Starting phenix.real_space_refine on Fri Oct 10 17:35:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w87_37347/10_2025/8w87_37347_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w87_37347/10_2025/8w87_37347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8w87_37347/10_2025/8w87_37347_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w87_37347/10_2025/8w87_37347_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w87_37347/10_2025/8w87_37347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w87_37347/10_2025/8w87_37347.map" } resolution = 2.8 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= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5235 2.51 5 N 1415 2.21 5 O 1515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8228 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1906 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2593 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2315 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'B40': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.91, per 1000 atoms: 0.23 Number of scatterers: 8228 At special positions: 0 Unit cell: (82.4, 98.88, 132.664, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1515 8.00 N 1415 7.00 C 5235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.26 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: 0.64 Conformation dependent library (CDL) restraints added in 522.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB B40 R 501 " Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 44.2% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 12 through 33 Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.934A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 223 removed outlier: 3.511A pdb=" N PHE A 222 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 239 through 253 Processing helix chain 'A' and resid 267 through 278 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 305 through 326 removed outlier: 3.749A pdb=" N ILE A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER A 326 " --> pdb=" O ILE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 365 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.524A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.812A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 20 through 51 Processing helix chain 'R' and resid 56 through 76 Processing helix chain 'R' and resid 76 through 87 Processing helix chain 'R' and resid 91 through 127 removed outlier: 4.282A pdb=" N PHE R 95 " --> pdb=" O PHE R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 135 Processing helix chain 'R' and resid 136 through 161 Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 168 through 180 Processing helix chain 'R' and resid 187 through 199 Processing helix chain 'R' and resid 199 through 231 removed outlier: 3.990A pdb=" N LEU R 231 " --> pdb=" O ALA R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 247 through 278 removed outlier: 3.610A pdb=" N PHE R 260 " --> pdb=" O VAL R 256 " (cutoff:3.500A) Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 284 through 305 removed outlier: 3.631A pdb=" N SER R 297 " --> pdb=" O GLY R 293 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 320 Processing sheet with id=AA1, first strand: chain 'A' and resid 191 through 198 removed outlier: 4.685A pdb=" N VAL A 208 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N GLY A 47 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA A 227 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE A 228 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N PHE A 264 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE A 230 " --> pdb=" O PHE A 264 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ASN A 266 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL A 232 " --> pdb=" O ASN A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.944A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.532A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.743A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.556A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.839A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.695A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.840A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.851A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 463 hydrogen bonds defined for protein. 