Starting phenix.real_space_refine on Mon Nov 17 17:30:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r0c_14221/11_2025/7r0c_14221.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r0c_14221/11_2025/7r0c_14221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r0c_14221/11_2025/7r0c_14221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r0c_14221/11_2025/7r0c_14221.map" model { file = "/net/cci-nas-00/data/ceres_data/7r0c_14221/11_2025/7r0c_14221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r0c_14221/11_2025/7r0c_14221.cif" } resolution = 4.73 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= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 39 5.16 5 C 4365 2.51 5 N 1158 2.21 5 O 1248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6816 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2181 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 15, 'TRANS': 268} Chain breaks: 4 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 3, 'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 2810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2810 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 324} Chain breaks: 1 Chain: "D" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1750 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 220} Chain breaks: 1 Time building chain proxies: 1.84, per 1000 atoms: 0.27 Number of scatterers: 6816 At special positions: 0 Unit cell: (83.2, 99.84, 139.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 6 15.00 O 1248 8.00 N 1158 7.00 C 4365 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 1 " - pdb=" SG CYS B 6 " distance=2.03 Simple disulfide: pdb=" SG CYS D 26 " - pdb=" SG CYS D 91 " distance=2.03 Simple disulfide: pdb=" SG CYS D 103 " - pdb=" SG CYS D 170 " distance=2.03 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 222 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 428.8 milliseconds 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1660 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 11 sheets defined 29.0% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 33 through 69 Processing helix chain 'A' and resid 72 through 103 removed outlier: 3.924A pdb=" N ILE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Proline residue: A 95 - end of helix Processing helix chain 'A' and resid 109 through 140 removed outlier: 4.001A pdb=" N ARG A 113 " --> pdb=" O ASP A 109 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLY A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 171 Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.582A pdb=" N PHE A 178 " --> pdb=" O GLN A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 228 removed outlier: 5.019A pdb=" N ALA A 216 " --> pdb=" O MET A 212 " (cutoff:3.500A) Proline residue: A 217 - end of helix removed outlier: 3.938A pdb=" N ILE A 228 " --> pdb=" O CYS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 296 Proline residue: A 286 - end of helix Processing helix chain 'A' and resid 304 through 311 removed outlier: 3.583A pdb=" N VAL A 308 " --> pdb=" O GLY A 304 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 310 " --> pdb=" O PRO A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 319 removed outlier: 5.570A pdb=" N SER A 315 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASN A 317 " --> pdb=" O ALA A 314 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS A 319 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 329 removed outlier: 3.574A pdb=" N PHE A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 Processing helix chain 'C' and resid 98 through 109 Processing helix chain 'C' and resid 159 through 161 No H-bonds generated for 'chain 'C' and resid 159 through 161' Processing helix chain 'C' and resid 277 through 282 removed outlier: 3.663A pdb=" N ASN C 280 " --> pdb=" O PHE C 277 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG C 282 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 86 removed outlier: 3.529A pdb=" N PHE D 86 " --> pdb=" O PRO D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 157 Processing helix chain 'D' and resid 188 through 191 Processing helix chain 'D' and resid 213 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 363 Processing sheet with id=AA2, first strand: chain 'C' and resid 26 through 28 removed outlier: 6.102A pdb=" N PHE C 27 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LYS C 170 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 10.265A pdb=" N VAL C 142 " --> pdb=" O LYS C 170 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL C 53 " --> pdb=" O SER C 86 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N PHE C 61 " --> pdb=" O ASP C 78 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASP C 78 " --> pdb=" O PHE C 