Starting phenix.real_space_refine on Tue Mar 3 13:56:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wsi_32759/03_2026/7wsi_32759.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsi_32759/03_2026/7wsi_32759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wsi_32759/03_2026/7wsi_32759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsi_32759/03_2026/7wsi_32759.map" model { file = "/net/cci-nas-00/data/ceres_data/7wsi_32759/03_2026/7wsi_32759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsi_32759/03_2026/7wsi_32759.cif" } resolution = 3.32 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= 0.000 sd= 0.001 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 43 5.16 5 C 3678 2.51 5 N 913 2.21 5 O 1067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5701 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2348 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 17, 'TRANS': 288} Chain: "H" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1669 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 15, 'TRANS': 205} Chain: "L" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1684 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 9, 'TRANS': 206} Time building chain proxies: 1.13, per 1000 atoms: 0.20 Number of scatterers: 5701 At special positions: 0 Unit cell: (87.15, 72.21, 141.93, 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 43 16.00 O 1067 8.00 N 913 7.00 C 3678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 345.2 milliseconds 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1376 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 9 sheets defined 38.0% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 removed outlier: 3.758A pdb=" N GLY A 19 " --> pdb=" O PRO A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 44 Processing helix chain 'A' and resid 47 through 57 removed outlier: 3.565A pdb=" N ILE A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 70 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 113 removed outlier: 3.888A pdb=" N VAL A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 142 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 156 through 180 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 183 through 211 removed outlier: 3.568A pdb=" N ALA A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 219 through 243 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 248 through 260 removed outlier: 3.587A pdb=" N ARG A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL A 254 " --> pdb=" O CYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 284 through 309 removed outlier: 3.675A pdb=" N LYS A 309 " --> pdb=" O TRP A 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 66 removed outlier: 3.520A pdb=" N LYS H 65 " --> pdb=" O GLU H 62 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY H 66 " --> pdb=" O LYS H 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 66' Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.104A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 199 removed outlier: 4.367A pdb=" N SER H 198 " --> pdb=" O SER H 194 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 132 removed outlier: 3.547A pdb=" N LEU L 130 " --> pdb=" O SER L 126 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR L 131 " --> pdb=" O SER L 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.610A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.599A pdb=" N GLU H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY H 57 " --> pdb=" O ASN H 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.599A pdb=" N GLU H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 128 through 132 removed outlier: 4.324A pdb=" N GLY H 147 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER H 187 " --> pdb=" O CYS H 148 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N MET H 185 " --> pdb=" O VAL H 150 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR H 184 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA H 176 " --> pdb=" O THR H 184 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER H 186 " --> pdb=" O PHE H 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 159 through 161 removed outlier: 3.868A pdb=" N CYS H 203 " --> pdb=" O LYS H 216 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS H 216 " --> pdb=" O CYS H 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.009A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 69 through 73 Processing sheet with id=AA8, first strand: chain 'L' and resid 122 through 123 removed outlier: 4.016A pdb=" N ASN L 143 " --> pdb=" O TYR L 178 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 158 through 159 removed outlier: 6.077A pdb=" N HIS L 203 " --> pdb=" O SER L 208 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N SER L 208 " --> pdb=" O HIS L 203 " (cutoff:3.500A) 275 hydrogen bonds defined for protein. 