1320 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: 1.41 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: 1.20 - 1.32: 1386 1.32 - 1.44: 2303 1.44 - 1.57: 4625 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 8406 Sorted by residual: bond pdb=" C THR R 102 " pdb=" N ASP R 103 " ideal model delta sigma weight residual 1.334 1.415 -0.082 1.23e-02 6.61e+03 4.39e+01 bond pdb=" C ASP R 103 " pdb=" N ILE R 104 " ideal model delta sigma weight residual 1.334 1.258 0.076 1.25e-02 6.40e+03 3.74e+01 bond pdb=" C ASP R 103 " pdb=" O ASP R 103 " ideal model delta sigma weight residual 1.236 1.200 0.036 1.15e-02 7.56e+03 9.89e+00 bond pdb=" CB ASP R 103 " pdb=" CG ASP R 103 " ideal model delta sigma weight residual 1.516 1.459 0.057 2.50e-02 1.60e+03 5.29e+00 bond pdb=" CA ASP R 103 " pdb=" CB ASP R 103 " ideal model delta sigma weight residual 1.530 1.557 -0.027 1.57e-02 4.06e+03 3.05e+00 ... (remaining 8401 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 11276 2.16 - 4.33: 97 4.33 - 6.49: 9 6.49 - 8.65: 0 8.65 - 10.82: 2 Bond angle restraints: 11384 Sorted by residual: angle pdb=" C ASP R 103 " pdb=" CA ASP R 103 " pdb=" CB ASP R 103 " ideal model delta sigma weight residual 110.96 105.05 5.91 1.54e+00 4.22e-01 1.47e+01 angle pdb=" CA B40 R 501 " pdb=" N B40 R 501 " pdb=" CM B40 R 501 " ideal model delta sigma weight residual 115.05 104.23 10.82 3.00e+00 1.11e-01 1.30e+01 angle pdb=" N B40 R 501 " pdb=" CA B40 R 501 " pdb=" C B40 R 501 " ideal model delta sigma weight residual 114.49 104.29 10.20 3.00e+00 1.11e-01 1.16e+01 angle pdb=" N VAL R 150 " pdb=" CA VAL R 150 " pdb=" C VAL R 150 " ideal model delta sigma weight residual 112.35 108.63 3.72 1.20e+00 6.94e-01 9.62e+00 angle pdb=" N SER B 331 " pdb=" CA SER B 331 " pdb=" C SER B 331 " ideal model delta sigma weight residual 108.60 112.56 -3.96 1.46e+00 4.69e-01 7.37e+00 ... (remaining 11379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.64: 4508 19.64 - 39.29: 381 39.29 - 58.93: 79 58.93 - 78.58: 16 78.58 - 98.22: 6 Dihedral angle restraints: 4990 sinusoidal: 1945 harmonic: 3045 Sorted by residual: dihedral pdb=" CA PHE B 292 " pdb=" C PHE B 292 " pdb=" N ASN B 293 " pdb=" CA ASN B 293 " ideal model delta harmonic sigma weight residual 180.00 161.73 18.27 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -162.49 -17.51 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CB B40 R 501 " pdb=" N B40 R 501 " pdb=" CA B40 R 501 " pdb=" CM B40 R 501 " ideal model delta sinusoidal sigma weight residual 168.08 -93.70 -98.22 1 3.00e+01 1.11e-03 1.22e+01 ... (remaining 4987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1106 0.056 - 0.113: 144 0.113 - 0.169: 23 0.169 - 0.226: 1 0.226 - 0.282: 1 Chirality restraints: 1275 Sorted by residual: chirality pdb=" CA B40 R 501 " pdb=" N B40 R 501 " pdb=" C B40 R 501 " pdb=" CB B40 R 501 " both_signs ideal model delta sigma weight residual False -2.42 -2.71 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA ASP R 103 " pdb=" N ASP R 103 " pdb=" C ASP R 103 " pdb=" CB ASP R 103 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CA PHE B 292 " pdb=" N PHE B 292 " pdb=" C PHE B 292 " pdb=" CB PHE B 292 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 1272 not shown) Planarity restraints: 1448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 284 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C THR R 284 " -0.059 2.00e-02 2.50e+03 pdb=" O THR R 284 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU R 285 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO R 282 " 0.056 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO R 283 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO R 283 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO R 283 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 19 " -0.182 9.50e-02 1.11e+02 8.20e-02 4.90e+00 pdb=" NE ARG B 19 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 19 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 19 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 19 " -0.002 2.00e-02 2.50e+03 ... (remaining 1445 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 594 2.73 - 3.28: 8380 3.28 - 3.82: 13939 3.82 - 4.36: 17219 4.36 - 4.90: 30105 Nonbonded interactions: 70237 Sorted by model distance: nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 196 " model vdw 2.193 3.040 nonbonded pdb=" O ASN A 188 " pdb=" OG SER A 189 " model vdw 2.226 3.040 nonbonded pdb=" C B40 R 501 " pdb=" CM B40 R 501 " model vdw 2.251 3.104 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.314 3.040 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.319 3.040 ... (remaining 70232 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 9.370 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.227 8407 Z= 0.220 Angle : 0.569 10.817 11386 Z= 0.321 Chirality : 0.041 0.282 1275 Planarity : 0.005 0.083 1448 Dihedral : 15.674 98.222 3019 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.45 % Allowed : 16.10 % Favored : 83.45 % 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 aren not related in a simple way. whole: 1.49 (0.27), residues: 1031 helix: 2.26 (0.25), residues: 416 sheet: 0.46 (0.34), residues: 228 loop : -0.01 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 19 TYR 0.008 0.001 TYR A 313 PHE 0.011 0.001 PHE R 70 TRP 0.013 0.001 TRP R 291 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8406) covalent geometry : angle 0.56066 (11384) SS BOND : bond 0.22739 ( 1) SS BOND : angle 7.39323 ( 2) hydrogen bonds : bond 0.14301 ( 463) hydrogen bonds : angle 6.60120 ( 1320) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 128 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 330 ARG cc_start: 0.7951 (mtm110) cc_final: 0.7653 (mtm110) REVERT: B 17 GLN cc_start: 0.6251 (tt0) cc_final: 0.6005 (tm130) outliers start: 4 outliers final: 3 residues processed: 130 average time/residue: 0.6588 time to fit residues: 90.4762 Evaluate side-chains 124 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 121 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain R residue 80 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.0020 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 237 ASN B 239 ASN R 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.150498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.105730 restraints weight = 9337.780| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.32 r_work: 0.3116 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8407 Z= 0.128 Angle : 0.525 6.467 11386 Z= 0.286 Chirality : 0.042 0.159 1275 Planarity : 0.004 0.065 1448 Dihedral : 5.522 58.690 1149 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.14 % Allowed : 14.08 % Favored : 83.78 % 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 aren not related in a simple way. whole: 1.69 (0.27), residues: 1031 helix: 2.39 (0.25), residues: 415 sheet: 0.59 (0.35), residues: 221 loop : 0.13 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 19 TYR 0.026 0.001 TYR R 27 PHE 0.021 0.001 PHE R 165 TRP 0.021 0.002 TRP B 169 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8406) covalent geometry : angle 0.52432 (11384) SS BOND : bond 0.00596 ( 1) SS BOND : angle 2.20609 ( 2) hydrogen bonds : bond 0.04131 ( 463) hydrogen bonds : angle 5.19107 ( 1320) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.8679 (mttp) cc_final: 0.8134 (mmtm) REVERT: A 213 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7638 (p0) REVERT: A 318 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7840 (mm-30) REVERT: A 321 ARG cc_start: 0.7241 (mtp85) cc_final: 0.7004 (mtm-85) REVERT: A 355 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7764 (t0) REVERT: B 214 ARG cc_start: 0.8302 (mmm-85) cc_final: 0.7368 (mpp80) REVERT: B 243 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.7988 (p) REVERT: R 80 SER cc_start: 0.7676 (t) cc_final: 0.6810 (p) outliers start: 19 outliers final: 7 residues processed: 150 average time/residue: 0.6501 time to fit residues: 103.2395 Evaluate side-chains 139 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain R residue 96 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 17 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 100 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.150360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.105432 restraints weight = 9302.645| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.31 r_work: 0.3112 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8407 Z= 0.137 Angle : 0.506 6.098 11386 Z= 0.274 Chirality : 0.042 0.156 1275 Planarity : 0.004 0.058 1448 Dihedral : 5.075 55.750 1148 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.59 % Allowed : 15.20 % Favored : 82.21 % 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 aren not related in a simple way. whole: 1.57 (0.27), residues: 1031 helix: 2.26 (0.25), residues: 421 sheet: 0.51 (0.36), residues: 215 loop : 0.08 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.009 0.001 TYR N 95 PHE 0.013 0.001 PHE A 196 TRP 0.015 0.002 TRP B 169 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8406) covalent geometry : angle 0.50482 (11384) SS BOND : bond 0.00745 ( 1) SS BOND : angle 2.10899 ( 2) hydrogen bonds : bond 0.03810 ( 463) hydrogen bonds : angle 4.95104 ( 1320) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.8691 (mttp) cc_final: 0.8148 (mmtm) REVERT: A 318 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7848 (mm-30) REVERT: A 321 ARG cc_start: 0.7290 (mtp85) cc_final: 0.7028 (mtm-85) REVERT: A 355 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7791 (t0) REVERT: B 175 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7300 (mp10) REVERT: B 214 ARG cc_start: 0.8264 (mmm-85) cc_final: 0.8040 (tpp80) outliers start: 23 outliers final: 11 residues processed: 157 average time/residue: 0.6327 time to fit residues: 104.9658 Evaluate side-chains 144 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 176 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 67 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.150244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.104999 restraints weight = 9461.402| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.33 r_work: 0.3131 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8407 Z= 0.136 Angle : 0.498 5.923 11386 Z= 0.270 Chirality : 0.042 0.152 1275 Planarity : 0.004 0.055 1448 Dihedral : 5.110 58.236 1148 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.04 % Allowed : 16.55 % Favored : 80.41 % 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 