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AA4, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 188 Processing sheet with id=AA6, first strand: chain 'C' and resid 207 through 208 removed outlier: 4.128A pdb=" N TYR C 321 " --> pdb=" O PHE C 349 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU C 351 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 9.194A pdb=" N VAL C 319 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE C 318 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA C 239 " --> pdb=" O ILE C 318 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER C 320 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N GLN C 237 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LYS C 322 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL C 235 " --> pdb=" O LYS C 322 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS C 324 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE C 233 " --> pdb=" O LYS C 324 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LYS C 326 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE C 231 " --> pdb=" O LYS C 326 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL C 328 " --> pdb=" O LYS C 229 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE C 231 " --> pdb=" O GLU C 257 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU C 257 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE C 233 " --> pdb=" O MET C 255 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N MET C 255 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C 235 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN C 237 " --> pdb=" O CYS C 251 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N CYS C 251 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 239 " --> pdb=" O TYR C 249 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 7 through 9 Processing sheet with id=AA8, first strand: chain 'D' and resid 56 through 57 removed outlier: 6.413A pdb=" N TRP D 38 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYR D 52 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL D 36 " --> pdb=" O TYR D 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 129 through 133 Processing sheet with id=AB1, first strand: chain 'D' and resid 136 through 138 removed outlier: 6.376A pdb=" N GLY D 136 " --> pdb=" O THR D 243 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE D 160 " --> pdb=" O SER D 176 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER D 176 " --> pdb=" O ILE D 160 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TRP D 162 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU D 172 " --> pdb=" O ARG D 164 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 136 through 138 removed outlier: 6.376A pdb=" N GLY D 136 " --> pdb=" O THR D 243 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N TYR D 235 " --> pdb=" O ARG D 224 " (cutoff:3.500A) 305 hydrogen bonds defined for protein. 828 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.80 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1179 1.32 - 1.45: 1796 1.45 - 1.57: 3926 1.57 - 1.69: 22 1.69 - 1.81: 52 Bond restraints: 6975 Sorted by residual: bond pdb=" OG1 TPO A 360 " pdb=" P TPO A 360 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" OG1 TPO A 359 " pdb=" P TPO A 359 " ideal model delta sigma weight residual 1.717 1.620 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" O1P TPO A 359 " pdb=" P TPO A 359 " ideal model delta sigma weight residual 1.525 1.610 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" O1P TPO A 360 " pdb=" P TPO A 360 " ideal model delta sigma weight residual 1.525 1.609 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" O3P TPO A 359 " pdb=" P TPO A 359 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.70e+01 ... (remaining 6970 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 9271 2.56 - 5.11: 193 5.11 - 7.67: 27 7.67 - 10.23: 6 10.23 - 12.78: 1 Bond angle restraints: 9498 Sorted by residual: angle pdb=" N ILE A 74 " pdb=" CA ILE A 74 " pdb=" C ILE A 74 " ideal model delta sigma weight residual 110.42 101.79 8.63 9.60e-01 1.09e+00 8.08e+01 angle pdb=" N VAL A 76 " pdb=" CA VAL A 76 " pdb=" C VAL A 76 " ideal model delta sigma weight residual 110.62 104.23 6.39 1.02e+00 9.61e-01 3.93e+01 angle pdb=" N PRO A 73 " pdb=" CA PRO A 73 " pdb=" C PRO A 73 " ideal model delta sigma weight residual 113.84 107.29 6.55 1.30e+00 5.92e-01 2.53e+01 angle pdb=" CA LYS D 202 " pdb=" CB LYS D 202 " pdb=" CG LYS D 202 " ideal model delta sigma weight residual 114.10 122.95 -8.85 2.00e+00 2.50e-01 1.96e+01 angle pdb=" C LEU C 68 " pdb=" N ASP C 69 " pdb=" CA ASP C 69 " ideal model delta sigma weight residual 122.61 129.40 -6.79 1.56e+00 4.11e-01 1.89e+01 ... (remaining 9493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 3812 16.88 - 33.77: 308 33.77 - 50.65: 