753 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: 0.75 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1736 1.35 - 1.46: 1445 1.46 - 1.58: 2593 1.58 - 1.70: 0 1.70 - 1.82: 65 Bond restraints: 5839 Sorted by residual: bond pdb=" CA GLY L 70 " pdb=" C GLY L 70 " ideal model delta sigma weight residual 1.520 1.513 0.008 7.30e-03 1.88e+04 1.06e+00 bond pdb=" N SER L 25 " pdb=" CA SER L 25 " ideal model delta sigma weight residual 1.457 1.471 -0.013 1.29e-02 6.01e+03 1.06e+00 bond pdb=" CA THR L 20 " pdb=" CB THR L 20 " ideal model delta sigma weight residual 1.527 1.541 -0.014 1.61e-02 3.86e+03 7.89e-01 bond pdb=" CA ALA H 16 " pdb=" CB ALA H 16 " ideal model delta sigma weight residual 1.530 1.515 0.015 1.69e-02 3.50e+03 7.72e-01 bond pdb=" SD MET A 122 " pdb=" CE MET A 122 " ideal model delta sigma weight residual 1.791 1.770 0.021 2.50e-02 1.60e+03 7.33e-01 ... (remaining 5834 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 7474 1.21 - 2.43: 343 2.43 - 3.64: 78 3.64 - 4.85: 26 4.85 - 6.07: 13 Bond angle restraints: 7934 Sorted by residual: angle pdb=" N ILE A 214 " pdb=" CA ILE A 214 " pdb=" C ILE A 214 " ideal model delta sigma weight residual 111.77 108.04 3.73 1.04e+00 9.25e-01 1.29e+01 angle pdb=" C PRO L 8 " pdb=" N SER L 9 " pdb=" CA SER L 9 " ideal model delta sigma weight residual 121.54 126.59 -5.05 1.91e+00 2.74e-01 6.98e+00 angle pdb=" CA CYS L 94 " pdb=" CB CYS L 94 " pdb=" SG CYS L 94 " ideal model delta sigma weight residual 114.40 120.23 -5.83 2.30e+00 1.89e-01 6.43e+00 angle pdb=" C ASP A 149 " pdb=" N LEU A 150 " pdb=" CA LEU A 150 " ideal model delta sigma weight residual 121.54 126.15 -4.61 1.91e+00 2.74e-01 5.82e+00 angle pdb=" N THR L 169 " pdb=" CA THR L 169 " pdb=" C THR L 169 " ideal model delta sigma weight residual 110.53 107.76 2.77 1.29e+00 6.01e-01 4.61e+00 ... (remaining 7929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.97: 3061 13.97 - 27.94: 325 27.94 - 41.91: 84 41.91 - 55.87: 12 55.87 - 69.84: 2 Dihedral angle restraints: 3484 sinusoidal: 1332 harmonic: 2152 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 94 " pdb=" CB CYS L 94 " ideal model delta sinusoidal sigma weight residual 93.00 158.44 -65.44 1 1.00e+01 1.00e-02 5.61e+01 dihedral pdb=" CB CYS H 148 " pdb=" SG CYS H 148 " pdb=" SG CYS H 203 " pdb=" CB CYS H 203 " ideal model delta sinusoidal sigma weight residual -86.00 -118.30 32.30 1 1.00e+01 1.00e-02 1.49e+01 dihedral pdb=" CA TYR L 92 " pdb=" C TYR L 92 " pdb=" N TYR L 93 " pdb=" CA TYR L 93 " ideal model delta harmonic sigma weight residual -180.00 -161.69 -18.31 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 3481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 559 0.032 - 0.064: 241 0.064 - 0.096: 77 0.096 - 0.127: 37 0.127 - 0.159: 4 Chirality restraints: 918 Sorted by residual: chirality pdb=" CA ILE L 54 " pdb=" N ILE L 54 " pdb=" C ILE L 54 " pdb=" CB ILE L 54 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CA ILE H 104 " pdb=" N ILE H 104 " pdb=" C ILE H 104 " pdb=" CB ILE H 104 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ILE A 145 " pdb=" N ILE A 145 " pdb=" C ILE A 145 " pdb=" CB ILE A 145 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 915 not shown) Planarity restraints: 981 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 64 " 0.041 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO L 65 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO L 65 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 65 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 180 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO A 181 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 49 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO L 50 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO L 50 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO L 50 " -0.020 5.00e-02 4.00e+02 ... (remaining 978 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 82 2.68 - 3.23: 5605 3.23 - 3.79: 8449 3.79 - 4.34: 11132 4.34 - 4.90: 18947 Nonbonded interactions: 44215 Sorted by model distance: nonbonded pdb=" OD1 ASP H 102 " pdb=" N GLY H 103 " model vdw 2.122 3.120 nonbonded pdb=" OG SER A 105 " pdb=" OE1 GLU A 257 " model vdw 2.229 3.040 nonbonded pdb=" NE2 GLN L 96 " pdb=" OG1 THR L 102 " model vdw 