 22 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO H 127 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C PRO H 127 " -0.034 2.00e-02 2.50e+03 pdb=" O PRO H 127 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO H 128 " 0.011 2.00e-02 2.50e+03 ... (remaining 956 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 153 2.70 - 3.25: 5491 3.25 - 3.80: 8712 3.80 - 4.35: 10633 4.35 - 4.90: 18554 Nonbonded interactions: 43543 Sorted by model distance: nonbonded pdb=" OG1 THR H 28 " pdb=" OD1 ASN H 31 " model vdw 2.156 3.040 nonbonded pdb=" O PRO H 132 " pdb=" OG SER L 120 " model vdw 2.210 3.040 nonbonded pdb=" OE1 GLN H 6 " pdb=" OG1 THR H 116 " model vdw 2.239 3.040 nonbonded pdb=" OG SER A 99 " pdb=" O ASN A 262 " model vdw 2.244 3.040 nonbonded pdb=" OG SER H 211 " pdb=" OG1 THR H 213 " model vdw 2.247 3.040 ... (remaining 43538 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 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: 0.660 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.930 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 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 0.170 5768 Z= 0.187 Angle : 0.662 16.328 7862 Z= 0.344 Chirality : 0.042 0.231 922 Planarity : 0.005 0.107 959 Dihedral : 18.637 120.190 2194 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.32 % Allowed : 21.08 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.33), residues: 721 helix: 1.57 (0.35), residues: 243 sheet: 0.55 (0.39), residues: 214 loop : -0.36 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 60 TYR 0.012 0.001 TYR H 184 PHE 0.021 0.001 PHE L 138 TRP 0.010 0.001 TRP L 162 HIS 0.002 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 5764) covalent geometry : angle 0.66174 ( 7854) SS BOND : bond 0.00327 ( 4) SS BOND : angle 0.49220 ( 8) hydrogen bonds : bond 0.18463 ( 273) hydrogen bonds : angle 7.71978 ( 771) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.200 Fit side-chains REVERT: A 151 LYS cc_start: 0.8340 (ptpt) cc_final: 0.7982 (tmtt) REVERT: A 269 ILE cc_start: 0.6364 (mm) cc_final: 0.5917 (mm) REVERT: A 303 MET cc_start: 0.7231 (mtt) cc_final: 0.6941 (mtt) outliers start: 2 outliers final: 1 residues processed: 126 average time/residue: 0.0691 time to fit residues: 11.7127 Evaluate side-chains 84 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 185 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 50.0000 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.0470 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 ASN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.186483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.140300 restraints weight = 6480.355| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.97 r_work: 0.3313 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 5768 Z= 0.211 Angle : 0.762 10.418 7862 Z= 0.368 Chirality : 0.050 0.307 922 Planarity : 0.005 0.056 959 Dihedral : 8.326 74.843 928 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.60 % Allowed : 20.60 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.32), residues: 721 helix: 1.17 (0.33), residues: 248 sheet: 0.46 (0.37), residues: 223 loop : -0.65 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 60 TYR 0.011 0.002 TYR A 141 PHE 0.022 0.002 PHE H 155 TRP 0.016 0.001 TRP L 162 HIS 0.005 0.001 HIS L 188 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 5764) covalent geometry : angle 0.76178 ( 7854) SS BOND : bond 0.00546 ( 4) SS BOND : angle 1.27366 ( 8) hydrogen bonds : bond 0.03945 ( 273) hydrogen bonds : angle 5.28634 ( 771) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.141 Fit side-chains REVERT: A 108 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.7959 (m-10) REVERT: A 192 MET cc_start: 0.4180 (mmp) cc_final: 0.3736 (mmm) REVERT: H 114 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8617 (mm) REVERT: H 124 LYS cc_start: 0.7020 (tttm) cc_final: 0.6728 (tppt) REVERT: L 7 SER cc_start: 0.8107 (m) cc_final: 0.7672 (p) REVERT: L 77 MET cc_start: 0.6571 (tpp) cc_final: 