54 50.65 - 67.54: 9 67.54 - 84.42: 8 Dihedral angle restraints: 4191 sinusoidal: 1628 harmonic: 2563 Sorted by residual: dihedral pdb=" CB CYS A 112 " pdb=" SG CYS A 112 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual -86.00 -141.74 55.74 1 1.00e+01 1.00e-02 4.20e+01 dihedral pdb=" CB CYS B 1 " pdb=" SG CYS B 1 " pdb=" SG CYS B 6 " pdb=" CB CYS B 6 " ideal model delta sinusoidal sigma weight residual 93.00 45.16 47.84 1 1.00e+01 1.00e-02 3.16e+01 dihedral pdb=" CA ARG D 226 " pdb=" C ARG D 226 " pdb=" N GLN D 227 " pdb=" CA GLN D 227 " ideal model delta harmonic sigma weight residual -180.00 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 4188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1040 0.108 - 0.215: 43 0.215 - 0.323: 1 0.323 - 0.430: 1 0.430 - 0.538: 1 Chirality restraints: 1086 Sorted by residual: chirality pdb=" CA ILE A 74 " pdb=" N ILE A 74 " pdb=" C ILE A 74 " pdb=" CB ILE A 74 " both_signs ideal model delta sigma weight residual False 2.43 2.97 -0.54 2.00e-01 2.50e+01 7.24e+00 chirality pdb=" CA TRP A 71 " pdb=" N TRP A 71 " pdb=" C TRP A 71 " pdb=" CB TRP A 71 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA VAL A 76 " pdb=" N VAL A 76 " pdb=" C VAL A 76 " pdb=" CB VAL A 76 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1083 not shown) Planarity restraints: 1191 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 99 " 0.015 2.00e-02 2.50e+03 1.55e-02 6.01e+00 pdb=" CG TRP A 99 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 99 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 99 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 99 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 99 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 99 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 99 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 99 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 99 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 94 " 0.040 5.00e-02 4.00e+02 6.03e-02 5.82e+00 pdb=" N PRO A 95 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 359 " 0.039 5.00e-02 4.00e+02 5.92e-02 5.60e+00 pdb=" N PRO C 360 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 360 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 360 " 0.032 5.00e-02 4.00e+02 ... (remaining 1188 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 180 2.66 - 3.22: 7059 3.22 - 3.78: 11171 3.78 - 4.34: 14375 4.34 - 4.90: 22454 Nonbonded interactions: 55239 Sorted by model distance: nonbonded pdb=" O ASN C 222 " pdb=" N SER C 265 " model vdw 2.100 3.120 nonbonded pdb=" OE1 GLN D 9 " pdb=" OG1 THR D 105 " model vdw 2.127 3.040 nonbonded pdb=" OG1 THR C 56 " pdb=" O ALA C 82 " model vdw 2.190 3.040 nonbonded pdb=" NZ LYS C 11 " pdb=" O ARG C 165 " model vdw 2.207 3.120 nonbonded pdb=" OD1 ASP C 204 " pdb=" OH TYR C 208 " model vdw 2.210 3.040 ... (remaining 55234 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.930 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 6981 Z= 0.290 Angle : 0.909 12.782 9508 Z= 0.523 Chirality : 0.052 0.538 1086 Planarity : 0.005 0.060 1191 Dihedral : 13.187 84.422 2516 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 26.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.14 % Allowed : 0.55 % Favored : 99.32 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.28), residues: 846 helix: -0.59 (0.32), residues: 209 sheet: -0.36 (0.34), residues: 245 loop : -0.59 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 64 TYR 0.020 0.002 TYR A 128 PHE 0.023 0.002 PHE D 228 TRP 0.042 0.003 TRP A 99 HIS 0.006 0.002 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 6975) covalent geometry : angle 0.90892 ( 9498) SS BOND : bond 0.00161 ( 5) SS BOND : angle 1.12490 ( 10) hydrogen bonds : bond 0.15121 ( 301) hydrogen bonds : angle 6.94444 ( 828) Misc. bond : bond 0.10138 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.9158 (ppp) cc_final: 0.8925 (ppp) REVERT: A 288 PHE cc_start: 0.8903 (m-80) cc_final: 0.8337 (m-80) REVERT: C 75 PHE cc_start: 0.6481 (m-80) cc_final: 0.5777 (m-10) REVERT: C 129 LEU cc_start: 0.9301 (mt) cc_final: 0.9092 (mt) REVERT: D 48 LYS cc_start: 0.9181 (tmtt) cc_final: 0.8828 (tmtt) REVERT: D 49 LEU cc_start: 0.8528 (tp) cc_final: 0.8281 (tp) REVERT: D 50 LEU cc_start: 0.8422 (mt) cc_final: 0.7654 (mt) REVERT: D 74 PHE cc_start: 0.9063 (m-80) cc_final: 0.8474 (m-80) REVERT: D 195 THR cc_start: 0.8680 (m) cc_final: 0.8416 (p) REVERT: D 209 MET cc_start: 0.6815 (mpp) cc_final: 0.6420 (mpp) outliers start: 1 outliers final: 1 residues processed: 131 average time/residue: 0.0789 time to fit residues: 13.7518 Evaluate side-chains 95 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN D 9 GLN D 165 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.110167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.088401 restraints weight = 28287.