aren not related in a simple way. whole: 1.53 (0.27), residues: 1031 helix: 2.26 (0.25), residues: 421 sheet: 0.48 (0.36), residues: 215 loop : 0.04 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.010 0.001 TYR N 95 PHE 0.018 0.001 PHE R 165 TRP 0.014 0.002 TRP B 169 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8406) covalent geometry : angle 0.49744 (11384) SS BOND : bond 0.00451 ( 1) SS BOND : angle 2.07169 ( 2) hydrogen bonds : bond 0.03664 ( 463) hydrogen bonds : angle 4.86223 ( 1320) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7564 (mptt) REVERT: A 200 LYS cc_start: 0.8685 (mttp) cc_final: 0.8161 (mmtm) REVERT: A 213 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7236 (p0) REVERT: A 318 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7836 (mm-30) REVERT: A 321 ARG cc_start: 0.7296 (mtp85) cc_final: 0.7020 (mtm-85) REVERT: A 330 ARG cc_start: 0.7712 (mtm110) cc_final: 0.7210 (mtm110) REVERT: A 355 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7792 (t0) REVERT: B 175 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7301 (mp10) REVERT: R 135 MET cc_start: 0.8431 (mmp) cc_final: 0.8109 (mmt) outliers start: 27 outliers final: 15 residues processed: 155 average time/residue: 0.6043 time to fit residues: 99.3153 Evaluate side-chains 151 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 182 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 66 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.151143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.105968 restraints weight = 9384.688| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.32 r_work: 0.3123 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8407 Z= 0.118 Angle : 0.476 5.791 11386 Z= 0.259 Chirality : 0.041 0.149 1275 Planarity : 0.004 0.055 1448 Dihedral : 4.931 55.610 1148 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.93 % Allowed : 17.23 % Favored : 79.84 % 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 aren not related in a simple way. whole: 1.58 (0.27), residues: 1031 helix: 2.32 (0.25), residues: 422 sheet: 0.52 (0.36), residues: 215 loop : 0.03 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.016 0.001 TYR R 27 PHE 0.013 0.001 PHE A 196 TRP 0.014 0.002 TRP A 218 HIS 0.003 0.001 HIS A 331 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8406) covalent geometry : angle 0.47534 (11384) SS BOND : bond 0.00426 ( 1) SS BOND : angle 1.95153 ( 2) hydrogen bonds : bond 0.03493 ( 463) hydrogen bonds : angle 4.76702 ( 1320) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7591 (mptt) REVERT: A 200 LYS cc_start: 0.8693 (mttp) cc_final: 0.8165 (mmtm) REVERT: A 213 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7265 (p0) REVERT: A 318 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7816 (mm-30) REVERT: A 321 ARG cc_start: 0.7283 (mtp85) cc_final: 0.6999 (mtm-85) REVERT: A 355 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7810 (t0) REVERT: B 175 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7397 (mp10) REVERT: R 23 ARG cc_start: 0.5769 (OUTLIER) cc_final: 0.5078 (ptt90) REVERT: R 83 ARG cc_start: 0.6253 (OUTLIER) cc_final: 0.5812 (ttm110) REVERT: R 135 MET cc_start: 0.8458 (mmp) cc_final: 0.8108 (mmt) outliers start: 26 outliers final: 14 residues processed: 155 average time/residue: 0.6255 time to fit residues: 102.8426 Evaluate side-chains 154 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 83 ARG Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 207 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 94 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 142 HIS B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.146072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.100736 restraints weight = 9441.775| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.30 r_work: 0.3071 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 8407 Z= 0.276 Angle : 0.600 7.243 11386 Z= 0.322 Chirality : 0.046 0.150 1275 Planarity : 0.005 0.054 1448 Dihedral : 5.354 56.263 1148 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.05 % Allowed : 17.12 % Favored : 78.83 % 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 aren not related in a simple way. whole: 1.14 (0.26), residues: 1031 helix: 1.88 (0.25), residues: 426 sheet: 0.41 (0.34), residues: 221 loop : -0.23 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 330 TYR 0.012 0.002 TYR R 279 PHE 0.019 0.002 PHE R 195 TRP 0.017 0.002 TRP A 218 HIS 0.006 0.001 HIS R 63 Details of bonding type rmsd covalent geometry : bond 0.00660 ( 8406) covalent geometry : angle 0.59949 (11384) SS BOND : bond 0.00534 ( 1) SS BOND : angle 2.60013 ( 2) hydrogen bonds : bond 0.04447 ( 463) hydrogen bonds : angle 5.15838 ( 1320) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7554 (mptt) REVERT: A 213 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7239 (p0) REVERT: A 355 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7831 (t0) REVERT: B 175 