Starting phenix.real_space_refine on Thu Oct 22 22:37:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/23ay_68820/10_2026/23ay_68820.cif Found real_map, /net/cci-nas-00/data/ceres_data/23ay_68820/10_2026/23ay_68820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/23ay_68820/10_2026/23ay_68820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/23ay_68820/10_2026/23ay_68820.map" model { file = "/net/cci-nas-00/data/ceres_data/23ay_68820/10_2026/23ay_68820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/23ay_68820/10_2026/23ay_68820.cif" } resolution = 2.27 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= 0.005 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4068 2.51 5 N 1086 2.21 5 O 1205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6396 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2312 Classifications: {'peptide': 296} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 278} Chain: "B" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1870 Classifications: {'peptide': 238} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 221} Chain: "C" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1896 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 231} Chain: "D" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 297 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 3, 'TRANS': 35} Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'SPH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.61, per 1000 atoms: 0.25 Number of scatterers: 6396 At special positions: 0 Unit cell: (92.169, 109.858, 86.583, 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 37 16.00 O 1205 8.00 N 1086 7.00 C 4068 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: 0.47 Conformation dependent library (CDL) restraints added in 376.8 milliseconds 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1536 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 12 sheets defined 16.2% alpha, 36.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 54 through 57 removed outlier: 3.560A pdb=" N THR A 57 " --> pdb=" O VAL A 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 54 through 57' Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 100 through 108 removed outlier: 3.547A pdb=" N LYS A 106 " --> pdb=" O GLN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.919A pdb=" N GLN A 164 " --> pdb=" O PHE A 161 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER A 165 " --> pdb=" O HIS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 43 through 47 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 167 through 173 removed outlier: 4.358A pdb=" N THR B 171 " --> pdb=" O ALA B 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 48 removed outlier: 4.164A pdb=" N VAL C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN C 48 " --> pdb=" O LEU C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 removed outlier: 3.710A pdb=" N LYS C 68 " --> pdb=" O GLU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 104 Processing helix chain 'C' and resid 143 through 148 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'D' and resid 34 through 38 Processing helix chain 'D' and resid 49 through 54 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA4, first strand: chain 'A' and resid 67 through 76 removed outlier: 6.600A pdb=" N VAL A 239 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS A 71 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL A 237 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER A 73 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL A 235 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU A 75 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE A 233 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE A 246 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARG A 114 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ALA A 248 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR A 112 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ALA A 250 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N PHE A 110 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA C 22 " --> pdb=" O ARG A 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 193 through 194 removed outlier: 4.754A pdb=" N PHE A 110 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ALA A 250 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR A 112 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ALA A 248 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARG A 114 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE A 246 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA A 248 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 90 through 94 removed outlier: 4.118A pdb=" N ALA A 169 " --> pdb=" O PHE A 147 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 14 through 18 Processing sheet with id=AA8, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.858A pdb=" N CYS B 32 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N