Starting phenix.real_space_refine on Wed Aug 5 09:07:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z7r_73878/08_2026/9z7r_73878.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z7r_73878/08_2026/9z7r_73878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9z7r_73878/08_2026/9z7r_73878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z7r_73878/08_2026/9z7r_73878.map" model { file = "/net/cci-nas-00/data/ceres_data/9z7r_73878/08_2026/9z7r_73878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z7r_73878/08_2026/9z7r_73878.cif" } resolution = 3.5 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= 0.001 sd= 0.031 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 Mg 2 5.21 5 S 21 5.16 5 C 2983 2.51 5 N 726 2.21 5 O 788 1.98 5 H 4479 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8999 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 4364 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 288} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'TYR:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "B" Number of atoms: 4625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4625 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 301} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2, 'water': 8} Link IDs: {None: 9} Time building chain proxies: 1.80, per 1000 atoms: 0.20 Number of scatterers: 8999 At special positions: 0 Unit cell: (64.35, 104.775, 70.125, 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) S 21 16.00 Mg 2 11.99 O 788 8.00 N 726 7.00 C 2983 6.00 H 4479 1.00 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: 0.56 Conformation dependent library (CDL) restraints added in 316.1 milliseconds 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1108 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 0 sheets defined 86.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 8 through 43 removed outlier: 3.916A pdb=" N SER A 21 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLY A 26 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A 27 " --> pdb=" O PHE A 23 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE A 28 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A 29 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 51 through 55 removed outlier: 3.854A pdb=" N LEU A 54 " --> pdb=" O HIS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 80 removed outlier: 3.568A pdb=" N TRP A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 Processing helix chain 'A' and resid 89 through 104 removed outlier: 3.986A pdb=" N VAL A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 138 through 146 removed outlier: 3.563A pdb=" N HIS A 144 " --> pdb=" O ASN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 168 removed outlier: 3.675A pdb=" N PHE A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 178 through 208 removed outlier: 3.883A pdb=" N ILE A 182 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 243 removed outlier: 3.971A pdb=" N TRP A 219 " --> pdb=" O HIS A 215 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP A 241 " --> pdb=" O ASN A 237 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE A 242 " --> pdb=" O ARG A 238 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 269 Proline residue: A 250 - end of helix Processing helix chain 'A' and resid 275 through 298 Processing helix chain 'B' and resid 7 through 43 removed outlier: 3.541A pdb=" N TYR B 11 " --> pdb=" O LYS B 7 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE B 28 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE B 29 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 51 through 55 removed outlier: 3.757A pdb=" N LEU B 54 " --> pdb=" O HIS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 77 removed outlier: 3.785A pdb=" N TRP B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 90 through 104 removed outlier: 3.785A pdb=" N LEU B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 130 Processing helix chain 'B' and resid 138 through 148 Processing helix chain 'B' and resid 148 through 168 Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 178 through 199 removed outlier: 3.881A pdb=" N ILE B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY B 189 " --> pdb=" O CYS B 185 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 243 removed outlier: 4.001A pdb=" N TRP B 219 " --> pdb=" O HIS B 215 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE B 242 " --> pdb=" O ARG B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 268 Proline residue: B 250 - end of helix Processing helix chain 'B' and resid 275 through 299 Processing helix chain 'B' and resid 308 through 318 removed outlier: 4.047A pdb=" N LYS B 315 " --> pdb=" O VAL B 311 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) 364 hydrogen bonds defined for protein. 