0.6131 (ttt) REVERT: L 80 GLU cc_start: 0.8399 (tp30) cc_final: 0.7851 (tt0) REVERT: L 162 TRP cc_start: 0.8035 (m-90) cc_final: 0.7775 (m-90) outliers start: 29 outliers final: 14 residues processed: 105 average time/residue: 0.0611 time to fit residues: 8.9158 Evaluate side-chains 88 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 145 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 0 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 14 optimal weight: 0.0970 chunk 66 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN H 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.186416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.138280 restraints weight = 6406.821| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.90 r_work: 0.3337 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5768 Z= 0.137 Angle : 0.607 8.054 7862 Z= 0.294 Chirality : 0.043 0.179 922 Planarity : 0.004 0.055 959 Dihedral : 6.862 74.606 927 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 5.07 % Allowed : 20.92 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.32), residues: 721 helix: 1.49 (0.34), residues: 243 sheet: 0.55 (0.36), residues: 223 loop : -0.62 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 60 TYR 0.015 0.001 TYR A 289 PHE 0.020 0.002 PHE H 155 TRP 0.010 0.001 TRP L 162 HIS 0.003 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 5764) covalent geometry : angle 0.60728 ( 7854) SS BOND : bond 0.00327 ( 4) SS BOND : angle 0.78726 ( 8) hydrogen bonds : bond 0.03650 ( 273) hydrogen bonds : angle 4.80024 ( 771) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 0.128 Fit side-chains REVERT: A 146 TYR cc_start: 0.8012 (t80) cc_final: 0.7799 (t80) REVERT: A 192 MET cc_start: 0.4216 (mmp) cc_final: 0.3754 (mmm) REVERT: A 277 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.7645 (pt0) REVERT: H 106 VAL cc_start: 0.7328 (OUTLIER) cc_final: 0.7001 (m) REVERT: H 124 LYS cc_start: 0.7143 (tttm) cc_final: 0.6883 (tppt) REVERT: L 7 SER cc_start: 0.8182 (m) cc_final: 0.7788 (p) REVERT: L 77 MET cc_start: 0.6952 (tpp) cc_final: 0.6288 (ttt) REVERT: L 78 GLU cc_start: 0.5897 (mm-30) cc_final: 0.5535 (mt-10) REVERT: L 174 MET cc_start: 0.6822 (tpt) cc_final: 0.6549 (tpt) outliers start: 32 outliers final: 19 residues processed: 96 average time/residue: 0.0619 time to fit residues: 8.3013 Evaluate side-chains 86 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 164 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.183298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.136747 restraints weight = 6341.796| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.81 r_work: 0.3291 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5768 Z= 0.156 Angle : 0.606 7.785 7862 Z= 0.296 Chirality : 0.043 0.129 922 Planarity : 0.004 0.055 959 Dihedral : 6.445 74.404 927 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 6.34 % Allowed : 20.76 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.32), residues: 721 helix: 1.39 (0.34), residues: 249 sheet: 0.42 (0.36), residues: 226 loop : -0.46 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 60 TYR 0.012 0.001 TYR H 80 PHE 0.020 0.002 PHE H 155 TRP 0.023 0.001 TRP L 162 HIS 0.004 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 5764) covalent geometry : angle 0.60533 ( 7854) SS BOND : bond 0.00344 ( 4) SS BOND : angle 0.77171 ( 8) hydrogen bonds : bond 0.03312 ( 273) hydrogen bonds : angle 4.55610 ( 771) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 69 time to evaluate : 0.208 Fit side-chains REVERT: A 79 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8036 (mp) REVERT: A 146 TYR cc_start: 0.8355 (t80) cc_final: 0.8110 (t80) REVERT: A 243 LEU cc_start: 0.6775 (tp) cc_final: 0.5882 (mt) REVERT: A 277 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.7720 (pt0) REVERT: A 299 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7542 (mt) REVERT: H 88 SER cc_start: 0.8864 (OUTLIER) cc_final: 0.8418 (p) REVERT: H 106 VAL cc_start: 0.7326 (OUTLIER) cc_final: 