HIS B 99 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLY B 241 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B 101 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE B 239 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ARG B 103 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N CYS B 237 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.858A pdb=" N CYS B 32 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N HIS B 99 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLY B 241 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B 101 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE B 239 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ARG B 103 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N CYS B 237 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 153 through 154 removed outlier: 3.508A pdb=" N TRP B 207 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA B 121 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLN B 119 " --> pdb=" O PRO B 216 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 80 through 85 removed outlier: 6.897A pdb=" N CYS C 194 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN C 83 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL C 192 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYS C 128 " --> pdb=" O GLN C 197 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASN C 199 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA C 126 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 176 through 177 removed outlier: 6.200A pdb=" N TYR C 106 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N MET C 227 " --> pdb=" O TYR C 106 " (cutoff:3.500A) 214 hydrogen bonds defined for protein. 510 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: 0.91 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2086 1.34 - 1.46: 1116 1.46 - 1.57: 3296 1.57 - 1.69: 0 1.69 - 1.80: 60 Bond restraints: 6558 Sorted by residual: bond pdb=" C2 SPH A 301 " pdb=" C3 SPH A 301 " ideal model delta sigma weight residual 1.544 1.517 0.027 2.00e-02 2.50e+03 1.87e+00 bond pdb=" CA GLY A 218 " pdb=" C GLY A 218 " ideal model delta sigma weight residual 1.524 1.511 0.013 1.20e-02 6.94e+03 1.13e+00 bond pdb=" CB LEU C 86 " pdb=" CG LEU C 86 " ideal model delta sigma weight residual 1.530 1.551 -0.021 2.00e-02 2.50e+03 1.08e+00 bond pdb=" CB GLU C 243 " pdb=" CG GLU C 243 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.55e-01 bond pdb=" CG GLU C 243 " pdb=" CD GLU C 243 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 8.06e-01 ... (remaining 6553 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 8784 1.81 - 3.61: 133 3.61 - 5.42: 15 5.42 - 7.22: 0 7.22 - 9.03: 3 Bond angle restraints: 8935 Sorted by residual: angle pdb=" N ILE C 88 " pdb=" CA ILE C 88 " pdb=" C ILE C 88 " ideal model delta sigma weight residual 112.29 108.20 4.09 9.40e-01 1.13e+00 1.89e+01 angle pdb=" N VAL B 48 " pdb=" CA VAL B 48 " pdb=" C VAL B 48 " ideal model delta sigma weight residual 111.62 109.27 2.35 7.90e-01 1.60e+00 8.82e+00 angle pdb=" C4 SPH A 301 " pdb=" C5 SPH A 301 " pdb=" C6 SPH A 301 " ideal model delta sigma weight residual 128.38 119.61 8.77 3.00e+00 1.11e-01 8.55e+00 angle pdb=" C3 SPH A 301 " pdb=" C4 SPH A 301 " pdb=" C5 SPH A 301 " ideal model delta sigma weight residual 127.69 119.11 8.58 3.00e+00 1.11e-01 8.18e+00 angle pdb=" CB GLU C 243 " pdb=" CG GLU C 243 " pdb=" CD GLU C 243 " ideal model delta sigma weight residual 112.60 117.39 -4.79 1.70e+00 3.46e-01 7.96e+00 ... (remaining 8930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 3480 17.83 - 35.66: 309 35.66 - 53.48: 78 53.48 - 71.31: 25 71.31 - 89.14: 10 Dihedral angle restraints: 3902 sinusoidal: 1525 harmonic: 2377 Sorted by residual: dihedral pdb=" CA LEU C 86 " pdb=" C LEU C 86 " pdb=" N ASP C 87 " pdb=" CA ASP C 87 " ideal model delta harmonic sigma weight residual -180.00 -160.88 -19.12 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ASN B 30 " pdb=" C ASN B 30 " pdb=" N TYR B 31 " pdb=" CA TYR B 31 " ideal model delta harmonic sigma weight residual 180.00 162.18 17.82 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA PHE A 100 " pdb=" C PHE A 100 " pdb=" N VAL A 101 " pdb=" CA VAL A 101 " ideal model delta harmonic sigma weight residual 180.00 -162.38 -17.62 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 3899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 741 0.043 - 0.086: 192 0.086 - 0.128: 71 0.128 - 0.171: 2 0.171 - 0.214: 1 Chirality restraints: 1007 Sorted by residual: chirality pdb=" CG LEU C 86 " pdb=" CB LEU C 86 " pdb=" CD1 LEU C 86 " pdb=" CD2 LEU C 86 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ILE C 153 " pdb=" N ILE C 153 " pdb=" C ILE C 153 " pdb=" CB ILE C 153 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA ILE A 294 " pdb=" N ILE A 294 " pdb=" C ILE A 294 " pdb=" CB ILE A 294 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 1004 not shown) Planarity restraints: 