Starting phenix.real_space_refine on Sat Apr 4 22:54:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xla_22237/04_2026/6xla_22237.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xla_22237/04_2026/6xla_22237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xla_22237/04_2026/6xla_22237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xla_22237/04_2026/6xla_22237.map" model { file = "/net/cci-nas-00/data/ceres_data/6xla_22237/04_2026/6xla_22237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xla_22237/04_2026/6xla_22237.cif" } resolution = 3.1 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= 0.003 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: 6 Type Number sf(0) Gaussians Sb 2 10.97 5 P 44 5.49 5 S 26 5.16 5 C 3339 2.51 5 N 912 2.21 5 O 1080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5403 Number of models: 1 Model: "" Number of chains: 6 Chain: "G" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2208 Classifications: {'peptide': 268} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 255} Chain: "H" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2208 Classifications: {'peptide': 268} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 255} Chain: "N" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 470 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain: "T" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 467 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'118': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'118': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.42, per 1000 atoms: 0.26 Number of scatterers: 5403 At special positions: 0 Unit cell: (116.35, 104.715, 71.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Sb 2 50.95 S 26 16.00 P 44 15.00 O 1080 8.00 N 912 7.00 C 3339 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 279.9 milliseconds 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1028 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 6 sheets defined 46.3% alpha, 27.6% beta 22 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'G' and resid 3 through 11 removed outlier: 3.607A pdb=" N LYS G 9 " --> pdb=" O GLY G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 25 removed outlier: 3.523A pdb=" N LEU G 18 " --> pdb=" O THR G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 57 removed outlier: 3.675A pdb=" N LEU G 46 " --> pdb=" O THR G 42 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN G 51 " --> pdb=" O MET G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 71 Processing helix chain 'G' and resid 75 through 110 removed outlier: 3.707A pdb=" N GLU G 79 " --> pdb=" O CYS G 75 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG G 80 " --> pdb=" O HIS G 76 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG G 81 " --> pdb=" O ILE G 77 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN G 88 " --> pdb=" O GLU G 84 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG G 90 " --> pdb=" O GLN G 86 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER G 97 " --> pdb=" O ALA G 93 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS G 108 " --> pdb=" O GLN G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 153 Proline residue: G 144 - end of helix removed outlier: 3.594A pdb=" N VAL G 150 " --> pdb=" O ILE G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 218 removed outlier: 3.930A pdb=" N SER G 218 " --> pdb=" O PRO G 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 215 through 218' Processing helix chain 'G' and resid 219 through 233 removed outlier: 3.633A pdb=" N TYR G 223 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR G 225 " --> pdb=" O ASN G 221 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU G 231 " --> pdb=" O MET G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 257 Processing helix chain 'H' and resid 3 through 12 removed outlier: 3.646A pdb=" N LYS H 9 " --> pdb=" O GLY H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 25 removed outlier: 3.835A pdb=" N LEU H 18 " --> pdb=" O THR H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 57 removed outlier: 3.919A pdb=" N GLN H 51 " --> pdb=" O MET H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 71 removed outlier: 4.039A pdb=" N GLN H 70 " --> pdb=" O VAL H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 109 removed outlier: 4.107A pdb=" N GLU H 79 " --> pdb=" O CYS H 75 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU H 84 " --> pdb=" O ARG H 80 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN H 86 " --> pdb=" O ARG H 82 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER H 97 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS H 108 " --> pdb=" O GLN H 104 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU H 109 " --> pdb=" O HIS