0.7017 (m) REVERT: L 77 MET cc_start: 0.6819 (tpp) cc_final: 0.6371 (ttt) REVERT: L 162 TRP cc_start: 0.8278 (m-90) cc_final: 0.8047 (m-90) outliers start: 40 outliers final: 28 residues processed: 106 average time/residue: 0.0548 time to fit residues: 8.3910 Evaluate side-chains 97 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 64 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain L residue 164 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 52 optimal weight: 0.0050 chunk 51 optimal weight: 0.2980 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.184177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.138243 restraints weight = 6369.536| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.89 r_work: 0.3297 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.5239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5768 Z= 0.113 Angle : 0.559 8.757 7862 Z= 0.270 Chirality : 0.041 0.140 922 Planarity : 0.004 0.055 959 Dihedral : 6.165 74.339 927 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.07 % Allowed : 23.45 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.32), residues: 721 helix: 1.68 (0.34), residues: 243 sheet: 0.45 (0.36), residues: 224 loop : -0.50 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 251 TYR 0.013 0.001 TYR H 154 PHE 0.015 0.001 PHE H 155 TRP 0.013 0.001 TRP L 162 HIS 0.004 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 5764) covalent geometry : angle 0.55903 ( 7854) SS BOND : bond 0.00276 ( 4) SS BOND : angle 0.79262 ( 8) hydrogen bonds : bond 0.03011 ( 273) hydrogen bonds : angle 4.40572 ( 771) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 74 time to evaluate : 0.193 Fit side-chains REVERT: A 79 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7924 (mp) REVERT: A 146 TYR cc_start: 0.8315 (t80) cc_final: 0.8091 (t80) REVERT: A 214 ILE cc_start: 0.6080 (OUTLIER) cc_final: 0.5720 (tt) REVERT: A 243 LEU cc_start: 0.6562 (tp) cc_final: 0.5680 (mt) REVERT: A 277 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.7646 (pt0) REVERT: A 299 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7484 (mt) REVERT: H 3 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.7042 (tt0) REVERT: H 55 ASN cc_start: 0.8703 (t0) cc_final: 0.8384 (t0) REVERT: H 106 VAL cc_start: 0.7274 (OUTLIER) cc_final: 0.6963 (m) REVERT: H 124 LYS cc_start: 0.7180 (tttm) cc_final: 0.6859 (tppt) REVERT: L 77 MET cc_start: 0.6842 (tpp) cc_final: 0.6533 (ttt) REVERT: L 162 TRP cc_start: 0.8293 (m-90) cc_final: 0.8041 (m-90) outliers start: 32 outliers final: 25 residues processed: 101 average time/residue: 0.0594 time to fit residues: 8.5134 Evaluate side-chains 103 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 72 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain L residue 164 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.184056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.137709 restraints weight = 6335.217| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.88 r_work: 0.3292 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5768 Z= 0.119 Angle : 0.562 8.569 7862 Z= 0.270 Chirality : 0.041 0.138 922 Planarity : 0.004 0.054 959 Dihedral : 6.141 74.703 927 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 6.34 % Allowed : 21.87 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.32), residues: 721 helix: 1.76 (0.34), residues: 243 sheet: 0.58 (0.37), residues: 211 loop : -0.53 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 251 TYR 0.011 0.001 TYR H 154 PHE 0.014 0.001 PHE H 155 TRP 0.011 0.001 TRP L 162 HIS 0.004 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 5764) covalent geometry : angle 0.56218 ( 7854) SS BOND : bond 0.00263 ( 4) SS BOND : angle 0.59266 ( 8) hydrogen bonds : bond 0.02931 ( 273) hydrogen bonds : angle 4.33392 ( 771) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 76 time to evaluate : 0.209 Fit side-chains REVERT: A 79 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7964 (mp) REVERT: A 146 TYR cc_start: 0.8398 (t80) cc_final: 0.8144 (t80) REVERT: A 214 ILE cc_start: 0.6151 (OUTLIER) cc_final: 0.5811 (tt) REVERT: A 243 LEU cc_start: 0.6595 (tp) cc_final: 0.5682 (mt) REVERT: A 277 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.7695 (pt0) REVERT: A 299 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7470 (mt) REVERT: H 3 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.7089 (tt0) REVERT: H 55 ASN cc_start: 0.8729 (t0) cc_final: 0.8417 (t0) REVERT: H 88 SER cc_start: 0.8820 (OUTLIER) cc_final: 0.8430 (p) REVERT: H 106 VAL cc_start: 0.7270 (OUTLIER) cc_final: 0.6964 (m) REVERT: H 124 LYS cc_start: 0.7103 (tttm) cc_final: 0.6802 (tppt) REVERT: L 77 MET cc_start: 0.6854 (tpp) cc_final: 0.6606 (ttt) REVERT: L 162 TRP cc_start: 0.8278 (m-90) cc_final: 0.8029 (m-90) outliers start: 40 outliers final: 31 residues processed: 106 average time/residue: 0.0529 time to fit residues: 8.1347 Evaluate side-chains 109 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 71 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain L residue 164 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 48 optimal weight: 0.0270 chunk 9 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 22 optimal weight: 0.0770 chunk 34 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.185595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.139448 restraints weight = 6346.190| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.79 r_work: 0.3329 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.5556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5768 Z= 0.104 Angle : 0.540 8.087 7862 Z= 0.261 Chirality : 0.040 0.136 922 Planarity : 0.004 0.054 959 Dihedral : 5.981 75.073 927 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 6.34 % Allowed : 22.35 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.32), residues: 721 helix: 1.93 (0.35), residues: 237 sheet: 0.71 (0.38), residues: 205 loop : -0.49 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 251 TYR 0.011 0.001 TYR H 154 PHE 0.014 0.001 PHE H 155 TRP 0.014 0.001 TRP H 112 HIS 0.004 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 5764) covalent geometry : angle 0.54054 ( 7854) SS BOND : bond 0.00249 ( 4) SS BOND : angle 0.49423 ( 8) hydrogen bonds : bond 0.02802 ( 273) hydrogen bonds : angle 4.23307 ( 771) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 75 time to evaluate : 0.207 Fit side-chains REVERT: A 79 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7976 (mp) REVERT: A 122 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7531 (mpp) REVERT: A 146 TYR cc_start: 0.8405 (t80) cc_final: 0.8186 (t80) REVERT: A 192 MET cc_start: 0.4453 (mmp) cc_final: 0.4006 (mmm) REVERT: A 214 ILE cc_start: 0.6045 (OUTLIER) cc_final: 0.5708 (tt) REVERT: A 243 LEU cc_start: 0.6547 (tp) cc_final: 0.5656 (mt) REVERT: A 247 ASN cc_start: 0.8430 (t0) cc_final: 0.8002 (t0) REVERT: A 299 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7474 (mt) REVERT: H 3 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.7044 (tt0) REVERT: H 34 MET cc_start: 0.8483 (ttm) cc_final: 0.8057 (mtp) REVERT: H 55 ASN cc_start: 0.8688 (t0) cc_final: 0.8387 (t0) REVERT: H 106 VAL cc_start: 0.7303 (OUTLIER) cc_final: 0.7065 (m) REVERT: H 124 LYS cc_start: 0.7069 (tttm) cc_final: 0.6763 (tppt) REVERT: L 77 MET cc_start: 0.6880 (tpp) cc_final: 0.6413 (ttt) outliers start: 40 outliers final: 31 residues processed: 107 average time/residue: 0.0520 time to fit residues: 8.2184 Evaluate side-chains 107 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 70 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 145 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 67 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN A 293 GLN L 197 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.182723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.137549 restraints weight = 6340.364| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.58 r_work: 0.3305 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5768 Z= 0.145 Angle : 0.581 