1156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP C 220 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.05e+00 pdb=" CG ASP C 220 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASP C 220 " 0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP C 220 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 148 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO A 149 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 149 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 149 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 92 " -0.017 5.00e-02 4.00e+02 2.57e-02 1.06e+00 pdb=" N PRO C 93 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO C 93 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 93 " -0.014 5.00e-02 4.00e+02 ... (remaining 1153 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 3579 3.02 - 3.49: 6071 3.49 - 3.96: 11085 3.96 - 4.43: 13079 4.43 - 4.90: 20349 Nonbonded interactions: 54163 Sorted by model distance: nonbonded pdb=" N GLU C 59 " pdb=" OE1 GLU C 59 " model vdw 2.548 3.120 nonbonded pdb=" N ASP A 159 " pdb=" OD1 ASP A 159 " model vdw 2.581 3.120 nonbonded pdb=" N ILE C 88 " pdb=" N GLN C 89 " model vdw 2.586 2.560 nonbonded pdb=" OH TYR A 112 " pdb=" OE2 GLU B 129 " model vdw 2.603 3.040 nonbonded pdb=" N ALA B 114 " pdb=" O ALA B 114 " model vdw 2.623 2.496 ... (remaining 54158 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.410 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 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 : 0.004 0.038 6558 Z= 0.175 Angle : 0.575 9.029 8935 Z= 0.307 Chirality : 0.044 0.214 1007 Planarity : 0.003 0.031 1156 Dihedral : 15.925 89.137 2366 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.71 % Allowed : 14.94 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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 (0.29), residues: 812 helix: -2.17 (0.55), residues: 65 sheet: 0.82 (0.38), residues: 198 loop : 0.07 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 104 TYR 0.016 0.001 TYR C 191 PHE 0.013 0.001 PHE C 222 TRP 0.008 0.001 TRP A 249 HIS 0.006 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 6558) covalent geometry : angle 0.57541 / 0.31 ( 8935) hydrogen bonds : bond 0.17519 / 11.25 ( 174) hydrogen bonds : angle 8.19695 / 5.64 ( 510) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.244 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 104 average time/residue: 0.5863 time to fit residues: 63.8443 Evaluate side-chains 101 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 86 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 GLN B 55 GLN B 206 GLN C 101 ASN C 197 GLN D 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.084708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.069148 restraints weight = 9566.222| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 2.09 r_work: 0.2680 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.0666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6558 Z= 0.175 Angle : 0.509 9.015 8935 Z= 0.263 Chirality : 0.044 0.214 1007 Planarity : 0.004 0.028 1156 Dihedral : 6.188 54.201 898 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.84 % Allowed : 12.23 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.01 (0.28), residues: 812 helix: -1.91 (0.57), residues: 68 sheet: 0.90 (0.37), residues: 198 loop : -0.02 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.014 0.001 TYR B 31 PHE 0.013 0.001 PHE C 222 TRP 0.008 0.001 TRP A 249 HIS 0.002 0.001 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 6558) covalent geometry : angle 0.50861 / 0.26 ( 8935) hydrogen bonds : bond 0.03747 / 2.46 ( 174) hydrogen bonds : angle 5.92334 / 4.17 ( 510) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.216 Fit side-chains REVERT: C 43 MET cc_start: 0.9502 (mmm) cc_final: 0.9061 (mmm) REVERT: C 205 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7571 (mt-10) REVERT: C 220 ASP cc_start: 0.8825 (p0) cc_final: 0.8581 (p0) outliers start: 20 outliers final: 8 residues processed: 113 average time/residue: 0.5524 time to fit residues: 65.5217 Evaluate side-chains 107 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 205 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [13, 31, 52, 68, 20, 40, 27, 53, 59, 35, 66] chunk 13 optimal weight: 9.9990 chunk 31 optimal weight: 0.0470 chunk 52 optimal weight: 0.0370 chunk 68 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 overall best weight: 2.