H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 143 removed outlier: 3.865A pdb=" N TYR H 139 " --> pdb=" O ASP H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 154 removed outlier: 3.830A pdb=" N GLY H 147 " --> pdb=" O ILE H 143 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL H 150 " --> pdb=" O ILE H 146 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET H 151 " --> pdb=" O GLY H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 218 through 233 removed outlier: 4.256A pdb=" N ALA H 222 " --> pdb=" O SER H 218 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR H 223 " --> pdb=" O LEU H 219 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET H 227 " --> pdb=" O TYR H 223 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU H 231 " --> pdb=" O MET H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 257 Processing sheet with id=AA1, first strand: chain 'G' and resid 31 through 32 removed outlier: 3.555A pdb=" N TYR G 31 " --> pdb=" O PHE G 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 117 through 121 removed outlier: 5.472A pdb=" N THR G 206 " --> pdb=" O VAL G 266 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU G 261 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N TYR G 245 " --> pdb=" O GLU G 261 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N GLN G 263 " --> pdb=" O GLU G 243 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N GLU G 243 " --> pdb=" O GLN G 263 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N CYS G 165 " --> pdb=" O TYR G 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 117 through 121 removed outlier: 5.472A pdb=" N THR G 206 " --> pdb=" O VAL G 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 31 through 32 Processing sheet with id=AA5, first strand: chain 'H' and resid 117 through 121 removed outlier: 5.457A pdb=" N THR H 206 " --> pdb=" O VAL H 266 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLU H 261 " --> pdb=" O TYR H 245 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N TYR H 245 " --> pdb=" O GLU H 261 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLN H 263 " --> pdb=" O GLU H 243 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N GLU H 243 " --> pdb=" O GLN H 263 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N CYS H 165 " --> pdb=" O TYR H 245 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 117 through 121 removed outlier: 5.457A pdb=" N THR H 206 " --> pdb=" O VAL H 266 " (cutoff:3.500A) 247 hydrogen bonds defined for protein. 684 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 0.88 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.40: 2328 1.40 - 1.58: 3160 1.58 - 1.77: 88 1.77 - 1.95: 42 1.95 - 2.13: 8 Bond restraints: 5626 Sorted by residual: bond pdb="SB 118 G 301 " pdb=" C1C 118 G 301 " ideal model delta sigma weight residual 2.092 2.134 -0.042 2.00e-02 2.50e+03 4.38e+00 bond pdb="SB 118 G 301 " pdb=" C1D 118 G 301 " ideal model delta sigma weight residual 2.092 2.131 -0.039 2.00e-02 2.50e+03 3.81e+00 bond pdb="SB 118 H 301 " pdb=" C1C 118 H 301 " ideal model delta sigma weight residual 2.092 2.130 -0.038 2.00e-02 2.50e+03 3.65e+00 bond pdb="SB 118 H 301 " pdb=" C1D 118 H 301 " ideal model delta sigma weight residual 2.092 2.129 -0.037 2.00e-02 2.50e+03 3.38e+00 bond pdb="SB 118 G 301 " pdb=" C1A 118 G 301 " ideal model delta sigma weight residual 2.093 2.129 -0.036 2.00e-02 2.50e+03 3.22e+00 ... (remaining 5621 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 7558 1.63 - 3.26: 227 3.26 - 4.89: 22 4.89 - 6.52: 5 6.52 - 8.16: 1 Bond angle restraints: 7813 Sorted by residual: angle pdb=" N ILE G 143 " pdb=" CA ILE G 143 " pdb=" C ILE G 143 " ideal model delta sigma weight residual 108.88 117.04 -8.16 2.16e+00 2.14e-01 1.43e+01 angle pdb=" N PRO H 144 " pdb=" CA PRO H 144 " pdb=" C PRO H 144 " ideal model delta sigma weight residual 110.70 115.28 -4.58 1.22e+00 6.72e-01 1.41e+01 angle pdb=" C3' DT N 61 " pdb=" O3' DT N 61 " pdb=" P DT N 62 " ideal model delta sigma weight residual 120.20 124.33 -4.13 1.50e+00 4.44e-01 7.60e+00 angle pdb=" CA ILE G 143 " pdb=" C ILE G 143 " pdb=" N PRO G 144 " ideal model delta sigma weight residual 118.88 122.79 -3.91 1.54e+00 4.22e-01 6.44e+00 angle pdb=" N ILE H 143 " pdb=" CA ILE H 143 " pdb=" C ILE H 143 " ideal model delta sigma weight residual 108.88 114.23 -5.35 2.16e+00 2.14e-01 6.14e+00 ... (remaining 7808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.48: 2958 31.48 - 62.95: 253 62.95 - 94.43: 14 94.43 - 125.91: 0 125.91 - 157.38: 1 Dihedral angle restraints: 3226 sinusoidal: 1630 harmonic: 1596 Sorted by residual: dihedral pdb=" CA VAL H 126 " pdb=" C VAL H 126 " pdb=" N TYR H 127 " pdb=" CA TYR H 127 " ideal model delta harmonic sigma weight residual 180.00 159.16 20.84 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ILE