9.181 7862 Z= 0.280 Chirality : 0.042 0.138 922 Planarity : 0.004 0.054 959 Dihedral : 6.041 74.773 927 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 6.34 % Allowed : 22.35 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.32), residues: 721 helix: 1.83 (0.34), residues: 241 sheet: 0.57 (0.37), residues: 211 loop : -0.57 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 252 TYR 0.014 0.001 TYR H 95 PHE 0.014 0.001 PHE A 108 TRP 0.027 0.001 TRP L 162 HIS 0.004 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 5764) covalent geometry : angle 0.58112 ( 7854) SS BOND : bond 0.00287 ( 4) SS BOND : angle 0.47896 ( 8) hydrogen bonds : bond 0.03066 ( 273) hydrogen bonds : angle 4.31674 ( 771) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 76 time to evaluate : 0.220 Fit side-chains REVERT: A 79 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8143 (mp) REVERT: A 122 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7466 (mpp) REVERT: A 146 TYR cc_start: 0.8423 (t80) cc_final: 0.8191 (t80) REVERT: A 214 ILE cc_start: 0.6174 (OUTLIER) cc_final: 0.5827 (tt) REVERT: A 243 LEU cc_start: 0.6727 (tp) cc_final: 0.5854 (mt) REVERT: A 277 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.7655 (pt0) REVERT: A 299 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7736 (mt) REVERT: H 3 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6982 (tt0) REVERT: H 55 ASN cc_start: 0.8730 (t0) cc_final: 0.8467 (t0) REVERT: H 88 SER cc_start: 0.8798 (OUTLIER) cc_final: 0.8539 (p) REVERT: H 106 VAL cc_start: 0.7379 (OUTLIER) cc_final: 0.7156 (m) REVERT: L 77 MET cc_start: 0.6908 (tpp) cc_final: 0.6599 (ttt) REVERT: L 138 PHE cc_start: 0.8383 (p90) cc_final: 0.8078 (p90) REVERT: L 162 TRP cc_start: 0.8338 (m-90) cc_final: 0.7985 (m-90) outliers start: 40 outliers final: 31 residues processed: 107 average time/residue: 0.0519 time to fit residues: 8.2709 Evaluate side-chains 113 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 74 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 145 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 67 optimal weight: 7.9990 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.181962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.139693 restraints weight = 6363.466| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.56 r_work: 0.3325 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.5969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5768 Z= 0.120 Angle : 0.552 8.395 7862 Z= 0.267 Chirality : 0.041 0.133 922 Planarity : 0.004 0.054 959 Dihedral : 5.973 74.706 927 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 6.34 % Allowed : 22.19 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.32), residues: 721 helix: 1.94 (0.35), residues: 236 sheet: 0.62 (0.37), residues: 211 loop : -0.44 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 60 TYR 0.011 0.001 TYR L 31 PHE 0.013 0.001 PHE H 155 TRP 0.016 0.001 TRP L 162 HIS 0.004 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 5764) covalent geometry : angle 0.55261 ( 7854) SS BOND : bond 0.00239 ( 4) SS BOND : angle 0.40748 ( 8) hydrogen bonds : bond 0.02880 ( 273) hydrogen bonds : angle 4.23566 ( 771) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 76 time to evaluate : 0.205 Fit side-chains REVERT: A 79 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8075 (mp) REVERT: A 122 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7423 (mpp) REVERT: A 184 MET cc_start: 0.3588 (OUTLIER) cc_final: 0.2171 (tpt) REVERT: A 192 MET cc_start: 0.4658 (mmp) cc_final: 0.4163 (mmm) REVERT: A 214 ILE cc_start: 0.6152 (OUTLIER) cc_final: 0.5819 (tt) REVERT: A 243 LEU cc_start: 0.6621 (tp) cc_final: 0.5771 (mt) REVERT: A 299 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7752 (mt) REVERT: H 3 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.6999 (tt0) REVERT: H 55 ASN cc_start: 0.8741 (t0) cc_final: 0.8468 (t0) REVERT: L 77 MET cc_start: 0.6960 (tpp) cc_final: 0.6679 (ttt) REVERT: L 138 PHE cc_start: 0.8360 (p90) cc_final: 0.8090 (p90) REVERT: L 162 TRP cc_start: 0.8328 (m-90) cc_final: 0.7905 (m-90) REVERT: L 174 MET cc_start: 0.8105 (tpt) cc_final: 0.7524 (tpt) outliers start: 40 outliers final: 31 residues processed: 107 average time/residue: 0.0496 time to fit residues: 7.8827 Evaluate side-chains 112 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 75 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 145 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 30.