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 ASN ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.086491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.071093 restraints weight = 9448.137| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.08 r_work: 0.2717 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6558 Z= 0.115 Angle : 0.477 8.909 8935 Z= 0.245 Chirality : 0.042 0.204 1007 Planarity : 0.003 0.027 1156 Dihedral : 5.660 54.465 896 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.84 % Allowed : 12.52 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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 (0.28), residues: 812 helix: -1.77 (0.59), residues: 68 sheet: 0.92 (0.37), residues: 198 loop : -0.02 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.011 0.001 TYR B 31 PHE 0.010 0.001 PHE A 91 TRP 0.007 0.001 TRP C 155 HIS 0.003 0.000 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 6558) covalent geometry : angle 0.47680 / 0.25 ( 8935) hydrogen bonds : bond 0.03200 / 2.11 ( 174) hydrogen bonds : angle 5.52216 / 3.90 ( 510) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.174 Fit side-chains REVERT: A 228 HIS cc_start: 0.8306 (OUTLIER) cc_final: 0.7776 (p-80) REVERT: C 43 MET cc_start: 0.9514 (mmm) cc_final: 0.9037 (mmm) REVERT: C 205 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7587 (mt-10) REVERT: C 220 ASP cc_start: 0.8770 (p0) cc_final: 0.8473 (p0) outliers start: 20 outliers final: 7 residues processed: 114 average time/residue: 0.5711 time to fit residues: 68.1618 Evaluate side-chains 106 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain D residue 46 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [65, 73, 64, 11, 19, 49, 52, 50, 5, 58, 74] chunk 65 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 50 optimal weight: 40.0000 chunk 5 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 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 = 0.2995 r_free = 0.2995 target = 0.083127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.067650 restraints weight = 9655.549| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 2.09 r_work: 0.2654 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6558 Z= 0.243 Angle : 0.543 8.685 8935 Z= 0.280 Chirality : 0.045 0.219 1007 Planarity : 0.004 0.030 1156 Dihedral : 5.940 56.099 896 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.70 % Allowed : 12.52 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.09 (0.28), residues: 812 helix: -1.82 (0.59), residues: 68 sheet: 0.84 (0.36), residues: 198 loop : -0.11 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.015 0.002 TYR C 191 PHE 0.012 0.001 PHE A 91 TRP 0.008 0.001 TRP C 155 HIS 0.004 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.24 ( 6558) covalent geometry : angle 0.54294 / 0.28 ( 8935) hydrogen bonds : bond 0.03721 / 2.44 ( 174) hydrogen bonds : angle 5.65471 / 4.00 ( 510) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.288 Fit side-chains REVERT: A 170 SER cc_start: 0.9549 (OUTLIER) cc_final: 0.9247 (m) REVERT: C 205 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7635 (mm-30) REVERT: C 220 ASP cc_start: 0.8856 (p0) cc_final: 0.8546 (p0) outliers start: 19 outliers final: 6 residues processed: 106 average time/residue: 0.5822 time to fit residues: 64.7597 Evaluate side-chains 103 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 205 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [77, 64, 20, 46, 15, 63, 62, 12, 8, 44, 33] chunk 77 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 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 = 0.2995 r_free = 0.2995 target = 0.082795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.067542 restraints weight = 9682.706| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 2.07 r_work: 0.2655 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 6558 Z= 0.239 Angle : 0.540 8.713 8935 Z= 0.279 Chirality : 0.045 0.218 1007 Planarity : 0.004 0.031 1156 Dihedral : 5.799 57.480 896 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.70 % Allowed : 12.66 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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 (0.28), residues: 812 helix: -1.77 (0.59), residues: 68 sheet: 0.80 (0.36), residues: 198 loop : -0.14 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.018 0.002 TYR C 191 PHE 0.012 0.001 PHE A 91 TRP 0.008 0.001 TRP A 249 HIS 0.004 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.24 ( 6558) covalent geometry : angle 0.53967 / 0.28 ( 8935) hydrogen bonds : bond 0.03651 / 2.40 ( 174) hydrogen bonds : angle 5.57944 / 3.95 ( 510) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.251 Fit side-chains REVERT: A 170 SER cc_start: 0.9550 (OUTLIER) cc_final: 0.9253 (m) REVERT: C 205 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7618 (mm-30) outliers start: 19 outliers final: 10 residues processed: 107 average time/residue: 0.5460 time to fit residues: 61.3829 Evaluate side-chains 107 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 226 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [8, 30, 77, 21, 18, 40, 26, 13, 68, 29, 52] chunk 8 optimal weight: 30.0000 chunk 30 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 68 optimal weight: 0.6980 chunk 29 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 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 = 0.3006 r_free = 0.3006 target = 0.083788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.068506 restraints weight = 