1074 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: 1.79 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 4469 1.02 - 1.22: 14 1.22 - 1.41: 1840 1.41 - 1.61: 2736 1.61 - 1.81: 32 Bond restraints: 9091 Sorted by residual: bond pdb=" C GLY A 89 " pdb=" O GLY A 89 " ideal model delta sigma weight residual 1.237 1.199 0.037 1.07e-02 8.73e+03 1.22e+01 bond pdb=" CA LEU A 91 " pdb=" C LEU A 91 " ideal model delta sigma weight residual 1.523 1.565 -0.042 1.35e-02 5.49e+03 9.50e+00 bond pdb=" N LEU A 84 " pdb=" CA LEU A 84 " ideal model delta sigma weight residual 1.456 1.429 0.028 1.28e-02 6.10e+03 4.72e+00 bond pdb=" C ALA A 90 " pdb=" O ALA A 90 " ideal model delta sigma weight residual 1.236 1.214 0.022 1.25e-02 6.40e+03 3.11e+00 bond pdb=" C THR A 83 " pdb=" O THR A 83 " ideal model delta sigma weight residual 1.236 1.213 0.023 1.29e-02 6.01e+03 3.09e+00 ... (remaining 9086 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 15532 1.18 - 2.36: 856 2.36 - 3.54: 33 3.54 - 4.72: 13 4.72 - 5.90: 6 Bond angle restraints: 16440 Sorted by residual: angle pdb=" C GLY A 89 " pdb=" N ALA A 90 " pdb=" CA ALA A 90 " ideal model delta sigma weight residual 120.28 125.39 -5.11 1.44e+00 4.82e-01 1.26e+01 angle pdb=" CA GLY A 89 " pdb=" C GLY A 89 " pdb=" N ALA A 90 " ideal model delta sigma weight residual 118.17 122.18 -4.01 1.26e+00 6.30e-01 1.01e+01 angle pdb=" CA LEU A 91 " pdb=" C LEU A 91 " pdb=" N SER A 92 " ideal model delta sigma weight residual 117.22 120.77 -3.55 1.17e+00 7.31e-01 9.20e+00 angle pdb=" O GLY A 89 " pdb=" C GLY A 89 " pdb=" N ALA A 90 " ideal model delta sigma weight residual 122.73 119.77 2.96 1.12e+00 7.97e-01 6.99e+00 angle pdb=" C LEU A 84 " pdb=" N VAL A 85 " pdb=" CA VAL A 85 " ideal model delta sigma weight residual 121.65 117.85 3.80 1.48e+00 4.57e-01 6.58e+00 ... (remaining 16435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 3908 16.97 - 33.94: 237 33.94 - 50.92: 72 50.92 - 67.89: 55 67.89 - 84.86: 9 Dihedral angle restraints: 4281 sinusoidal: 2207 harmonic: 2074 Sorted by residual: dihedral pdb=" CA ILE B 166 " pdb=" C ILE B 166 " pdb=" N PHE B 167 " pdb=" CA PHE B 167 " ideal model delta harmonic sigma weight residual -180.00 -163.73 -16.27 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA GLN B 272 " pdb=" C GLN B 272 " pdb=" N ASP B 273 " pdb=" CA ASP B 273 " ideal model delta harmonic sigma weight residual -180.00 -163.83 -16.17 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA ILE A 166 " pdb=" C ILE A 166 " pdb=" N PHE A 167 " pdb=" CA PHE A 167 " ideal model delta harmonic sigma weight residual 180.00 -164.69 -15.31 0 5.00e+00 4.00e-02 9.37e+00 ... (remaining 4278 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 426 0.024 - 0.047: 210 0.047 - 0.070: 95 0.070 - 0.094: 30 0.094 - 0.117: 11 Chirality restraints: 772 Sorted by residual: chirality pdb=" CA LEU A 88 " pdb=" N LEU A 88 " pdb=" C LEU A 88 " pdb=" CB LEU A 88 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.43e-01 chirality pdb=" CA ALA A 82 " pdb=" N ALA A 82 " pdb=" C ALA A 82 " pdb=" CB ALA A 82 " both_signs ideal model delta sigma weight residual False 2.48 2.37 0.12 2.00e-01 2.50e+01 3.43e-01 chirality pdb=" CA THR A 249 " pdb=" N THR A 249 " pdb=" C THR A 249 " pdb=" CB THR A 249 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.40e-01 ... (remaining 769 not shown) Planarity restraints: 1335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 84 " -0.023 2.00e-02 2.50e+03 4.45e-02 1.98e+01 pdb=" N VAL A 85 " 0.076 2.00e-02 2.50e+03 pdb=" CA VAL A 85 " -0.019 2.00e-02 2.50e+03 pdb=" H VAL A 85 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 88 " 0.019 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C LEU A 88 " -0.066 2.00e-02 2.50e+03 pdb=" O LEU A 88 " 0.024 2.00e-02 2.50e+03 pdb=" N GLY A 89 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 82 " 0.015 2.00e-02 2.50e+03 2.72e-02 7.38e+00 pdb=" N THR A 83 " -0.047 2.00e-02 2.50e+03 pdb=" CA THR A 83 " 0.012 2.00e-02 2.50e+03 pdb=" H THR A 83 " 0.020 2.00e-02 2.50e+03 ... (remaining 1332 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 503 2.21 - 2.81: 18520 2.81 - 3.40: 25043 3.40 - 4.00: 30714 4.00 - 4.60: 48359 Nonbonded interactions: 123139 Sorted by model distance: nonbonded pdb=" H GLY B 47 " pdb=" OD2 ASP B 241 " model vdw 1.609 2.450 nonbonded pdb=" O GLN B 175 " pdb=" HG1 THR B 176 " model vdw 1.673 2.450 nonbonded pdb=" HG SER A 92 " pdb=" O HOH A 502 " model vdw 1.704 2.450 