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.091469 restraints weight = 17812.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.093606 restraints weight = 12730.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.095033 restraints weight = 9934.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.096042 restraints weight = 8296.688| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6981 Z= 0.179 Angle : 0.677 7.827 9508 Z= 0.349 Chirality : 0.045 0.175 1086 Planarity : 0.005 0.058 1191 Dihedral : 6.454 74.689 965 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.14 % Allowed : 5.88 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.29), residues: 846 helix: -0.06 (0.34), residues: 211 sheet: -0.28 (0.34), residues: 244 loop : -0.69 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 236 TYR 0.014 0.002 TYR A 128 PHE 0.024 0.002 PHE D 228 TRP 0.026 0.002 TRP A 99 HIS 0.006 0.002 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 6975) covalent geometry : angle 0.67627 ( 9498) SS BOND : bond 0.00161 ( 5) SS BOND : angle 0.96432 ( 10) hydrogen bonds : bond 0.04136 ( 301) hydrogen bonds : angle 6.07802 ( 828) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.9094 (ppp) cc_final: 0.8821 (ppp) REVERT: A 272 MET cc_start: 0.8488 (ppp) cc_final: 0.8261 (ppp) REVERT: A 288 PHE cc_start: 0.8953 (m-80) cc_final: 0.8429 (m-80) REVERT: C 10 LYS cc_start: 0.7749 (pttt) cc_final: 0.7183 (pmtt) REVERT: C 75 PHE cc_start: 0.6577 (m-80) cc_final: 0.5778 (m-10) REVERT: C 172 GLN cc_start: 0.8678 (mp-120) cc_final: 0.8006 (mp-120) REVERT: C 223 ASN cc_start: 0.8090 (m-40) cc_final: 0.7734 (p0) REVERT: C 233 ILE cc_start: 0.9020 (mm) cc_final: 0.8747 (mm) REVERT: C 315 LEU cc_start: 0.9186 (mm) cc_final: 0.8983 (mm) REVERT: D 74 PHE cc_start: 0.9025 (m-80) cc_final: 0.8621 (m-80) REVERT: D 195 THR cc_start: 0.8724 (m) cc_final: 0.8520 (p) REVERT: D 209 MET cc_start: 0.6927 (mpp) cc_final: 0.6360 (mpp) outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 0.0765 time to fit residues: 13.0969 Evaluate side-chains 87 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 53 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 ASN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.107929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.085812 restraints weight = 28455.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.088717 restraints weight = 18027.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.090775 restraints weight = 13004.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.092148 restraints weight = 10241.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.092993 restraints weight = 8625.157| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6981 Z= 0.194 Angle : 0.672 7.553 9508 Z= 0.348 Chirality : 0.045 0.155 1086 Planarity : 0.005 0.059 1191 Dihedral : 6.493 77.659 965 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.29), residues: 846 helix: 0.10 (0.34), residues: 211 sheet: -0.57 (0.34), residues: 256 loop : -0.57 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 193 TYR 0.026 0.002 TYR D 52 PHE 0.025 0.002 PHE D 228 TRP 0.042 0.002 TRP A 99 HIS 0.005 0.002 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 6975) covalent geometry : angle 0.67081 ( 9498) SS BOND : bond 0.00282 ( 5) SS BOND : angle 1.34550 ( 10) hydrogen bonds : bond 0.04256 ( 301) hydrogen bonds : angle 6.00678 ( 828) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.7417 (mmp) cc_final: 0.7099 (mmp) REVERT: A 133 MET cc_start: 0.9016 (ppp) cc_final: 0.8757 (ppp) REVERT: A 276 ILE cc_start: 0.9343 (pt) cc_final: 0.8827 (pt) REVERT: A 288 PHE cc_start: 0.8835 (m-80) cc_final: 0.8432 (m-80) REVERT: C 172 GLN cc_start: 0.8669 (mp-120) cc_final: 0.8187 (mp-120) REVERT: C 223 ASN cc_start: 0.8140 (m-40) cc_final: 0.7868 (p0) REVERT: D 48 LYS cc_start: 0.8848 (tmtt) cc_final: 0.8565 (tmtt) REVERT: D 49 LEU cc_start: 0.8574 (tp) cc_final: 0.8194 (tp) REVERT: D 50 LEU cc_start: 0.8799 (mt) cc_final: 0.7991 (mm) REVERT: D 65 PHE cc_start: 0.8274 (m-10) cc_final: 0.7926 (m-80) REVERT: D 74 PHE cc_start: 0.8883 (m-80) cc_final: 0.8500 (m-80) REVERT: D 195 THR cc_start: 0.8782 (m) cc_final: 0.8537 (p) REVERT: D 209 MET cc_start: 0.7082 (mpp) cc_final: 0.6475 (mmm) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.0728 time to fit residues: 11.9591 Evaluate side-chains 87 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 0.0770 chunk 84 optimal weight: 0.4980 chunk 83 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 16 optimal weight: 0.0570 chunk 15 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 ASN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.114444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.092463 restraints weight = 28882.