H 143 " pdb=" C ILE H 143 " pdb=" N PRO H 144 " pdb=" CA PRO H 144 " ideal model delta harmonic sigma weight residual -180.00 -159.73 -20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" C4' DT N 61 " pdb=" C3' DT N 61 " pdb=" O3' DT N 61 " pdb=" P DT N 62 " ideal model delta sinusoidal sigma weight residual 220.00 62.62 157.38 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 3223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 493 0.031 - 0.063: 250 0.063 - 0.094: 75 0.094 - 0.125: 24 0.125 - 0.156: 12 Chirality restraints: 854 Sorted by residual: chirality pdb=" CA ILE H 132 " pdb=" N ILE H 132 " pdb=" C ILE H 132 " pdb=" CB ILE H 132 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CA VAL H 210 " pdb=" N VAL H 210 " pdb=" C VAL H 210 " pdb=" CB VAL H 210 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CB ILE G 143 " pdb=" CA ILE G 143 " pdb=" CG1 ILE G 143 " pdb=" CG2 ILE G 143 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.55e-01 ... (remaining 851 not shown) Planarity restraints: 832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO H 144 " 0.041 5.00e-02 4.00e+02 6.16e-02 6.08e+00 pdb=" N PRO H 145 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO H 145 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 145 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA N 51 " -0.024 2.00e-02 2.50e+03 1.01e-02 2.82e+00 pdb=" N9 DA N 51 " 0.021 2.00e-02 2.50e+03 pdb=" C8 DA N 51 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DA N 51 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA N 51 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA N 51 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA N 51 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DA N 51 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA N 51 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA N 51 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA N 51 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO G 144 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO G 145 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO G 145 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 145 " 0.023 5.00e-02 4.00e+02 ... (remaining 829 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1288 2.80 - 3.33: 4457 3.33 - 3.85: 8610 3.85 - 4.38: 10617 4.38 - 4.90: 16575 Nonbonded interactions: 41547 Sorted by model distance: nonbonded pdb=" OH TYR G 127 " pdb=" OE1 GLU G 185 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR H 61 " pdb=" OE1 GLU H 64 " model vdw 2.288 3.040 nonbonded pdb=" OG1 THR G 61 " pdb=" OE2 GLU G 64 " model vdw 2.305 3.040 nonbonded pdb=" N6 DA N 51 " pdb=" O4 DT T 38 " model vdw 2.332 3.120 nonbonded pdb=" NZ LYS H 108 " pdb=" OE2 GLU H 109 " model vdw 2.358 3.120 ... (remaining 41542 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 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'N' and (resid 41 through 50 or resid 52 through 61)) selection = (chain 'T' and (resid 28 through 37 or resid 39 through 48)) } 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: 3.840 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.320 Find NCS groups from input model: 0.070 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 0.051 5626 Z= 0.230 Angle : 0.651 8.156 7813 Z= 0.387 Chirality : 0.043 0.156 854 Planarity : 0.005 0.062 832 Dihedral : 19.958 157.382 2198 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -2.59 (0.32), residues: 532 helix: -1.71 (0.29), residues: 216 sheet: -0.87 (0.48), residues: 104 loop : -1.99 (0.38), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 90 TYR 0.019 0.001 TYR G 127 PHE 0.017 0.002 PHE G 131 TRP 0.014 0.002 TRP H 229 HIS 0.004 0.001 HIS G 101 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 5626) covalent geometry : angle 0.65134 ( 7813) hydrogen bonds : bond 0.14768 ( 280) hydrogen bonds : angle 6.78445 ( 802) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: G 192 LYS cc_start: 0.6916 (mmtt) cc_final: 0.6500 (mtmt) REVERT: H 105 HIS cc_start: 0.7643 (t70) cc_final: 0.7331 (t-90) REVERT: H 232 ASP cc_start: 0.7786 (t0) cc_final: 0.7506 (t0) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1297 time to fit residues: 10.2712 Evaluate side-chains 46 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.0770 chunk 50 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 22 ASN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 105 HIS G 178 ASN G 233 ASN H 3 GLN H 101 HIS H 105 HIS H 233 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.128197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.107730 restraints weight = 5516.455| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.41 r_work: 0.3335 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5626 Z= 0.149 Angle : 0.540 6.693 7813 Z= 