nonbonded pdb=" O LEU A 179 " pdb=" HG1 THR A 183 " model vdw 1.718 2.450 nonbonded pdb=" HG SER B 20 " pdb=" O GLY B 69 " model vdw 1.747 2.450 ... (remaining 123134 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 'A' and (resid 6 through 73 or (resid 74 through 75 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 76 through 128 \ or (resid 129 and (name N or name CA or name C or name O or name CB or name CG \ or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 \ or name HB3 or name HD1 or name HD2 or name HE1)) or resid 130 through 131 or ( \ resid 132 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 133 or (resid 134 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 135 or (resid 136 through 137 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 1 \ 38 through 147 or (resid 148 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 149 through 191 or (resid 192 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 193 or \ (resid 194 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 195 through 206 or resid 209 through 212 or (resid 213 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 214 through 263 or (resid 264 and (name N or name CA or name C or name O or name \ CB or name OG or name H or name HA )) or resid 265 through 301 or (resid 302 an \ d (name N or name CA or name C or name O or name CB or name CG1 or name CG2)))) selection = (chain 'B' and (resid 6 or (resid 7 through 8 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 9 through 18 or (resid 19 t \ hrough 20 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 21 through 31 or (resid 32 through 33 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 34 through 35 or ( \ resid 36 through 37 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 38 through 39 or (resid 40 through 41 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 42 or (r \ esid 43 through 45 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 46 through 47 or (resid 48 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 49 through 54 or (re \ sid 55 through 56 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 57 through 63 or (resid 64 and (name N or name CA or na \ me C or name O or name CB )) or resid 65 through 102 or (resid 103 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 104 th \ rough 138 or (resid 139 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 140 through 152 or (resid 153 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 154 through \ 204 or (resid 205 through 206 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 209 through 211 or (resid 212 through 213 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 214 or (resid 215 and (name N or name CA or name C or name O or name CB or \ name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or \ name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 216 through \ 245 or (resid 246 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 247 through 302)) } 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 group one per residue 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: 1.220 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: 0.070 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.280 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4612 Z= 0.162 Angle : 0.519 5.896 6288 Z= 0.316 Chirality : 0.035 0.117 772 Planarity : 0.003 0.038 765 Dihedral : 11.351 84.860 1541 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.36), residues: 604 helix: 2.30 (0.25), residues: 467 sheet: None (None), residues: 0 loop : -1.04 (0.51), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 107 TYR 0.014 0.001 TYR A 77 PHE 0.015 0.001 PHE A 10 TRP 0.013 0.001 TRP B 271 HIS 0.004 0.001 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.16 ( 4612) covalent geometry : angle 0.51852 / 0.32 ( 6288) hydrogen bonds : bond 0.13430 / 9.42 ( 364) hydrogen bonds : angle 5.69745 / 4.44 ( 1074) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 7 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue SER 264 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.5910 (tpp) cc_final: 0.5648 (tpp) REVERT: B 222 LEU cc_start: 0.8560 (tp) cc_final: 0.8338 (tt) REVERT: B 273 ASP cc_start: 0.7683 (t0) cc_final: 0.7369 (t0) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1607 time to fit residues: 21.4165 Evaluate side-chains 84 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 GLN B 111 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.166584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.134249 restraints weight = 15693.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.141012 restraints weight = 7206.