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.095751 restraints weight = 17664.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.097991 restraints weight = 12426.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.099478 restraints weight = 9583.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.100601 restraints weight = 7924.066| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6981 Z= 0.119 Angle : 0.632 8.512 9508 Z= 0.317 Chirality : 0.045 0.164 1086 Planarity : 0.004 0.057 1191 Dihedral : 6.156 77.585 965 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.29), residues: 846 helix: 0.30 (0.34), residues: 210 sheet: -0.40 (0.33), residues: 263 loop : -0.56 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 62 TYR 0.010 0.001 TYR C 238 PHE 0.020 0.001 PHE D 228 TRP 0.031 0.002 TRP D 38 HIS 0.005 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 6975) covalent geometry : angle 0.63179 ( 9498) SS BOND : bond 0.00118 ( 5) SS BOND : angle 0.74004 ( 10) hydrogen bonds : bond 0.03657 ( 301) hydrogen bonds : angle 5.49446 ( 828) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.9094 (ppp) cc_final: 0.8828 (ppp) REVERT: A 134 THR cc_start: 0.9266 (p) cc_final: 0.9055 (p) REVERT: A 288 PHE cc_start: 0.8915 (m-80) cc_final: 0.8625 (m-80) REVERT: C 29 ASP cc_start: 0.8193 (t0) cc_final: 0.7676 (t0) REVERT: C 172 GLN cc_start: 0.8695 (mp-120) cc_final: 0.8163 (mm-40) REVERT: C 315 LEU cc_start: 0.9205 (mm) cc_final: 0.8994 (mm) REVERT: D 39 TYR cc_start: 0.6994 (m-10) cc_final: 0.6749 (m-10) REVERT: D 49 LEU cc_start: 0.8508 (tp) cc_final: 0.8279 (tp) REVERT: D 50 LEU cc_start: 0.8878 (mt) cc_final: 0.8153 (mt) REVERT: D 57 LEU cc_start: 0.8795 (pp) cc_final: 0.8553 (pp) REVERT: D 65 PHE cc_start: 0.8207 (m-10) cc_final: 0.7994 (m-80) REVERT: D 74 PHE cc_start: 0.8917 (m-80) cc_final: 0.8596 (m-80) REVERT: D 75 THR cc_start: 0.8480 (p) cc_final: 0.8190 (p) REVERT: D 195 THR cc_start: 0.8667 (m) cc_final: 0.8414 (p) REVERT: D 209 MET cc_start: 0.6920 (mpp) cc_final: 0.6418 (mmm) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1000 time to fit residues: 17.3044 Evaluate side-chains 95 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 0.2980 chunk 0 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 63 optimal weight: 0.0020 chunk 38 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 ASN ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.113343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.090822 restraints weight = 28332.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.094094 restraints weight = 17258.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.096248 restraints weight = 12105.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.097747 restraints weight = 9402.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.098728 restraints weight = 7819.689| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6981 Z= 0.125 Angle : 0.636 6.636 9508 Z= 0.320 Chirality : 0.045 0.175 1086 Planarity : 0.005 0.057 1191 Dihedral : 6.107 78.882 965 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.14 % Allowed : 3.01 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.29), residues: 846 helix: 0.36 (0.34), residues: 211 sheet: -0.35 (0.33), residues: 265 loop : -0.52 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 213 TYR 0.025 0.001 TYR D 52 PHE 0.016 0.001 PHE D 228 TRP 0.059 0.003 TRP A 99 HIS 0.013 0.002 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 6975) covalent geometry : angle 0.63417 ( 9498) SS BOND : bond 0.00614 ( 5) SS BOND : angle 1.45978 ( 10) hydrogen bonds : bond 0.03612 ( 301) hydrogen bonds : angle 5.36768 ( 828) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.9185 (ppp) cc_final: 0.8926 (ppp) REVERT: A 288 PHE cc_start: 0.8811 (m-80) cc_final: 0.8508 (m-80) REVERT: C 29 ASP cc_start: 0.8130 (t0) cc_final: 0.7705 (t0) REVERT: C 172 GLN cc_start: 0.8650 (mp-120) cc_final: 0.7885 (mp-120) REVERT: C 223 ASN cc_start: 0.8047 (m-40) cc_final: 0.7765 (p0) REVERT: C 315 LEU cc_start: 0.9133 (mm) cc_final: 0.8898 (mm) REVERT: D 39 TYR cc_start: 0.7064 (m-10) cc_final: 0.6858 (m-10) REVERT: D 65 PHE cc_start: 0.8071 (m-10) cc_final: 0.7857 (m-80) REVERT: D 74 PHE cc_start: 0.8904 (m-80) cc_final: 0.8658 (m-80) REVERT: D 106 LYS cc_start: 0.8875 (tptp) cc_final: 0.8647 (tptt) REVERT: D 193 ARG cc_start: 0.8116 (ttt180) cc_final: 0.7863 (ttt180) REVERT: D 195 THR cc_start: 0.8590 (m) cc_final: 0.8324 (p) REVERT: D 209 MET cc_start: 0.7130 (mpp) cc_final: 0.6639 (mmm) outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 0.0812 time to fit residues: 14.4710 Evaluate side-chains 99 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 47 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 chunk 74 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 14 optimal weight: 0.0980 chunk 35 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 0.0270 chunk 80 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** 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 = 0.3983 r_free = 0.3983 target = 0.115579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.093445 restraints weight = 27370.