9525.309| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 2.07 r_work: 0.2669 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6558 Z= 0.180 Angle : 0.510 8.662 8935 Z= 0.264 Chirality : 0.044 0.212 1007 Planarity : 0.004 0.029 1156 Dihedral : 5.516 57.034 896 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.56 % Allowed : 13.23 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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 (0.28), residues: 812 helix: -1.72 (0.60), residues: 68 sheet: 0.75 (0.37), residues: 195 loop : -0.12 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.016 0.001 TYR C 191 PHE 0.012 0.001 PHE A 91 TRP 0.008 0.001 TRP A 249 HIS 0.002 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 ( 6558) covalent geometry : angle 0.50985 / 0.26 ( 8935) hydrogen bonds : bond 0.03403 / 2.26 ( 174) hydrogen bonds : angle 5.45597 / 3.86 ( 510) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.216 Fit side-chains REVERT: A 19 GLU cc_start: 0.8296 (pm20) cc_final: 0.8029 (pm20) REVERT: A 170 SER cc_start: 0.9530 (OUTLIER) cc_final: 0.9221 (m) REVERT: C 205 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7653 (mm-30) REVERT: C 220 ASP cc_start: 0.8769 (p0) cc_final: 0.8434 (p0) outliers start: 18 outliers final: 10 residues processed: 104 average time/residue: 0.5489 time to fit residues: 59.9110 Evaluate side-chains 108 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 205 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [30, 51, 35, 69, 27, 74, 39, 61, 28, 59, 8] chunk 30 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 8 optimal weight: 30.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 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 = 0.2965 r_free = 0.2965 target = 0.080950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.065869 restraints weight = 9782.960| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 2.06 r_work: 0.2624 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 6558 Z= 0.356 Angle : 0.599 8.334 8935 Z= 0.311 Chirality : 0.048 0.233 1007 Planarity : 0.004 0.032 1156 Dihedral : 5.816 51.390 896 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.28 % Allowed : 13.51 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.25 (0.28), residues: 812 helix: -1.81 (0.59), residues: 67 sheet: 0.72 (0.37), residues: 195 loop : -0.25 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 144 TYR 0.025 0.002 TYR C 191 PHE 0.014 0.002 PHE A 91 TRP 0.009 0.002 TRP C 155 HIS 0.003 0.001 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00840 / 0.36 ( 6558) covalent geometry : angle 0.59908 / 0.31 ( 8935) hydrogen bonds : bond 0.04102 / 2.68 ( 174) hydrogen bonds : angle 5.72238 / 4.05 ( 510) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.255 Fit side-chains REVERT: B 30 ASN cc_start: 0.9465 (OUTLIER) cc_final: 0.9249 (t0) REVERT: C 205 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7573 (mm-30) outliers start: 16 outliers final: 6 residues processed: 101 average time/residue: 0.5513 time to fit residues: 58.4436 Evaluate side-chains 101 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 205 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [78, 49, 10, 54, 66, 5, 58, 14, 15, 61, 24] chunk 78 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 219 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 = 0.3011 r_free = 0.3011 target = 0.083795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.068719 restraints weight = 9557.515| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 2.06 r_work: 0.2673 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6558 Z= 0.160 Angle : 0.511 8.564 8935 Z= 0.265 Chirality : 0.044 0.211 1007 Planarity : 0.004 0.030 1156 Dihedral : 5.438 51.887 896 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.71 % Allowed : 14.22 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.19 (0.28), residues: 812 helix: -1.78 (0.59), residues: 68 sheet: 0.73 (0.37), residues: 195 loop : -0.18 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 104 TYR 0.020 0.001 TYR C 191 PHE 0.012 0.001 PHE A 91 TRP 0.008 0.001 TRP A 249 HIS 0.002 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 6558) covalent geometry : angle 0.51138 / 0.26 ( 8935) hydrogen bonds : bond 0.03315 / 2.20 ( 174) hydrogen bonds : angle 5.40518 / 3.83 ( 510) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.209 Fit side-chains REVERT: A 19 GLU cc_start: 0.8333 (pm20) cc_final: 0.8085 (tp30) REVERT: C 43 MET cc_start: 0.9509 (mmm) cc_final: 0.9079 (mmm) REVERT: C 205 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7610 (mm-30) REVERT: C 220 ASP cc_start: 0.8784 (p0) cc_final: 0.8427 (p0) outliers start: 12 outliers final: 6 residues processed: 104 average time/residue: 0.5841 time to fit residues: 63.5627 Evaluate side-chains 103 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 205 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [0, 49, 39, 34, 9, 24, 31, 74, 17, 54, 53] chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 