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.145363 restraints weight = 4596.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.148125 restraints weight = 3454.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.149955 restraints weight = 2834.264| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4612 Z= 0.132 Angle : 0.473 5.325 6288 Z= 0.265 Chirality : 0.035 0.143 772 Planarity : 0.003 0.035 765 Dihedral : 3.546 15.850 635 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.22 % Allowed : 6.72 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.69 (0.36), residues: 604 helix: 2.46 (0.25), residues: 469 sheet: None (None), residues: 0 loop : -0.74 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 37 TYR 0.008 0.001 TYR A 253 PHE 0.015 0.001 PHE A 10 TRP 0.008 0.001 TRP B 271 HIS 0.004 0.001 HIS A 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 4612) covalent geometry : angle 0.47253 / 0.27 ( 6288) hydrogen bonds : bond 0.04067 / 2.88 ( 364) hydrogen bonds : angle 4.47137 / 3.48 ( 1074) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 7 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue SER 264 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ILE cc_start: 0.8500 (tt) cc_final: 0.8194 (mt) REVERT: B 44 MET cc_start: 0.6199 (tpp) cc_final: 0.5994 (tpp) REVERT: B 222 LEU cc_start: 0.8607 (tp) cc_final: 0.8353 (tt) REVERT: B 273 ASP cc_start: 0.7885 (t0) cc_final: 0.7518 (t0) outliers start: 1 outliers final: 1 residues processed: 92 average time/residue: 0.1477 time to fit residues: 17.6475 Evaluate side-chains 87 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.167580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.135207 restraints weight = 15902.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.142188 restraints weight = 7072.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.146245 restraints weight = 4422.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.149283 restraints weight = 3346.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.150926 restraints weight = 2720.983| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4612 Z= 0.119 Angle : 0.448 5.373 6288 Z= 0.250 Chirality : 0.035 0.129 772 Planarity : 0.003 0.049 765 Dihedral : 3.495 15.233 635 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.08 % Allowed : 7.38 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.36), residues: 604 helix: 2.56 (0.25), residues: 468 sheet: None (None), residues: 0 loop : -0.79 (0.56), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 238 TYR 0.007 0.001 TYR A 253 PHE 0.012 0.001 PHE B 151 TRP 0.007 0.001 TRP B 271 HIS 0.004 0.001 HIS B 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 4612) covalent geometry : angle 0.44780 / 0.25 ( 6288) hydrogen bonds : bond 0.03669 / 2.59 ( 364) hydrogen bonds : angle 4.19316 / 3.27 ( 1074) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 7 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue SER 264 is missing expected H atoms. Skipping. Evaluate side-chains 96 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ILE cc_start: 0.8502 (tt) cc_final: 0.8197 (mt) REVERT: A 288 THR cc_start: 0.8745 (t) cc_final: 0.8282 (m) REVERT: B 222 LEU cc_start: 0.8576 (tp) cc_final: 0.8316 (tt) REVERT: B 273 ASP cc_start: 0.7785 (t0) cc_final: 0.7442 (t0) outliers start: 5 outliers final: 2 residues processed: 93 average time/residue: 0.1326 time to fit residues: 16.3639 Evaluate side-chains 87 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain B residue 196 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.164153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.132517 restraints weight = 16161.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.139202 restraints weight = 7222.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.143497 restraints weight = 4540.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.146152 restraints weight = 3376.