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.096657 restraints weight = 17015.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.098754 restraints weight = 12097.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.100298 restraints weight = 9460.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.101329 restraints weight = 7873.477| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6981 Z= 0.115 Angle : 0.634 6.728 9508 Z= 0.316 Chirality : 0.045 0.165 1086 Planarity : 0.005 0.079 1191 Dihedral : 5.949 79.260 965 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.30), residues: 846 helix: 0.64 (0.36), residues: 202 sheet: 0.00 (0.35), residues: 248 loop : -0.48 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 236 TYR 0.015 0.001 TYR A 325 PHE 0.017 0.001 PHE D 228 TRP 0.035 0.003 TRP A 99 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 6975) covalent geometry : angle 0.63228 ( 9498) SS BOND : bond 0.00236 ( 5) SS BOND : angle 1.39430 ( 10) hydrogen bonds : bond 0.03458 ( 301) hydrogen bonds : angle 5.13337 ( 828) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.7588 (mmp) cc_final: 0.7352 (mmp) REVERT: A 130 ILE cc_start: 0.9652 (mm) cc_final: 0.9437 (mm) REVERT: A 133 MET cc_start: 0.9112 (ppp) cc_final: 0.8873 (ppp) REVERT: A 280 TYR cc_start: 0.8881 (t80) cc_final: 0.8501 (t80) REVERT: A 284 TRP cc_start: 0.8014 (m-10) cc_final: 0.7542 (m100) REVERT: A 288 PHE cc_start: 0.8840 (m-80) cc_final: 0.7931 (m-80) REVERT: C 29 ASP cc_start: 0.7917 (t0) cc_final: 0.7531 (t0) REVERT: C 172 GLN cc_start: 0.8687 (mp-120) cc_final: 0.7887 (mp-120) REVERT: C 223 ASN cc_start: 0.8013 (m-40) cc_final: 0.7734 (p0) REVERT: C 315 LEU cc_start: 0.9053 (mm) cc_final: 0.8795 (mm) REVERT: D 73 ASP cc_start: 0.8737 (m-30) cc_final: 0.8277 (m-30) REVERT: D 74 PHE cc_start: 0.8986 (m-80) cc_final: 0.8222 (m-80) REVERT: D 193 ARG cc_start: 0.8097 (ttt180) cc_final: 0.7691 (ttt-90) REVERT: D 195 THR cc_start: 0.8576 (m) cc_final: 0.8299 (p) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.0863 time to fit residues: 14.7421 Evaluate side-chains 101 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 25 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 80 optimal weight: 0.1980 chunk 79 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** 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 = 0.3924 r_free = 0.3924 target = 0.111825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.089789 restraints weight = 28038.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.092882 restraints weight = 17526.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.094918 restraints weight = 12485.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.096417 restraints weight = 9809.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.097476 restraints weight = 8172.500| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6981 Z= 0.149 Angle : 0.643 6.817 9508 Z= 0.327 Chirality : 0.044 0.146 1086 Planarity : 0.006 0.077 1191 Dihedral : 6.070 79.738 965 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.29), residues: 846 helix: 0.59 (0.35), residues: 203 sheet: -0.03 (0.36), residues: 234 loop : -0.58 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 164 TYR 0.027 0.002 TYR D 52 PHE 0.018 0.002 PHE D 228 TRP 0.067 0.003 TRP A 99 HIS 0.006 0.001 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6975) covalent geometry : angle 0.64184 ( 9498) SS BOND : bond 0.00216 ( 5) SS BOND : angle 1.54731 ( 10) hydrogen bonds : bond 0.03626 ( 301) hydrogen bonds : angle 5.24875 ( 828) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.7542 (mmp) cc_final: 0.7212 (mmp) REVERT: A 134 THR cc_start: 0.9390 (m) cc_final: 0.9072 (m) REVERT: A 288 PHE cc_start: 0.8869 (m-80) cc_final: 0.8419 (m-80) REVERT: C 29 ASP cc_start: 0.8031 (t0) cc_final: 0.7596 (t0) REVERT: C 37 VAL cc_start: 0.9001 (t) cc_final: 0.8796 (p) REVERT: C 172 GLN cc_start: 0.8636 (mp-120) cc_final: 0.7958 (mp-120) REVERT: D 50 LEU cc_start: 0.8887 (mp) cc_final: 0.8455 (mp) REVERT: D 65 PHE cc_start: 0.7434 (m-80) cc_final: 0.7180 (m-80) REVERT: D 73 ASP cc_start: 0.8843 (m-30) cc_final: 0.8405 (m-30) REVERT: D 74 PHE cc_start: 0.9017 (m-80) cc_final: 0.8273 (m-80) REVERT: D 193 ARG cc_start: 0.8147 (ttt180) cc_final: 0.7714 (ttt-90) REVERT: D 195 THR cc_start: 0.8675 (m) cc_final: 0.8424 (p) REVERT: D 209 MET cc_start: 0.6976 (mpp) cc_final: 0.6253 (mmm) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.0735 time to fit residues: 12.5620 Evaluate side-chains 98 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 50 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 17 optimal weight: 0.0770 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 58 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 HIS ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.113329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.091541 restraints weight = 28180.