0.314 Chirality : 0.040 0.142 854 Planarity : 0.004 0.056 832 Dihedral : 21.678 156.874 1084 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.02 % Allowed : 8.78 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.81 (0.36), residues: 532 helix: 0.48 (0.34), residues: 218 sheet: -0.76 (0.49), residues: 106 loop : -1.42 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 12 TYR 0.013 0.001 TYR G 127 PHE 0.013 0.001 PHE G 131 TRP 0.008 0.001 TRP G 229 HIS 0.008 0.001 HIS G 105 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 5626) covalent geometry : angle 0.54011 ( 7813) hydrogen bonds : bond 0.04845 ( 280) hydrogen bonds : angle 4.48013 ( 802) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.149 Fit side-chains REVERT: G 192 LYS cc_start: 0.7116 (mmtt) cc_final: 0.6400 (mtmt) REVERT: H 220 ARG cc_start: 0.8338 (ttm-80) cc_final: 0.8072 (ttm-80) outliers start: 5 outliers final: 2 residues processed: 55 average time/residue: 0.0705 time to fit residues: 5.1528 Evaluate side-chains 47 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 208 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 41 optimal weight: 0.0170 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.0370 chunk 34 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 GLN G 105 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.128897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.108445 restraints weight = 5462.251| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.40 r_work: 0.3345 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5626 Z= 0.144 Angle : 0.527 6.430 7813 Z= 0.305 Chirality : 0.039 0.144 854 Planarity : 0.004 0.051 832 Dihedral : 21.638 156.851 1084 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.02 % Allowed : 10.61 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.36), residues: 532 helix: 1.23 (0.35), residues: 224 sheet: -0.26 (0.53), residues: 98 loop : -1.42 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 12 TYR 0.012 0.001 TYR G 127 PHE 0.011 0.001 PHE G 131 TRP 0.011 0.001 TRP G 229 HIS 0.009 0.001 HIS G 105 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 5626) covalent geometry : angle 0.52748 ( 7813) hydrogen bonds : bond 0.04357 ( 280) hydrogen bonds : angle 4.19025 ( 802) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: G 192 LYS cc_start: 0.7058 (mmtt) cc_final: 0.6342 (mtmt) REVERT: G 227 MET cc_start: 0.8479 (mmm) cc_final: 0.8227 (mmt) outliers start: 5 outliers final: 2 residues processed: 55 average time/residue: 0.0835 time to fit residues: 5.9971 Evaluate side-chains 50 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 83 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.125448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.105220 restraints weight = 5471.658| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.40 r_work: 0.3296 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5626 Z= 0.213 Angle : 0.591 9.906 7813 Z= 0.334 Chirality : 0.041 0.150 854 Planarity : 0.004 0.048 832 Dihedral : 21.842 157.749 1084 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.22 % Allowed : 13.06 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.33 (0.36), residues: 532 helix: 1.25 (0.35), residues: 224 sheet: -0.61 (0.49), residues: 112 loop : -1.69 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 56 TYR 0.016 0.001 TYR G 127 PHE 0.012 0.002 PHE H 49 TRP 0.012 0.002 TRP G 229 HIS 0.003 0.001 HIS G 101 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 5626) covalent geometry : angle 0.59074 ( 7813) hydrogen bonds : bond 0.05342 ( 280) hydrogen bonds : angle 4.37798 ( 802) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.222 Fit side-chains REVERT: G 192 LYS cc_start: 0.7054 (mmtt) cc_final: 0.6363 (mtmt) outliers start: 6 outliers final: 3 residues processed: 54 average time/residue: 0.0816 time to fit residues: 5.6986 Evaluate side-chains 50 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 171 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 50 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 51 optimal weight: 0.0040 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.128495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.108017 restraints weight = 5601.662| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.42 r_work: 0.3338 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5626 Z= 0.142 Angle : 0.524 6.143 7813 Z= 0.302 Chirality : 0.039 0.146 854 Planarity : 0.004 0.047 832 Dihedral : 21.532 157.023 1084 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.61 % Allowed : 15.10 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.36), residues: 532 helix: 1.67 (0.35), residues: 224 sheet: -0.22 (0.53), residues: 102 loop : -1.58 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 220 TYR 0.011 0.001 