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.148092 restraints weight = 2770.322| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4612 Z= 0.131 Angle : 0.454 5.326 6288 Z= 0.253 Chirality : 0.035 0.146 772 Planarity : 0.003 0.030 765 Dihedral : 3.491 14.953 635 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.30 % Allowed : 7.81 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.00 (0.37), residues: 604 helix: 2.83 (0.25), residues: 459 sheet: None (None), residues: 0 loop : -0.98 (0.54), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 238 TYR 0.010 0.001 TYR A 77 PHE 0.011 0.001 PHE A 10 TRP 0.007 0.001 TRP B 271 HIS 0.003 0.001 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 4612) covalent geometry : angle 0.45415 / 0.25 ( 6288) hydrogen bonds : bond 0.03589 / 2.53 ( 364) hydrogen bonds : angle 4.11688 / 3.21 ( 1074) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 7 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue SER 264 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ILE cc_start: 0.8499 (tt) cc_final: 0.8184 (mt) REVERT: B 142 MET cc_start: 0.8523 (tmm) cc_final: 0.8281 (tpp) REVERT: B 273 ASP cc_start: 0.7780 (t0) cc_final: 0.7461 (t0) outliers start: 6 outliers final: 5 residues processed: 96 average time/residue: 0.1377 time to fit residues: 17.2588 Evaluate side-chains 88 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 267 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 HIS ** 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 = 0.3825 r_free = 0.3825 target = 0.161822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.130007 restraints weight = 16228.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.136722 restraints weight = 7277.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.141032 restraints weight = 4583.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.143841 restraints weight = 3404.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.145627 restraints weight = 2782.509| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4612 Z= 0.162 Angle : 0.479 5.375 6288 Z= 0.269 Chirality : 0.036 0.162 772 Planarity : 0.003 0.030 765 Dihedral : 3.558 14.755 635 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.52 % Allowed : 10.41 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.92 (0.37), residues: 604 helix: 2.79 (0.25), residues: 459 sheet: None (None), residues: 0 loop : -1.04 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 37 TYR 0.010 0.001 TYR B 235 PHE 0.011 0.001 PHE A 10 TRP 0.006 0.001 TRP B 271 HIS 0.004 0.001 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 4612) covalent geometry : angle 0.47907 / 0.27 ( 6288) hydrogen bonds : bond 0.03765 / 2.65 ( 364) hydrogen bonds : angle 4.13126 / 3.22 ( 1074) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 7 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue SER 264 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ILE cc_start: 0.8492 (tt) cc_final: 0.8187 (mt) REVERT: B 142 MET cc_start: 0.8590 (tmm) cc_final: 0.8298 (tpp) REVERT: B 273 ASP cc_start: 0.7908 (t0) cc_final: 0.7566 (t0) outliers start: 7 outliers final: 7 residues processed: 94 average time/residue: 0.1364 time to fit residues: 16.9790 Evaluate side-chains 95 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 267 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 21 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 20 optimal weight: 0.0000 chunk 57 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 HIS ** 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 = 0.3866 r_free = 0.3866 target = 0.165416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.133506 restraints weight = 16069.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.140408 restraints weight = 7160.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.144799 restraints weight = 4484.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.147562 restraints weight = 3332.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.149523 restraints weight = 2724.348| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4612 Z= 0.099 Angle : 0.433 5.213 6288 Z= 0.236 Chirality : 0.034 0.126 772 Planarity : 0.003 0.027 765 Dihedral : 3.448 14.581 635 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.08 % Allowed : 11.28 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.13 (0.37), residues: 604 helix: 2.97 (0.25), residues: 458 sheet: None (None), residues: 0 loop : -1.06 (0.54), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 238 TYR 0.008 0.001 TYR A 77 PHE 0.009 0.001 PHE A 10 TRP 0.009 0.001 TRP A 59 HIS 0.003 0.001 HIS A 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 ( 4612) covalent geometry : angle 0.43253 / 0.24 ( 6288) hydrogen bonds : bond 0.03336 / 2.34 ( 364) hydrogen bonds : angle 3.94956 / 3.09 ( 1074) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 7 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue SER 264 is missing expected H atoms. Skipping. Evaluate side-chains 95 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ILE cc_start: 0.8446 (tt) cc_final: 0.8142 (mt) REVERT: B 273 ASP cc_start: 0.7800 (t0) cc_final: 0.7487 (t0) outliers start: 5 outliers final: 4 residues processed: 93 average time/residue: 0.1460 time to fit residues: 17.8314 Evaluate side-chains 90 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 196 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 59 optimal weight: 0.0670 chunk 37 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 HIS ** 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 = 0.3865 r_free = 0.3865 target = 0.165075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.133486 restraints weight = 16174.