2.328 3.120 nonbonded pdb=" NH1 ARG L 160 " pdb=" O ASN L 162 " model vdw 2.340 3.120 nonbonded pdb=" O TYR L 55 " pdb=" OG1 THR L 59 " model vdw 2.354 3.040 ... (remaining 44210 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: 0.480 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.650 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 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 0.027 5842 Z= 0.142 Angle : 0.668 6.068 7940 Z= 0.349 Chirality : 0.043 0.159 918 Planarity : 0.005 0.063 981 Dihedral : 12.247 69.843 2099 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.23 (0.32), residues: 737 helix: 0.97 (0.34), residues: 241 sheet: 0.43 (0.39), residues: 195 loop : -1.50 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 180 TYR 0.017 0.002 TYR A 69 PHE 0.018 0.001 PHE A 292 TRP 0.010 0.001 TRP L 41 HIS 0.002 0.001 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 5839) covalent geometry : angle 0.66803 ( 7934) SS BOND : bond 0.00348 ( 3) SS BOND : angle 0.81728 ( 6) hydrogen bonds : bond 0.17774 ( 271) hydrogen bonds : angle 6.60305 ( 753) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 TRP cc_start: 0.5403 (m-10) cc_final: 0.5077 (m-10) REVERT: H 3 GLN cc_start: 0.7813 (pp30) cc_final: 0.7395 (pp30) REVERT: H 117 LEU cc_start: 0.8462 (tt) cc_final: 0.8099 (tp) REVERT: L 42 TYR cc_start: 0.8120 (m-80) cc_final: 0.7786 (m-80) REVERT: L 44 GLN cc_start: 0.8043 (tt0) cc_final: 0.7615 (tt0) REVERT: L 128 GLU cc_start: 0.7847 (pm20) cc_final: 0.7550 (pm20) REVERT: L 143 ASN cc_start: 0.8175 (m-40) cc_final: 0.7957 (m-40) REVERT: L 160 ARG cc_start: 0.8007 (ptm-80) cc_final: 0.7635 (ptp90) REVERT: L 168 TRP cc_start: 0.8956 (m-90) cc_final: 0.8650 (m-90) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.0702 time to fit residues: 27.3284 Evaluate side-chains 234 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 0.0570 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN H 39 GLN L 6 GLN L 215 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.143513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.114175 restraints weight = 10752.493| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.68 r_work: 0.3256 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5842 Z= 0.151 Angle : 0.730 7.725 7940 Z= 0.366 Chirality : 0.045 0.155 918 Planarity : 0.005 0.077 981 Dihedral : 4.605 16.617 794 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.06 % Favored : 92.81 % Rotamer: Outliers : 4.48 % Allowed : 16.23 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.44 (0.31), residues: 737 helix: 0.87 (0.33), residues: 253 sheet: 0.46 (0.40), residues: 182 loop : -1.81 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 60 TYR 0.020 0.002 TYR L 98 PHE 0.016 0.001 PHE A 292 TRP 0.016 0.001 TRP H 196 HIS 0.001 0.000 HIS L 203 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 5839) covalent geometry : angle 0.72996 ( 7934) SS BOND : bond 0.00198 ( 3) SS BOND : angle 0.91056 ( 6) hydrogen bonds : bond 0.04069 ( 271) hydrogen bonds : angle 5.13903 ( 753) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 230 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8709 (t80) cc_final: 0.8403 (t80) REVERT: A 176 LEU cc_start: 0.8395 (tt) cc_final: 0.7697 (tt) REVERT: A 180 ARG cc_start: 0.7814 (tmt170) cc_final: 0.7304 (ttp80) REVERT: A 246 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7596 (mm) REVERT: A 256 MET cc_start: 0.8038 (ttm) cc_final: 0.7762 (ttm) REVERT: H 3 GLN cc_start: 0.8939 (pp30) cc_final: 0.7982 (pp30) REVERT: H 130 TYR cc_start: 0.9059 (m-10) cc_final: 0.8460 (m-80) REVERT: L 27 GLN cc_start: 0.8416 (pm20) cc_final: 0.8129 (pm20) REVERT: L 29 LEU cc_start: 0.9580 (pp) cc_final: 0.9359 (pp) REVERT: L 48 GLN cc_start: 0.7997 (mp10) cc_final: 0.7771 (mp10) REVERT: L 87 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8501 (pp20) REVERT: L 128 GLU cc_start: 0.8525 (pm20) cc_final: 0.8232 (pm20) REVERT: L 160 ARG cc_start: 0.8326 (ptm-80) cc_final: 0.7932 (ptp90) REVERT: L 198 THR cc_start: 0.8853 (m) cc_final: 0.8598 (p) REVERT: L 200 GLU cc_start: 0.7306 (tt0) cc_final: 0.7088 (tt0) outliers start: 29 outliers final: 18 residues processed: 240 average time/residue: 0.0642 time to fit residues: 21.1470 Evaluate side-chains 230 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 210 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 136 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 43 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 247 ASN L 215 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.139479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.109623 