TYR G 127 PHE 0.011 0.001 PHE G 131 TRP 0.010 0.001 TRP H 229 HIS 0.003 0.001 HIS G 101 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 5626) covalent geometry : angle 0.52412 ( 7813) hydrogen bonds : bond 0.04185 ( 280) hydrogen bonds : angle 4.10970 ( 802) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.165 Fit side-chains REVERT: G 192 LYS cc_start: 0.6989 (mmtt) cc_final: 0.6301 (mtmt) REVERT: G 227 MET cc_start: 0.8486 (mmm) cc_final: 0.8232 (mmt) REVERT: H 123 GLU cc_start: 0.8113 (pt0) cc_final: 0.7849 (mt-10) outliers start: 3 outliers final: 3 residues processed: 56 average time/residue: 0.0801 time to fit residues: 5.9307 Evaluate side-chains 53 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 208 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 3 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.129817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.109819 restraints weight = 5642.130| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.40 r_work: 0.3389 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5626 Z= 0.186 Angle : 0.566 7.499 7813 Z= 0.320 Chirality : 0.041 0.149 854 Planarity : 0.004 0.045 832 Dihedral : 21.701 157.486 1084 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.82 % Allowed : 16.33 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.03 (0.37), residues: 532 helix: 1.66 (0.35), residues: 224 sheet: -0.47 (0.50), residues: 108 loop : -1.60 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 56 TYR 0.015 0.001 TYR G 127 PHE 0.012 0.002 PHE H 49 TRP 0.011 0.001 TRP H 229 HIS 0.003 0.001 HIS G 101 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 5626) covalent geometry : angle 0.56570 ( 7813) hydrogen bonds : bond 0.04812 ( 280) hydrogen bonds : angle 4.22949 ( 802) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.176 Fit side-chains REVERT: G 192 LYS cc_start: 0.7020 (mmtt) cc_final: 0.6379 (mtmt) outliers start: 4 outliers final: 3 residues processed: 54 average time/residue: 0.0783 time to fit residues: 5.5339 Evaluate side-chains 53 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain H residue 171 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.130009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.109951 restraints weight = 5709.915| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.40 r_work: 0.3390 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5626 Z= 0.179 Angle : 0.560 7.595 7813 Z= 0.318 Chirality : 0.040 0.149 854 Planarity : 0.004 0.045 832 Dihedral : 21.673 157.424 1084 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.43 % Allowed : 15.92 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.37), residues: 532 helix: 1.74 (0.35), residues: 224 sheet: -0.44 (0.50), residues: 108 loop : -1.58 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 220 TYR 0.014 0.001 TYR G 127 PHE 0.011 0.001 PHE H 49 TRP 0.012 0.001 TRP H 229 HIS 0.003 0.001 HIS G 101 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 5626) covalent geometry : angle 0.56039 ( 7813) hydrogen bonds : bond 0.04731 ( 280) hydrogen bonds : angle 4.20835 ( 802) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.148 Fit side-chains REVERT: G 192 LYS cc_start: 0.7023 (mmtt) cc_final: 0.6377 (mtmt) REVERT: H 105 HIS cc_start: 0.8097 (OUTLIER) cc_final: 0.7520 (t-90) outliers start: 7 outliers final: 5 residues processed: 56 average time/residue: 0.0680 time to fit residues: 5.0237 Evaluate side-chains 56 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 105 HIS Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 208 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 50 optimal weight: 0.0000 chunk 19 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.131979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.111820 restraints weight = 5603.324| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.41 r_work: 0.3422 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5626 Z= 0.144 Angle : 0.533 8.210 7813 Z= 0.302 Chirality : 0.039 0.146 854 Planarity : 0.003 0.045 832 Dihedral : 21.519 157.070 1084 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.22 % Allowed : 16.33 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.36 (0.37), residues: 532 helix: 1.99 (0.35), residues: 224 sheet: -0.09 (0.48), residues: 126 loop : -1.80 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 220 TYR 0.012 0.001 TYR G 127 PHE 0.011 0.001 PHE G 136 TRP 0.011 0.001 TRP H 229 HIS 0.003 0.001 HIS G 101 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 5626) covalent geometry : angle 0.53307 ( 7813) hydrogen bonds : bond 0.04065 ( 280) hydrogen bonds : angle 4.05048 ( 802) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.193 Fit side-chains REVERT: G 192 LYS cc_start: 0.6983 (mmtt) cc_final: 0.6332 (mtmt) REVERT: H 105 HIS cc_start: 