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.140294 restraints weight = 7200.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.144617 restraints weight = 4509.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.147299 restraints weight = 3346.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.149231 restraints weight = 2737.870| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4612 Z= 0.108 Angle : 0.444 5.255 6288 Z= 0.243 Chirality : 0.035 0.178 772 Planarity : 0.003 0.024 765 Dihedral : 3.414 14.357 635 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.52 % Allowed : 11.71 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.14 (0.37), residues: 604 helix: 2.96 (0.25), residues: 460 sheet: None (None), residues: 0 loop : -1.04 (0.55), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 238 TYR 0.010 0.001 TYR A 77 PHE 0.009 0.001 PHE B 151 TRP 0.007 0.001 TRP B 271 HIS 0.003 0.001 HIS A 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 4612) covalent geometry : angle 0.44442 / 0.24 ( 6288) hydrogen bonds : bond 0.03287 / 2.31 ( 364) hydrogen bonds : angle 3.91874 / 3.06 ( 1074) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 7 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue SER 264 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ILE cc_start: 0.8443 (tt) cc_final: 0.8137 (mt) REVERT: B 273 ASP cc_start: 0.7797 (t0) cc_final: 0.7481 (t0) outliers start: 7 outliers final: 6 residues processed: 91 average time/residue: 0.1453 time to fit residues: 17.4102 Evaluate side-chains 91 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 196 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 57 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 HIS ** 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 = 0.3849 r_free = 0.3849 target = 0.163844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.132307 restraints weight = 16084.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.139070 restraints weight = 7253.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.143326 restraints weight = 4558.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.146025 restraints weight = 3393.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.147875 restraints weight = 2769.589| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4612 Z= 0.125 Angle : 0.450 5.258 6288 Z= 0.248 Chirality : 0.035 0.168 772 Planarity : 0.003 0.024 765 Dihedral : 3.417 14.426 635 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.74 % Allowed : 11.50 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.13 (0.37), residues: 604 helix: 2.95 (0.25), residues: 460 sheet: None (None), residues: 0 loop : -1.03 (0.55), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 37 TYR 0.009 0.001 TYR A 77 PHE 0.012 0.001 PHE B 151 TRP 0.007 0.001 TRP B 271 HIS 0.003 0.001 HIS A 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 4612) covalent geometry : angle 0.45009 / 0.25 ( 6288) hydrogen bonds : bond 0.03376 / 2.37 ( 364) hydrogen bonds : angle 3.93682 / 3.07 ( 1074) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 7 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue SER 264 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ILE cc_start: 0.8434 (tt) cc_final: 0.8118 (mt) REVERT: B 273 ASP cc_start: 0.7829 (t0) cc_final: 0.7499 (t0) outliers start: 8 outliers final: 7 residues processed: 94 average time/residue: 0.1329 time to fit residues: 16.3833 Evaluate side-chains 92 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 196 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 3 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 53 optimal weight: 0.0970 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 HIS ** 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 = 0.3865 r_free = 0.3865 target = 0.165252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.133419 restraints weight = 16159.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.140286 restraints weight = 7212.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.144620 restraints weight = 4535.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.147215 restraints weight = 3367.