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.094759 restraints weight = 17530.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.096942 restraints weight = 12427.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.098463 restraints weight = 9643.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.099531 restraints weight = 7982.500| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6981 Z= 0.130 Angle : 0.640 6.925 9508 Z= 0.321 Chirality : 0.044 0.143 1086 Planarity : 0.005 0.058 1191 Dihedral : 6.027 79.458 965 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.30), residues: 846 helix: 0.63 (0.35), residues: 202 sheet: -0.12 (0.35), residues: 248 loop : -0.51 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 213 TYR 0.009 0.001 TYR C 173 PHE 0.022 0.002 PHE D 228 TRP 0.048 0.003 TRP A 99 HIS 0.004 0.001 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 6975) covalent geometry : angle 0.63785 ( 9498) SS BOND : bond 0.00192 ( 5) SS BOND : angle 1.61895 ( 10) hydrogen bonds : bond 0.03559 ( 301) hydrogen bonds : angle 5.16683 ( 828) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.8862 (ppp) cc_final: 0.8650 (ppp) REVERT: A 134 THR cc_start: 0.9443 (m) cc_final: 0.9101 (m) REVERT: A 272 MET cc_start: 0.8492 (ppp) cc_final: 0.8291 (ppp) REVERT: A 280 TYR cc_start: 0.9008 (t80) cc_final: 0.8631 (t80) REVERT: A 284 TRP cc_start: 0.8185 (m-10) cc_final: 0.7604 (m100) REVERT: A 288 PHE cc_start: 0.8862 (m-80) cc_final: 0.7759 (m-80) REVERT: C 29 ASP cc_start: 0.7905 (t0) cc_final: 0.7509 (t0) REVERT: C 172 GLN cc_start: 0.8596 (mp-120) cc_final: 0.7932 (mp-120) REVERT: D 48 LYS cc_start: 0.8435 (tmtt) cc_final: 0.8221 (tptt) REVERT: D 65 PHE cc_start: 0.7438 (m-80) cc_final: 0.7201 (m-80) REVERT: D 73 ASP cc_start: 0.8802 (m-30) cc_final: 0.8371 (m-30) REVERT: D 74 PHE cc_start: 0.8942 (m-80) cc_final: 0.8097 (m-80) REVERT: D 75 THR cc_start: 0.8476 (p) cc_final: 0.8219 (p) REVERT: D 191 LYS cc_start: 0.8361 (mmtp) cc_final: 0.7818 (mmpt) REVERT: D 193 ARG cc_start: 0.8067 (ttt180) cc_final: 0.7725 (ttt-90) REVERT: D 195 THR cc_start: 0.8652 (m) cc_final: 0.8445 (p) REVERT: D 209 MET cc_start: 0.6940 (mpp) cc_final: 0.6292 (mmm) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.0751 time to fit residues: 12.6934 Evaluate side-chains 99 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 30 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** 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 = 0.3864 r_free = 0.3864 target = 0.107650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.085820 restraints weight = 29260.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.088709 restraints weight = 18609.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.090696 restraints weight = 13435.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.092010 restraints weight = 10591.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.092978 restraints weight = 8975.080| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6981 Z= 0.225 Angle : 0.730 7.642 9508 Z= 0.376 Chirality : 0.047 0.151 1086 Planarity : 0.006 0.059 1191 Dihedral : 6.528 80.768 965 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 24.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.30), residues: 846 helix: 0.25 (0.35), residues: 202 sheet: -0.55 (0.34), residues: 237 loop : -0.44 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 213 TYR 0.030 0.002 TYR D 52 PHE 0.027 0.003 PHE C 27 TRP 0.052 0.003 TRP D 38 HIS 0.008 0.002 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 6975) covalent geometry : angle 0.72865 ( 9498) SS BOND : bond 0.00242 ( 5) SS BOND : angle 1.67986 ( 10) hydrogen bonds : bond 0.04300 ( 301) hydrogen bonds : angle 5.79396 ( 828) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.8888 (ppp) cc_final: 0.8647 (ppp) REVERT: A 134 THR cc_start: 0.9534 (m) cc_final: 0.9168 (m) REVERT: A 280 TYR cc_start: 0.9022 (t80) cc_final: 0.8755 (t80) REVERT: A 284 TRP cc_start: 0.8492 (m-10) cc_final: 0.7962 (m-10) REVERT: A 288 PHE cc_start: 0.8898 (m-80) cc_final: 0.8583 (m-80) REVERT: D 57 LEU cc_start: 0.8960 (pp) cc_final: 0.8693 (pp) REVERT: D 65 PHE cc_start: 0.7448 (m-80) cc_final: 0.7198 (m-80) REVERT: D 74 PHE cc_start: 0.9085 (m-80) cc_final: 0.8417 (m-80) REVERT: D 195 THR cc_start: 0.8697 (m) cc_final: 0.8433 (p) REVERT: D 202 LYS cc_start: 0.9247 (tppt) cc_final: 0.9021 (tppt) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.0734 time to fit residues: 11.7022 Evaluate side-chains 92 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 64 optimal weight: 0.9980 chunk 23 optimal weight: 0.0050 chunk 77 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 2 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 26 optimal weight: 0.0970 chunk 13 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** 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 = 0.3960 r_free = 0.3960 target = 0.114103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.092020 restraints weight = 27897.