restraints weight = 10754.929| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.69 r_work: 0.3178 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5842 Z= 0.170 Angle : 0.706 10.593 7940 Z= 0.350 Chirality : 0.045 0.150 918 Planarity : 0.004 0.043 981 Dihedral : 4.620 17.263 794 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 5.26 % Allowed : 20.87 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.41 (0.31), residues: 737 helix: 0.88 (0.34), residues: 255 sheet: 0.60 (0.41), residues: 172 loop : -1.81 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 60 TYR 0.023 0.002 TYR H 183 PHE 0.018 0.001 PHE A 292 TRP 0.008 0.001 TRP H 196 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 5839) covalent geometry : angle 0.70622 ( 7934) SS BOND : bond 0.00319 ( 3) SS BOND : angle 0.76590 ( 6) hydrogen bonds : bond 0.03680 ( 271) hydrogen bonds : angle 4.71695 ( 753) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 214 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7242 (t80) REVERT: A 133 MET cc_start: 0.8782 (ppp) cc_final: 0.8554 (ppp) REVERT: A 143 ARG cc_start: 0.8482 (ttt180) cc_final: 0.7560 (mmt90) REVERT: A 223 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8180 (mt) REVERT: A 246 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7094 (mp) REVERT: A 256 MET cc_start: 0.8186 (ttm) cc_final: 0.7984 (ttm) REVERT: H 3 GLN cc_start: 0.8982 (pp30) cc_final: 0.7973 (pp30) REVERT: H 130 TYR cc_start: 0.9102 (m-10) cc_final: 0.8312 (m-80) REVERT: L 27 GLN cc_start: 0.8561 (pm20) cc_final: 0.8216 (pm20) REVERT: L 48 GLN cc_start: 0.8117 (mp10) cc_final: 0.7440 (mp10) REVERT: L 87 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8560 (pp20) REVERT: L 123 PHE cc_start: 0.9279 (m-80) cc_final: 0.8973 (m-80) REVERT: L 161 GLN cc_start: 0.8964 (tm-30) cc_final: 0.8676 (tm-30) REVERT: L 180 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8086 (tpp) outliers start: 34 outliers final: 23 residues processed: 227 average time/residue: 0.0625 time to fit residues: 19.4867 Evaluate side-chains 237 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 209 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 181 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 66 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 46 optimal weight: 0.1980 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 247 ASN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.140454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.110625 restraints weight = 10663.989| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.74 r_work: 0.3204 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5842 Z= 0.130 Angle : 0.682 11.713 7940 Z= 0.333 Chirality : 0.044 0.152 918 Planarity : 0.004 0.043 981 Dihedral : 4.432 16.700 794 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 4.33 % Allowed : 23.80 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.27 (0.31), residues: 737 helix: 1.09 (0.34), residues: 250 sheet: 0.72 (0.42), residues: 165 loop : -1.76 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 180 TYR 0.020 0.002 TYR H 183 PHE 0.018 0.001 PHE A 292 TRP 0.007 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 5839) covalent geometry : angle 0.68217 ( 7934) SS BOND : bond 0.00260 ( 3) SS BOND : angle 0.65031 ( 6) hydrogen bonds : bond 0.03288 ( 271) hydrogen bonds : angle 4.60220 ( 753) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8140 (m-30) cc_final: 0.7932 (m-30) REVERT: A 33 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7260 (t80) REVERT: A 50 LYS cc_start: 0.8465 (mmmt) cc_final: 0.7982 (mttp) REVERT: A 133 MET cc_start: 0.8742 (ppp) cc_final: 0.8518 (ppp) REVERT: A 167 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8236 (tt) REVERT: A 176 LEU cc_start: 0.8653 (tt) cc_final: 0.8219 (tt) REVERT: A 223 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8148 (mt) REVERT: A 246 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7394 (mm) REVERT: H 3 GLN cc_start: 0.8986 (pp30) cc_final: 0.7965 (pp30) REVERT: H 130 TYR cc_start: 0.9125 (m-10) cc_final: 0.8327 (m-80) REVERT: L 27 GLN cc_start: 0.8531 (pm20) cc_final: 0.8032 (pm20) REVERT: L 29 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9204 (pp) REVERT: L 48 GLN cc_start: 0.8114 (mp10) cc_final: 0.7501 (mp10) REVERT: L 87 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8646 (pp20) REVERT: L 123 PHE cc_start: 0.9264 (m-80) cc_final: 0.8956 (m-80) REVERT: L 161 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8517 (tm-30) REVERT: L 168 TRP cc_start: 