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.149031 restraints weight = 2771.847| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4612 Z= 0.103 Angle : 0.440 5.204 6288 Z= 0.241 Chirality : 0.035 0.180 772 Planarity : 0.003 0.023 765 Dihedral : 3.401 15.656 635 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.52 % Allowed : 11.71 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.19 (0.37), residues: 604 helix: 2.99 (0.25), residues: 460 sheet: None (None), residues: 0 loop : -1.03 (0.55), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 37 TYR 0.017 0.001 TYR B 235 PHE 0.013 0.001 PHE B 151 TRP 0.007 0.001 TRP B 271 HIS 0.003 0.001 HIS A 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 4612) covalent geometry : angle 0.43965 / 0.24 ( 6288) hydrogen bonds : bond 0.03209 / 2.25 ( 364) hydrogen bonds : angle 3.88692 / 3.03 ( 1074) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 7 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue SER 264 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ILE cc_start: 0.8402 (tt) cc_final: 0.8097 (mt) REVERT: B 273 ASP cc_start: 0.7771 (t0) cc_final: 0.7454 (t0) outliers start: 7 outliers final: 7 residues processed: 90 average time/residue: 0.1447 time to fit residues: 17.0494 Evaluate side-chains 90 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 37 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 HIS ** 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 = 0.3856 r_free = 0.3856 target = 0.164552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.132596 restraints weight = 16023.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.139254 restraints weight = 7245.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.143663 restraints weight = 4588.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.146385 restraints weight = 3408.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.148315 restraints weight = 2785.306| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4612 Z= 0.111 Angle : 0.448 5.223 6288 Z= 0.246 Chirality : 0.035 0.183 772 Planarity : 0.003 0.023 765 Dihedral : 3.391 15.311 635 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.52 % Allowed : 12.15 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.18 (0.37), residues: 604 helix: 2.97 (0.25), residues: 461 sheet: None (None), residues: 0 loop : -0.99 (0.55), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 37 TYR 0.015 0.001 TYR B 235 PHE 0.012 0.001 PHE B 151 TRP 0.007 0.001 TRP B 271 HIS 0.006 0.001 HIS A 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 4612) covalent geometry : angle 0.44786 / 0.25 ( 6288) hydrogen bonds : bond 0.03226 / 2.26 ( 364) hydrogen bonds : angle 3.90321 / 3.04 ( 1074) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 7 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue SER 264 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ILE cc_start: 0.8378 (tt) cc_final: 0.8065 (mt) REVERT: B 273 ASP cc_start: 0.7784 (t0) cc_final: 0.7466 (t0) outliers start: 7 outliers final: 7 residues processed: 89 average time/residue: 0.1409 time to fit residues: 16.3406 Evaluate side-chains 89 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 10 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 HIS ** 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 = 0.3866 r_free = 0.3866 target = 0.165263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.133402 restraints weight = 15863.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.140156 restraints weight = 7207.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.144530 restraints weight = 4565.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.147298 restraints weight = 3395.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.148987 restraints weight = 2768.058| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4612 Z= 0.112 Angle : 0.444 5.203 6288 Z= 0.244 Chirality : 0.035 0.162 772 Planarity : 0.003 0.023 765 Dihedral : 3.383 14.991 635 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.52 % Allowed : 11.93 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.23 (0.37), residues: 604 helix: 2.99 (0.25), residues: 461 sheet: None (None), residues: 0 loop : -0.93 (0.57), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 37 TYR 0.014 0.001 TYR B 235 PHE 0.012 0.001 PHE B 151 TRP 0.007 0.001 TRP A 271 HIS 0.006 0.001 HIS A 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 4612) covalent geometry : angle 0.44449 / 0.24 ( 6288) hydrogen bonds : bond 0.03202 / 2.24 ( 364) hydrogen bonds : angle 3.88833 / 3.03 ( 1074) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1767.56 seconds wall clock time: 30 minutes 45.86 seconds (1845.86 seconds total)