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7411 (mp10) REVERT: N 108 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.7649 (m-80) REVERT: R 23 ARG cc_start: 0.5789 (OUTLIER) cc_final: 0.5091 (ptt90) REVERT: R 80 SER cc_start: 0.7850 (t) cc_final: 0.6723 (p) REVERT: R 83 ARG cc_start: 0.6307 (OUTLIER) cc_final: 0.5663 (ttm110) outliers start: 36 outliers final: 17 residues processed: 154 average time/residue: 0.6225 time to fit residues: 101.5029 Evaluate side-chains 150 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 83 ARG Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 271 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 20 optimal weight: 0.0170 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.151352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.106136 restraints weight = 9412.204| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.34 r_work: 0.3124 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8407 Z= 0.107 Angle : 0.475 5.862 11386 Z= 0.259 Chirality : 0.041 0.148 1275 Planarity : 0.004 0.054 1448 Dihedral : 4.830 56.217 1148 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.70 % Allowed : 18.69 % Favored : 78.60 % 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 aren not related in a simple way. whole: 1.41 (0.26), residues: 1031 helix: 2.25 (0.25), residues: 420 sheet: 0.40 (0.36), residues: 215 loop : -0.13 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 19 TYR 0.010 0.001 TYR R 279 PHE 0.011 0.001 PHE A 196 TRP 0.016 0.002 TRP R 291 HIS 0.003 0.001 HIS A 331 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 8406) covalent geometry : angle 0.47492 (11384) SS BOND : bond 0.00356 ( 1) SS BOND : angle 1.72484 ( 2) hydrogen bonds : bond 0.03407 ( 463) hydrogen bonds : angle 4.77451 ( 1320) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7117 (tmtt) REVERT: A 200 LYS cc_start: 0.8706 (mttp) cc_final: 0.8156 (mmtm) REVERT: A 213 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7196 (p0) REVERT: A 317 ASP cc_start: 0.8233 (m-30) cc_final: 0.7949 (m-30) REVERT: A 355 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7795 (t0) REVERT: B 175 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7383 (mp10) REVERT: B 292 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.8368 (m-10) REVERT: R 23 ARG cc_start: 0.5782 (OUTLIER) cc_final: 0.5061 (ptt90) outliers start: 24 outliers final: 11 residues processed: 151 average time/residue: 0.6097 time to fit residues: 97.5081 Evaluate side-chains 146 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 43 ILE Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 176 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 4 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 73 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.150728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.105813 restraints weight = 9369.443| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.31 r_work: 0.3120 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8407 Z= 0.119 Angle : 0.491 6.812 11386 Z= 0.266 Chirality : 0.041 0.148 1275 Planarity : 0.004 0.064 1448 Dihedral : 4.670 55.724 1148 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.70 % Allowed : 18.92 % Favored : 78.38 % 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 aren not related in a simple way. whole: 1.49 (0.26), residues: 1031 helix: 2.30 (0.25), residues: 421 sheet: 0.45 (0.36), residues: 215 loop : -0.08 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 19 TYR 0.009 0.001 TYR R 279 PHE 0.015 0.001 PHE R 165 TRP 0.014 0.002 TRP R 291 HIS 0.003 0.001 HIS R 63 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8406) covalent geometry : angle 0.49056 (11384) SS BOND : bond 0.00484 ( 1) SS BOND : angle 1.80869 ( 2) hydrogen bonds : bond 0.03447 ( 463) hydrogen bonds : angle 4.74584 ( 1320) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7116 (tmtt) REVERT: A 200 LYS cc_start: 0.8701 (mttp) cc_final: 0.8162 (mmtm) REVERT: A 213 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7167 (p0) REVERT: A 317 ASP cc_start: 0.8254 (m-30) cc_final: 0.7969 (m-30) REVERT: A 355 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7783 (t0) REVERT: B 175 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7368 (mp10) REVERT: B 220 GLN cc_start: 0.8065 (mt0) cc_final: 0.7856 (mt0) REVERT: R 23 ARG cc_start: 0.5707 (OUTLIER) cc_final: 0.5012 (ptt90) outliers start: 24 outliers final: 12 residues processed: 147 average time/residue: 0.5899 time to fit residues: 91.7797 Evaluate side-chains 145 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 182 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 75 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.151121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.106097 restraints weight = 9330.952| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.32 r_work: 0.3124 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8407 Z= 0.118 Angle : 0.486 6.978 