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.095304 restraints weight = 17199.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.097575 restraints weight = 12090.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.099155 restraints weight = 9297.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.100270 restraints weight = 7642.359| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6981 Z= 0.123 Angle : 0.688 9.609 9508 Z= 0.339 Chirality : 0.046 0.168 1086 Planarity : 0.005 0.058 1191 Dihedral : 6.095 78.776 965 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.30), residues: 846 helix: 0.33 (0.35), residues: 202 sheet: -0.23 (0.35), residues: 244 loop : -0.48 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 213 TYR 0.022 0.002 TYR A 325 PHE 0.021 0.002 PHE D 228 TRP 0.055 0.003 TRP D 38 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 6975) covalent geometry : angle 0.68625 ( 9498) SS BOND : bond 0.00294 ( 5) SS BOND : angle 1.62049 ( 10) hydrogen bonds : bond 0.03699 ( 301) hydrogen bonds : angle 5.32368 ( 828) Misc. bond : bond 0.00001 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 THR cc_start: 0.9468 (m) cc_final: 0.9159 (m) REVERT: A 166 PHE cc_start: 0.7438 (t80) cc_final: 0.7231 (t80) REVERT: A 214 PHE cc_start: 0.8054 (m-80) cc_final: 0.6952 (m-80) REVERT: A 272 MET cc_start: 0.8504 (ppp) cc_final: 0.8278 (ppp) REVERT: A 280 TYR cc_start: 0.9037 (t80) cc_final: 0.8683 (t80) REVERT: A 284 TRP cc_start: 0.8179 (m-10) cc_final: 0.7653 (m100) REVERT: C 29 ASP cc_start: 0.7965 (t0) cc_final: 0.7608 (t0) REVERT: C 172 GLN cc_start: 0.8687 (mp-120) cc_final: 0.8076 (mp-120) REVERT: C 212 GLU cc_start: 0.8784 (mp0) cc_final: 0.8576 (mp0) REVERT: C 232 LYS cc_start: 0.8860 (tppt) cc_final: 0.8431 (tppt) REVERT: C 260 ASP cc_start: 0.8999 (m-30) cc_final: 0.8148 (t70) REVERT: D 48 LYS cc_start: 0.8499 (tmtt) cc_final: 0.8295 (tptt) REVERT: D 65 PHE cc_start: 0.7457 (m-80) cc_final: 0.7233 (m-80) REVERT: D 73 ASP cc_start: 0.8796 (m-30) cc_final: 0.8250 (m-30) REVERT: D 74 PHE cc_start: 0.9015 (m-80) cc_final: 0.8140 (m-80) REVERT: D 90 TYR cc_start: 0.7659 (m-10) cc_final: 0.7197 (m-80) REVERT: D 191 LYS cc_start: 0.8332 (mmtp) cc_final: 0.7749 (mmpt) REVERT: D 193 ARG cc_start: 0.8217 (ttt180) cc_final: 0.7780 (ttt-90) REVERT: D 195 THR cc_start: 0.8713 (m) cc_final: 0.8474 (p) REVERT: D 202 LYS cc_start: 0.9201 (tppt) cc_final: 0.8898 (tppt) REVERT: D 209 MET cc_start: 0.6937 (mpp) cc_final: 0.6383 (mmm) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.0863 time to fit residues: 14.9854 Evaluate side-chains 107 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 56 optimal weight: 0.3980 chunk 52 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 HIS ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.112061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.090506 restraints weight = 27939.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.093451 restraints weight = 17320.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.095645 restraints weight = 12414.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.097137 restraints weight = 9664.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.098169 restraints weight = 8025.433| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6981 Z= 0.136 Angle : 0.662 6.951 9508 Z= 0.334 Chirality : 0.045 0.150 1086 Planarity : 0.005 0.059 1191 Dihedral : 6.043 79.015 965 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.30), residues: 846 helix: 0.19 (0.34), residues: 211 sheet: -0.05 (0.35), residues: 239 loop : -0.50 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 145 TYR 0.016 0.002 TYR D 52 PHE 0.020 0.002 PHE D 228 TRP 0.055 0.003 TRP D 38 HIS 0.003 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 6975) covalent geometry : angle 0.66017 ( 9498) SS BOND : bond 0.00248 ( 5) SS BOND : angle 1.70233 ( 10) hydrogen bonds : bond 0.03683 ( 301) hydrogen bonds : angle 5.35386 ( 828) Misc. bond : bond 0.00001 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1231.01 seconds wall clock time: 22 minutes 5.93 seconds (1325.93 seconds total)