219 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 = 0.2992 r_free = 0.2992 target = 0.082649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.067512 restraints weight = 9752.501| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.07 r_work: 0.2651 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6558 Z= 0.234 Angle : 0.546 8.441 8935 Z= 0.283 Chirality : 0.045 0.222 1007 Planarity : 0.004 0.030 1156 Dihedral : 5.535 48.005 896 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.71 % Allowed : 14.22 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.21 (0.28), residues: 812 helix: -1.82 (0.59), residues: 68 sheet: 0.76 (0.36), residues: 198 loop : -0.21 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 144 TYR 0.026 0.002 TYR C 191 PHE 0.012 0.001 PHE A 91 TRP 0.007 0.001 TRP C 155 HIS 0.003 0.001 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.23 ( 6558) covalent geometry : angle 0.54593 / 0.28 ( 8935) hydrogen bonds : bond 0.03632 / 2.40 ( 174) hydrogen bonds : angle 5.49989 / 3.90 ( 510) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.250 Fit side-chains REVERT: C 148 MET cc_start: 0.9245 (OUTLIER) cc_final: 0.8478 (pp-130) REVERT: C 205 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7614 (mm-30) REVERT: C 220 ASP cc_start: 0.8822 (p0) cc_final: 0.8471 (p0) outliers start: 12 outliers final: 7 residues processed: 99 average time/residue: 0.5892 time to fit residues: 61.1262 Evaluate side-chains 104 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 205 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [73, 67, 70, 22, 26, 23, 46, 48, 53, 39, 21] chunk 73 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 70 optimal weight: 0.1980 chunk 22 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 219 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 = 0.3013 r_free = 0.3013 target = 0.084254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.069067 restraints weight = 9497.157| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.08 r_work: 0.2678 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6558 Z= 0.156 Angle : 0.507 8.545 8935 Z= 0.262 Chirality : 0.044 0.212 1007 Planarity : 0.004 0.030 1156 Dihedral : 5.290 44.663 896 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.85 % Allowed : 14.08 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.14 (0.28), residues: 812 helix: -1.74 (0.59), residues: 68 sheet: 0.78 (0.36), residues: 198 loop : -0.15 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 65 TYR 0.023 0.001 TYR C 191 PHE 0.011 0.001 PHE A 91 TRP 0.008 0.001 TRP B 79 HIS 0.002 0.001 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 6558) covalent geometry : angle 0.50659 / 0.26 ( 8935) hydrogen bonds : bond 0.03256 / 2.16 ( 174) hydrogen bonds : angle 5.34548 / 3.79 ( 510) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.252 Fit side-chains REVERT: A 19 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8081 (pm20) REVERT: C 43 MET cc_start: 0.9507 (mmm) cc_final: 0.9073 (mmm) REVERT: C 148 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8399 (pp-130) REVERT: C 205 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7649 (mm-30) REVERT: D 50 SER cc_start: 0.9117 (p) cc_final: 0.8869 (p) outliers start: 13 outliers final: 6 residues processed: 103 average time/residue: 0.5904 time to fit residues: 63.5755 Evaluate side-chains 104 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 205 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [16, 38, 62, 8, 15, 63, 6, 35, 40, 77, 30] chunk 16 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 15 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 35 optimal weight: 0.0270 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 overall best weight: 5.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 219 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 = 0.2995 r_free = 0.2995 target = 0.083125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.067883 restraints weight = 9677.396| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 2.08 r_work: 0.2655 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6558 Z= 0.220 Angle : 0.537 8.429 8935 Z= 0.278 Chirality : 0.045 0.219 1007 Planarity : 0.004 0.030 1156 Dihedral : 5.437 42.824 896 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.56 % Allowed : 14.65 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.18 (0.28), residues: 812 helix: -1.77 (0.59), residues: 68 sheet: 0.77 (0.36), residues: 198 loop : -0.20 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 65 TYR 0.027 0.002 TYR C 191 PHE 0.012 0.001 PHE A 91 TRP 0.007 0.001 TRP A 249 HIS 0.003 0.001 HIS C 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.22 ( 6558) covalent geometry : angle 0.53748 / 0.28 ( 8935) hydrogen bonds : bond 0.03549 / 2.35 ( 174) hydrogen bonds : angle 5.45070 / 3.87 ( 510) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2667.23 seconds wall clock time: 46 minutes 10.83 seconds (2770.83 seconds total)