11386 Z= 0.263 Chirality : 0.041 0.147 1275 Planarity : 0.004 0.078 1448 Dihedral : 4.556 55.465 1146 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.04 % Allowed : 18.92 % Favored : 78.04 % 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 aren not related in a simple way. whole: 1.51 (0.26), residues: 1031 helix: 2.30 (0.25), residues: 422 sheet: 0.48 (0.36), residues: 215 loop : -0.07 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 19 TYR 0.012 0.001 TYR R 27 PHE 0.013 0.001 PHE R 154 TRP 0.014 0.002 TRP R 291 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8406) covalent geometry : angle 0.48529 (11384) SS BOND : bond 0.00429 ( 1) SS BOND : angle 1.71336 ( 2) hydrogen bonds : bond 0.03379 ( 463) hydrogen bonds : angle 4.70444 ( 1320) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7082 (tmtt) REVERT: A 200 LYS cc_start: 0.8633 (mttp) cc_final: 0.8069 (mmtt) REVERT: A 213 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7150 (p0) REVERT: A 317 ASP cc_start: 0.8171 (m-30) cc_final: 0.7881 (m-30) REVERT: A 355 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7714 (t0) REVERT: B 217 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7978 (ppp) REVERT: B 220 GLN cc_start: 0.7997 (mt0) cc_final: 0.7783 (mt0) REVERT: R 23 ARG cc_start: 0.5692 (OUTLIER) cc_final: 0.4933 (ptm-80) REVERT: R 135 MET cc_start: 0.8335 (mmp) cc_final: 0.7884 (mmt) outliers start: 27 outliers final: 14 residues processed: 149 average time/residue: 0.5870 time to fit residues: 92.7221 Evaluate side-chains 148 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 6 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 0.0970 chunk 44 optimal weight: 0.0070 chunk 35 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.152681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.107841 restraints weight = 9349.920| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.32 r_work: 0.3145 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8407 Z= 0.102 Angle : 0.473 7.428 11386 Z= 0.256 Chirality : 0.040 0.145 1275 Planarity : 0.004 0.080 1448 Dihedral : 4.411 55.040 1146 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.14 % Allowed : 19.93 % Favored : 77.93 % 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 aren not related in a simple way. whole: 1.58 (0.26), residues: 1031 helix: 2.37 (0.25), residues: 422 sheet: 0.47 (0.36), residues: 217 loop : -0.02 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 19 TYR 0.012 0.001 TYR R 279 PHE 0.015 0.001 PHE R 154 TRP 0.015 0.002 TRP R 291 HIS 0.002 0.001 HIS A 331 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 8406) covalent geometry : angle 0.47239 (11384) SS BOND : bond 0.00423 ( 1) SS BOND : angle 1.56159 ( 2) hydrogen bonds : bond 0.03210 ( 463) hydrogen bonds : angle 4.61106 ( 1320) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7144 (ttpt) REVERT: A 200 LYS cc_start: 0.8642 (mttp) cc_final: 0.8098 (mmtt) REVERT: A 213 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7104 (p0) REVERT: A 317 ASP cc_start: 0.8131 (m-30) cc_final: 0.7803 (m-30) REVERT: A 355 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7726 (t0) REVERT: B 220 GLN cc_start: 0.7985 (mt0) cc_final: 0.7778 (mt0) REVERT: N 46 GLU cc_start: 0.8075 (tt0) cc_final: 0.7701 (pt0) REVERT: N 123 GLN cc_start: 0.8352 (tp40) cc_final: 0.8150 (mm-40) REVERT: R 23 ARG cc_start: 0.5656 (OUTLIER) cc_final: 0.4931 (ptm-80) outliers start: 19 outliers final: 11 residues processed: 148 average time/residue: 0.5592 time to fit residues: 87.9442 Evaluate side-chains 142 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 182 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 4 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 71 optimal weight: 0.4980 chunk 79 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.151884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.106817 restraints weight = 9387.342| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.32 r_work: 0.3131 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 8407 Z= 0.115 Angle : 0.493 6.391 11386 Z= 0.268 Chirality : 0.041 0.145 1275 Planarity : 0.004 0.056 1448 Dihedral : 4.422 54.720 1146 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.91 % Allowed : 20.38 % Favored : 77.70 % 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 aren not related in a simple way. whole: 1.55 (0.26), residues: 1031 helix: 2.33 (0.25), residues: 422 sheet: 0.43 (0.35), residues: 217 loop : 0.01 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 19 TYR 0.014 0.001 TYR R 279 PHE 0.012 0.001 PHE A 196 TRP 0.014 0.002 TRP R 291 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8406) covalent geometry : angle 0.49251 (11384) SS BOND : bond 0.00392 ( 1) SS BOND : angle 1.60201 ( 2) hydrogen bonds : bond 0.03300 ( 463) hydrogen bonds : angle 4.68686 ( 1320) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3659.38 seconds wall clock time: 62 minutes 56.49 seconds (3776.49 seconds total)