0.9438 (m-90) cc_final: 0.8960 (m-90) REVERT: L 180 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.7328 (tpt) outliers start: 28 outliers final: 18 residues processed: 235 average time/residue: 0.0592 time to fit residues: 19.1707 Evaluate side-chains 237 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 212 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 180 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 62 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 57 optimal weight: 0.4980 chunk 72 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 247 ASN L 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.140122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.110445 restraints weight = 10888.731| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.77 r_work: 0.3210 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5842 Z= 0.138 Angle : 0.696 12.070 7940 Z= 0.337 Chirality : 0.044 0.169 918 Planarity : 0.004 0.035 981 Dihedral : 4.405 17.127 794 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 5.41 % Allowed : 25.19 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.22 (0.32), residues: 737 helix: 1.03 (0.34), residues: 255 sheet: 0.83 (0.43), residues: 165 loop : -1.72 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 180 TYR 0.022 0.002 TYR H 183 PHE 0.019 0.001 PHE A 292 TRP 0.007 0.001 TRP L 168 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 5839) covalent geometry : angle 0.69643 ( 7934) SS BOND : bond 0.00273 ( 3) SS BOND : angle 0.64900 ( 6) hydrogen bonds : bond 0.03231 ( 271) hydrogen bonds : angle 4.56818 ( 753) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 216 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8827 (t80) cc_final: 0.8551 (t80) REVERT: A 24 ASP cc_start: 0.8142 (m-30) cc_final: 0.7933 (m-30) REVERT: A 33 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7264 (t80) REVERT: A 46 MET cc_start: 0.9081 (mtt) cc_final: 0.8789 (mtp) REVERT: A 50 LYS cc_start: 0.8563 (mmmt) cc_final: 0.8098 (mttp) REVERT: A 133 MET cc_start: 0.8730 (ppp) cc_final: 0.8493 (ppp) REVERT: A 223 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8136 (mt) REVERT: A 246 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7466 (mt) REVERT: H 3 GLN cc_start: 0.9001 (pp30) cc_final: 0.7970 (pp30) REVERT: H 117 LEU cc_start: 0.9381 (tp) cc_final: 0.9176 (tt) REVERT: H 130 TYR cc_start: 0.8964 (m-10) cc_final: 0.8481 (m-80) REVERT: L 27 GLN cc_start: 0.8577 (pm20) cc_final: 0.8090 (pm20) REVERT: L 29 LEU cc_start: 0.9643 (OUTLIER) cc_final: 0.9223 (pp) REVERT: L 48 GLN cc_start: 0.8175 (mp10) cc_final: 0.7574 (mp10) REVERT: L 87 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8596 (pp20) REVERT: L 123 PHE cc_start: 0.9197 (m-80) cc_final: 0.8945 (m-80) REVERT: L 161 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8481 (tm-30) REVERT: L 168 TRP cc_start: 0.9452 (m-90) cc_final: 0.8945 (m-90) REVERT: L 180 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7296 (tpt) outliers start: 35 outliers final: 22 residues processed: 225 average time/residue: 0.0635 time to fit residues: 19.5877 Evaluate side-chains 234 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 206 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 180 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 39 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 6 optimal weight: 0.0980 chunk 24 optimal weight: 1.9990 chunk 51 optimal weight: 0.0170 chunk 53 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 chunk 32 optimal weight: 3.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN L 6 GLN L 129 GLN L 166 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.141996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.112630 restraints weight = 10799.233| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.76 r_work: 0.3238 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5842 Z= 0.120 Angle : 0.675 11.788 7940 Z= 0.325 Chirality : 0.044 0.174 918 Planarity : 0.004 0.037 981 Dihedral : 4.323 15.524 794 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 5.26 % Allowed : 25.04 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.32), residues: 737 helix: 1.17 (0.34), residues: 254 sheet: 0.84 (0.43), residues: 165 loop : -1.73 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 160 TYR 0.021 0.002 TYR L 98 PHE 0.019 0.001 PHE A 292 TRP 0.007 0.001 TRP L 168 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 5839) covalent geometry : angle 0.67452 ( 7934) SS BOND : bond 0.00540 ( 3) SS BOND : angle 0.89136 ( 6) hydrogen bonds : bond 0.03039 ( 271) hydrogen bonds : angle 4.45335 ( 753) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 226 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8859 (t80) cc_final: 0.8589 (t80) REVERT: A 24 ASP cc_start: 0.8145 (m-30) cc_final: 0.7881 (m-30) REVERT: A 50 LYS cc_start: 0.8553 (mmmt) cc_final: 0.8114 (mttp) REVERT: A 167 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8217 (tt) REVERT: A 223 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8046 (mt) REVERT: H 3 GLN cc_start: 0.9008 (pp30) cc_final: 0.7993 (pp30) REVERT: H 28 THR cc_start: 0.9284 (m) cc_final: 0.9081 (p) REVERT: H 98 ARG cc_start: 0.8821 (tmm-80) cc_final: 0.8491 (tmm-80) REVERT: H 130 TYR cc_start: 0.8882 (m-10) cc_final: 0.8282 (m-80) REVERT: H 215 ASP cc_start: 0.8604 (t0) cc_final: 0.7818 (p0) REVERT: L 27 GLN cc_start: 0.8536 (pm20) cc_final: 0.8055 (pm20) REVERT: L 29 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9195 (pp) REVERT: L 48 GLN cc_start: 0.8198 (mp10) cc_final: 0.7599 (mp10) REVERT: L 160 ARG cc_start: 0.8531 (ptm-80) cc_final: 0.7606 (ptm-80) REVERT: L 161 GLN cc_start: 0.8907 (tm-30) cc_final: 0.8409 (tm-30) REVERT: L 168 TRP cc_start: 0.9452 (m-90) cc_final: 0.8984 (m-90) REVERT: L 180 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7503 (tpt) outliers start: 34 outliers final: 23 residues processed: 237 average time/residue: 0.0597 time to fit residues: 19.2573 Evaluate side-chains 248 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 221 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 181 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 0.3980 chunk 72 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.139899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.110060 restraints weight = 10857.594| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.77 r_work: 0.3212 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5842 Z= 0.141 Angle : 0.697 11.389 7940 Z= 0.335 Chirality : 0.044 0.174 918 Planarity : 0.004 0.035 981 Dihedral : 4.378 15.787 794 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 5.41 % Allowed : 25.97 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.16 (0.32), residues: 737 helix: 1.23 (0.34), residues: 250 sheet: 0.82 (0.43), residues: 165 loop : -1.76 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 60 TYR 0.022 0.002 TYR L 98 PHE 0.022 0.001 PHE A 292 TRP 0.007 0.001 TRP L 168 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 5839) covalent geometry : angle 0.69657 ( 7934) SS BOND : bond 0.00263 ( 3) SS BOND : angle 0.67117 ( 6) hydrogen bonds : bond 0.03168 ( 271) hydrogen bonds : angle 4.43579 ( 753) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8589 (mmmt) cc_final: 0.8141 (mttp) REVERT: A 141 TYR cc_start: 0.9008 (m-80) cc_final: 0.8279 (m-80) REVERT: A 223 ILE cc_start: 0.8305 (mt) cc_final: 0.8052 (mt) REVERT: A 246 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7458 (mt) REVERT: H 3 GLN cc_start: 0.8986 (pp30) cc_final: 0.7978 (pp30) REVERT: H 90 ASP cc_start: 0.9108 (OUTLIER) cc_final: 0.8812 (m-30) REVERT: H 117 LEU cc_start: 0.9386 (tp) cc_final: 0.9175 (tt) REVERT: H 130 TYR cc_start: 0.8871 (m-10) cc_final: 0.8471 (m-80) REVERT: H 215 ASP cc_start: 0.8599 (t0) cc_final: 0.7854 (p0) REVERT: L 29 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9224 (pp) REVERT: L 48 GLN cc_start: 0.8219 (mp10) cc_final: 0.7603 (mp10) REVERT: L 87 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8674 (pp20) REVERT: L 110 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8223 (mp0) REVERT: L 161 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8354 (tm-30) REVERT: L 168 TRP cc_start: 0.9420 (m-90) cc_final: 0.8876 (m-90) REVERT: L 180 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7563 (tpt) outliers start: 35 outliers final: 23 residues processed: 222 average time/residue: 0.0595 time to fit residues: 18.1703 Evaluate side-chains 231 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 203 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 181 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 33 optimal weight: 3.9990 chunk 46 optimal weight: 0.0010 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 0.0070 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 23 optimal weight: 0.1980 overall best weight: 0.2804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN L 6 GLN L 166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.143670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.115346 restraints weight = 10755.263| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.52 r_work: 