0.8044 (OUTLIER) cc_final: 0.7444 (t-90) outliers start: 6 outliers final: 5 residues processed: 54 average time/residue: 0.0701 time to fit residues: 5.0370 Evaluate side-chains 55 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 105 HIS Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 208 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.0270 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 0.0010 chunk 45 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 overall best weight: 0.4644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.132950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.112871 restraints weight = 5586.617| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.40 r_work: 0.3439 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5626 Z= 0.133 Angle : 0.519 8.752 7813 Z= 0.295 Chirality : 0.038 0.145 854 Planarity : 0.003 0.042 832 Dihedral : 21.439 156.727 1084 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.22 % Allowed : 16.12 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.48 (0.38), residues: 532 helix: 2.15 (0.35), residues: 224 sheet: -0.11 (0.48), residues: 128 loop : -1.78 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 220 TYR 0.012 0.001 TYR H 139 PHE 0.009 0.001 PHE G 131 TRP 0.010 0.001 TRP H 229 HIS 0.003 0.001 HIS G 101 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 5626) covalent geometry : angle 0.51881 ( 7813) hydrogen bonds : bond 0.03754 ( 280) hydrogen bonds : angle 3.95172 ( 802) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.200 Fit side-chains REVERT: G 192 LYS cc_start: 0.6976 (mmtt) cc_final: 0.6326 (mtmt) REVERT: H 105 HIS cc_start: 0.8021 (OUTLIER) cc_final: 0.7354 (t-90) outliers start: 6 outliers final: 4 residues processed: 53 average time/residue: 0.0794 time to fit residues: 5.5824 Evaluate side-chains 54 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 105 HIS Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 208 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 0.2980 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.132174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.112159 restraints weight = 5681.496| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.40 r_work: 0.3427 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5626 Z= 0.142 Angle : 0.541 11.989 7813 Z= 0.301 Chirality : 0.039 0.146 854 Planarity : 0.003 0.043 832 Dihedral : 21.485 156.753 1084 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.02 % Allowed : 16.53 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.49 (0.38), residues: 532 helix: 2.14 (0.35), residues: 224 sheet: -0.09 (0.48), residues: 128 loop : -1.74 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 220 TYR 0.011 0.001 TYR G 127 PHE 0.011 0.001 PHE G 136 TRP 0.010 0.001 TRP H 229 HIS 0.003 0.001 HIS G 101 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 5626) covalent geometry : angle 0.54068 ( 7813) hydrogen bonds : bond 0.03939 ( 280) hydrogen bonds : angle 3.98174 ( 802) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.220 Fit side-chains REVERT: G 192 LYS cc_start: 0.7007 (mmtt) cc_final: 0.6359 (mtmt) REVERT: G 227 MET cc_start: 0.8398 (mmm) cc_final: 0.8169 (mmt) REVERT: H 105 HIS cc_start: 0.8021 (OUTLIER) cc_final: 0.7351 (t-90) outliers start: 5 outliers final: 4 residues processed: 52 average time/residue: 0.0826 time to fit residues: 5.6441 Evaluate side-chains 53 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 105 HIS Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 208 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 1 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 3 optimal weight: 0.0970 chunk 21 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.132424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.112464 restraints weight = 5654.463| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.40 r_work: 0.3431 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5626 Z= 0.135 Angle : 0.536 11.447 7813 Z= 0.299 Chirality : 0.038 0.146 854 Planarity : 0.003 0.044 832 Dihedral : 21.469 156.891 1084 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.02 % Allowed : 16.53 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.53 (0.38), residues: 532 helix: 2.16 (0.35), residues: 224 sheet: -0.08 (0.48), residues: 128 loop : -1.71 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 220 TYR 0.014 0.001 TYR H 139 PHE 0.010 0.001 PHE G 136 TRP 0.010 0.001 TRP H 229 HIS 0.003 0.001 HIS G 101 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 5626) covalent geometry : angle 0.53630 ( 7813) hydrogen bonds : bond 0.03860 ( 280) hydrogen bonds : angle 3.96684 ( 802) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1567.01 seconds wall clock time: 27 minutes 24.36 seconds (1644.36 seconds total)