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.181904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.146134 restraints weight = 6380.935| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.30 r_work: 0.3345 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.6095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5768 Z= 0.123 Angle : 0.558 8.831 7862 Z= 0.270 Chirality : 0.041 0.134 922 Planarity : 0.004 0.054 959 Dihedral : 5.943 74.642 927 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.86 % Allowed : 22.82 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.32), residues: 721 helix: 1.97 (0.35), residues: 236 sheet: 0.64 (0.37), residues: 211 loop : -0.44 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 60 TYR 0.012 0.001 TYR L 31 PHE 0.013 0.001 PHE H 155 TRP 0.020 0.001 TRP L 162 HIS 0.004 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 5764) covalent geometry : angle 0.55861 ( 7854) SS BOND : bond 0.00251 ( 4) SS BOND : angle 0.40651 ( 8) hydrogen bonds : bond 0.02893 ( 273) hydrogen bonds : angle 4.21256 ( 771) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 78 time to evaluate : 0.221 Fit side-chains REVERT: A 79 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8089 (mp) REVERT: A 122 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7377 (mpp) REVERT: A 184 MET cc_start: 0.3517 (OUTLIER) cc_final: 0.2144 (tpt) REVERT: A 214 ILE cc_start: 0.6192 (OUTLIER) cc_final: 0.5876 (tt) REVERT: A 243 LEU cc_start: 0.6687 (tp) cc_final: 0.5864 (mt) REVERT: A 299 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7860 (mt) REVERT: H 3 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.6988 (tt0) REVERT: H 11 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7909 (mm) REVERT: H 55 ASN cc_start: 0.8746 (t0) cc_final: 0.8466 (t0) REVERT: L 138 PHE cc_start: 0.8383 (p90) cc_final: 0.8117 (p90) REVERT: L 162 TRP cc_start: 0.8317 (m-90) cc_final: 0.7870 (m-90) REVERT: L 174 MET cc_start: 0.8090 (tpt) cc_final: 0.7623 (tpt) outliers start: 37 outliers final: 29 residues processed: 107 average time/residue: 0.0525 time to fit residues: 8.2905 Evaluate side-chains 113 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 77 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 145 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 31 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.183900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3500 r_free = 0.3500 target = 0.137343 restraints weight = 6207.660| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.42 r_work: 0.3376 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.6186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5768 Z= 0.114 Angle : 0.559 8.538 7862 Z= 0.269 Chirality : 0.041 0.133 922 Planarity : 0.004 0.054 959 Dihedral : 5.911 74.799 927 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 6.18 % Allowed : 22.19 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.33), residues: 721 helix: 2.02 (0.35), residues: 236 sheet: 0.68 (0.37), residues: 212 loop : -0.42 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 251 TYR 0.013 0.001 TYR A 146 PHE 0.013 0.001 PHE H 155 TRP 0.018 0.001 TRP L 162 HIS 0.004 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 5764) covalent geometry : angle 0.55921 ( 7854) SS BOND : bond 0.00236 ( 4) SS BOND : angle 0.41285 ( 8) hydrogen bonds : bond 0.02827 ( 273) hydrogen bonds : angle 4.16598 ( 771) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1576.14 seconds wall clock time: 27 minutes 41.49 seconds (1661.49 seconds total)