0.3291 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5842 Z= 0.118 Angle : 0.692 11.763 7940 Z= 0.330 Chirality : 0.043 0.180 918 Planarity : 0.004 0.036 981 Dihedral : 4.289 21.329 794 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 4.17 % Allowed : 27.67 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.12 (0.32), residues: 737 helix: 1.27 (0.34), residues: 250 sheet: 0.85 (0.43), residues: 165 loop : -1.76 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 160 TYR 0.020 0.001 TYR L 98 PHE 0.019 0.001 PHE A 292 TRP 0.007 0.001 TRP L 168 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 5839) covalent geometry : angle 0.69218 ( 7934) SS BOND : bond 0.00190 ( 3) SS BOND : angle 0.54733 ( 6) hydrogen bonds : bond 0.02969 ( 271) hydrogen bonds : angle 4.37785 ( 753) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 230 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8511 (mmmt) cc_final: 0.8087 (mttp) REVERT: A 141 TYR cc_start: 0.8948 (m-80) cc_final: 0.8346 (m-80) REVERT: A 223 ILE cc_start: 0.8205 (mt) cc_final: 0.7973 (mt) REVERT: H 3 GLN cc_start: 0.8925 (pp30) cc_final: 0.7846 (pp30) REVERT: H 90 ASP cc_start: 0.9011 (OUTLIER) cc_final: 0.8794 (m-30) REVERT: H 189 VAL cc_start: 0.9019 (p) cc_final: 0.8776 (m) REVERT: H 215 ASP cc_start: 0.8626 (t70) cc_final: 0.7864 (p0) REVERT: L 29 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9216 (pp) REVERT: L 48 GLN cc_start: 0.8191 (mp10) cc_final: 0.7632 (mp10) REVERT: L 110 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8182 (mp0) REVERT: L 129 GLN cc_start: 0.8495 (tm-30) cc_final: 0.7866 (tm-30) REVERT: L 160 ARG cc_start: 0.8307 (ptm-80) cc_final: 0.7319 (ptm-80) REVERT: L 161 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8246 (tm-30) REVERT: L 168 TRP cc_start: 0.9417 (m-90) cc_final: 0.8945 (m-90) REVERT: L 180 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.7615 (tpt) outliers start: 27 outliers final: 21 residues processed: 239 average time/residue: 0.0564 time to fit residues: 18.7514 Evaluate side-chains 247 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 181 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 17 optimal weight: 0.0070 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.141188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.111810 restraints weight = 10894.209| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.77 r_work: 0.3234 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5842 Z= 0.128 Angle : 0.710 11.831 7940 Z= 0.337 Chirality : 0.044 0.190 918 Planarity : 0.004 0.033 981 Dihedral : 4.320 16.693 794 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 4.33 % Allowed : 27.20 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.04 (0.32), residues: 737 helix: 1.35 (0.35), residues: 248 sheet: 0.91 (0.44), residues: 165 loop : -1.70 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 60 TYR 0.022 0.002 TYR L 98 PHE 0.021 0.001 PHE A 292 TRP 0.008 0.001 TRP L 168 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 5839) covalent geometry : angle 0.71012 ( 7934) SS BOND : bond 0.00242 ( 3) SS BOND : angle 0.67097 ( 6) hydrogen bonds : bond 0.03101 ( 271) hydrogen bonds : angle 4.40120 ( 753) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 PHE cc_start: 0.8358 (t80) cc_final: 0.8044 (t80) REVERT: A 50 LYS cc_start: 0.8565 (mmmt) cc_final: 0.8131 (mttp) REVERT: A 112 MET cc_start: 0.7953 (mmp) cc_final: 0.7179 (tpp) REVERT: A 141 TYR cc_start: 0.8963 (m-80) cc_final: 0.8366 (m-80) REVERT: A 223 ILE cc_start: 0.8206 (mt) cc_final: 0.7971 (mt) REVERT: A 277 GLU cc_start: 0.8625 (mp0) cc_final: 0.8398 (mp0) REVERT: H 3 GLN cc_start: 0.8943 (pp30) cc_final: 0.7940 (pp30) REVERT: H 81 MET cc_start: 0.9141 (ttt) cc_final: 0.8846 (ttm) REVERT: H 90 ASP cc_start: 0.9072 (OUTLIER) cc_final: 0.8840 (m-30) REVERT: H 117 LEU cc_start: 0.9391 (tp) cc_final: 0.9186 (tt) REVERT: H 189 VAL cc_start: 0.9041 (p) cc_final: 0.8787 (m) REVERT: L 29 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9239 (pp) REVERT: L 48 GLN cc_start: 0.8223 (mp10) cc_final: 0.7671 (mp10) REVERT: L 87 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8608 (pp20) REVERT: L 110 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8234 (mp0) REVERT: L 129 GLN cc_start: 0.8512 (tm-30) cc_final: 0.7869 (tm-30) REVERT: L 160 ARG cc_start: 0.8378 (ptm-80) cc_final: 0.7494 (ptm-80) REVERT: L 161 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8246 (tm-30) REVERT: L 168 TRP cc_start: 0.9420 (m-90) cc_final: 0.8930 (m-90) REVERT: L 180 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.7592 (tpt) outliers start: 28 outliers final: 21 residues processed: 241 average time/residue: 0.0553 time to fit residues: 18.6814 Evaluate side-chains 246 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 221 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 181 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 20 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 0.0270 chunk 25 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 209 ASN L 166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.140754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.110923 restraints weight = 10923.904| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.79 r_work: 0.3222 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5842 Z= 0.138 Angle : 0.734 11.792 7940 Z= 0.346 Chirality : 0.044 0.188 918 Planarity : 0.004 0.034 981 Dihedral : 4.366 17.752 794 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 4.33 % Allowed : 28.28 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.07 (0.32), residues: 737 helix: 1.30 (0.34), residues: 253 sheet: 0.84 (0.43), residues: 166 loop : -1.72 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 60 TYR 0.022 0.002 TYR L 98 PHE 0.023 0.001 PHE A 292 TRP 0.008 0.001 TRP L 153 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 5839) covalent geometry : angle 0.73422 ( 7934) SS BOND : bond 0.00258 ( 3) SS BOND : angle 0.60341 ( 6) hydrogen bonds : bond 0.03169 ( 271) hydrogen bonds : angle 4.40986 ( 753) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 PHE cc_start: 0.8413 (t80) cc_final: 0.8150 (t80) REVERT: A 46 MET cc_start: 0.8840 (mtt) cc_final: 0.8400 (mtp) REVERT: A 50 LYS cc_start: 0.8534 (mmmt) cc_final: 0.8129 (mttp) REVERT: A 106 ASN cc_start: 0.8818 (m110) cc_final: 0.8134 (m-40) REVERT: A 141 TYR cc_start: 0.8991 (m-80) cc_final: 0.8390 (m-80) REVERT: A 223 ILE cc_start: 0.8225 (mt) cc_final: 0.7987 (mt) REVERT: A 277 GLU cc_start: 0.8661 (mp0) cc_final: 0.8427 (mp0) REVERT: H 3 GLN cc_start: 0.8949 (pp30) cc_final: 0.7921 (pp30) REVERT: H 81 MET cc_start: 0.9127 (ttt) cc_final: 0.8828 (ttm) REVERT: H 90 ASP cc_start: 0.9106 (OUTLIER) cc_final: 0.8863 (m-30) REVERT: H 117 LEU cc_start: 0.9417 (tp) cc_final: 0.9186 (tt) REVERT: H 189 VAL cc_start: 0.9045 (p) cc_final: 0.8791 (m) REVERT: L 29 LEU cc_start: 0.9648 (OUTLIER) cc_final: 0.9234 (pp) REVERT: L 48 GLN cc_start: 0.8319 (mp10) cc_final: 0.7690 (mp10) REVERT: L 87 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8676 (pp20) REVERT: L 110 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8259 (mp0) REVERT: L 129 GLN cc_start: 0.8496 (tm-30) cc_final: 0.7947 (tm-30) REVERT: L 160 ARG cc_start: 0.8297 (ptm-80) cc_final: 0.7289 (ptm-80) REVERT: L 161 GLN cc_start: 0.8745 (tm-30) cc_final: 0.8139 (tm-30) REVERT: L 168 TRP cc_start: 0.9436 (m-90) cc_final: 0.8957 (m-90) REVERT: L 180 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.7598 (tpt) outliers start: 28 outliers final: 20 residues processed: 240 average time/residue: 0.0581 time to fit residues: 19.4649 Evaluate side-chains 246 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 222 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 181 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 19 optimal weight: 0.8980 chunk 72 optimal weight: 30.0000 chunk 57 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 chunk 23 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 209 ASN H 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.139248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.109750 restraints weight = 10715.329| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.71 r_work: 0.3210 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5842 Z= 0.140 Angle : 0.737 11.449 7940 Z= 0.348 Chirality : 0.044 0.195 918 Planarity : 0.004 0.033 981 Dihedral : 4.365 16.396 794 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 4.33 % Allowed : 28.90 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.06 (0.32), residues: 737 helix: 1.29 (0.34), residues: 254 sheet: 0.86 (0.43), residues: 166 loop : -1.73 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 249 TYR 0.023 0.002 TYR L 191 PHE 0.022 0.001 PHE A 292 TRP 0.007 0.001 TRP L 168 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 5839) covalent geometry : angle 0.73758 ( 7934) SS BOND : bond 0.00241 ( 3) SS BOND : angle 0.58444 ( 6) hydrogen bonds : bond 0.03135 ( 271) hydrogen bonds : angle 4.40066 ( 753) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1450.88 seconds wall clock time: 25 minutes 35.62 seconds (1535.62 seconds total)