Starting phenix.real_space_refine on Wed Sep 17 12:02:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kdf_62274/09_2025/9kdf_62274.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kdf_62274/09_2025/9kdf_62274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kdf_62274/09_2025/9kdf_62274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kdf_62274/09_2025/9kdf_62274.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kdf_62274/09_2025/9kdf_62274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kdf_62274/09_2025/9kdf_62274.map" } resolution = 3.3 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= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1431 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Fe 1 7.16 5 Zn 1 6.06 5 S 49 5.16 5 C 4801 2.51 5 N 1214 2.21 5 O 1329 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7399 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 6383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 6383 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 763} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "A" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 135 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' CA': 4, ' FE': 1, ' ZN': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'FK5': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.87, per 1000 atoms: 0.25 Number of scatterers: 7399 At special positions: 0 Unit cell: (67.396, 95.284, 146.412, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 1 26.01 Ca 4 19.99 S 49 16.00 O 1329 8.00 N 1214 7.00 C 4801 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 255 " 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=0, symmetry=0 Links applied ASP_CG-ANY_N " ASP A 9 " - " GLY A 1 " Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 362.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R1506 " pdb="ZN ZN R1506 " - pdb=" ND1 HIS R1257 " pdb="ZN ZN R1506 " - pdb=" NE2 HIS R1175 " 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1724 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 7 sheets defined 57.8% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'R' and resid 93 through 129 removed outlier: 4.495A pdb=" N TYR R 102 " --> pdb=" O GLU R 98 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE R 103 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 163 removed outlier: 3.729A pdb=" N ILE R 140 " --> pdb=" O PRO R 136 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N HIS R 150 " --> pdb=" O GLY R 146 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE R 153 " --> pdb=" O LEU R 149 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE R 155 " --> pdb=" O ILE R 151 " (cutoff:3.500A) Proline residue: R 156 - end of helix Processing helix chain 'R' and resid 170 through 204 Proline residue: R 178 - end of helix Processing helix chain 'R' and resid 216 through 238 Proline residue: R 235 - end of helix Processing helix chain 'R' and resid 263 through 272 Processing helix chain 'R' and resid 272 through 280 Processing helix chain 'R' and resid 282 through 303 removed outlier: 3.716A pdb=" N LEU R 286 " --> pdb=" O PHE R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 320 Processing helix chain 'R' and resid 328 through 334 Processing helix chain 'R' and resid 335 through 341 removed outlier: 4.017A pdb=" N GLN R 340 " --> pdb=" O GLU R 337 " (cutoff:3.500A) Processing helix chain 'R' and resid 343 through 352 Processing helix chain 'R' and resid 360 through 370 removed outlier: 3.578A pdb=" N GLN R 370 " --> pdb=" O GLU R 366 " (cutoff:3.500A) Processing helix chain 'R' and resid 376 through 389 removed outlier: 3.580A pdb=" N LYS R 380 " --> pdb=" O ASP R 376 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR R 388 " --> pdb=" O ALA R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 397 through 410 Processing helix chain 'R' and resid 414 through 430 Processing helix chain 'R' and resid 439 through 446 Processing helix chain 'R' and resid 447 through 455 removed outlier: 4.324A pdb=" N ASP R 450 " --> pdb=" O GLY R 447 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE R 451 " --> pdb=" O GLY R 448 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N HIS R 452 " --> pdb=" O LEU R 449 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS R 453 " --> pdb=" O ASP R 450 " (cutoff:3.500A) Processing helix chain 'R' and resid 466 through 483 Processing helix chain 'R' and resid 483 through 497 removed outlier: 3.598A pdb=" N HIS R 487 " --> pdb=" O TRP R 483 " (cutoff:3.500A) Processing helix chain 'R' and resid 504 through 526 removed outlier: 3.948A pdb=" N VAL R 513 " --> pdb=" O SER R 509 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER R 526 " --> pdb=" O ALA R 522 " (cutoff:3.500A) Processing helix chain 'R' and resid 528 through 537 Processing helix chain 'R' and resid 537 through 549 Processing helix chain 'R' and resid 1006 through 1011 Processing helix chain 'R' and resid 1018 through 1028 Processing helix chain 'R' and resid 1033 through 1050 removed outlier: 3.952A pdb=" N GLN R1050 " --> pdb=" O SER R1046 " (cutoff:3.500A) Processing helix chain 'R' and resid 1070 through 1082 Processing helix chain 'R' and resid 1101 through 1116 removed outlier: 3.545A pdb=" N CYS R1105 " --> pdb=" O PHE R1101 " (cutoff:3.500A) Processing helix chain 'R' and resid 1129 through 1136 Processing helix chain 'R' and resid 1137 through 1146 Processing helix chain 'R' and resid 1147 through 1160 removed outlier: 3.519A pdb=" N TYR R1151 " --> pdb=" O SER R1147 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS R1160 " --> pdb=" O ASP R1156 " (cutoff:3.500A) Processing helix chain 'R' and resid 1184 through 1190 removed outlier: 3.900A pdb=" N ILE R1188 " --> pdb=" O THR R1184 " (cutoff:3.500A) Processing helix chain 'R' and resid 1201 through 1209 Processing helix chain 'R' and resid 1237 through 1249 Processing helix chain 'R' and resid 1286 through 1290 Processing helix chain 'R' and resid 1319 through 1323 removed outlier: 3.733A pdb=" N MET R1323 " --> pdb=" O PRO R1320 " (cutoff:3.500A) Processing helix chain 'R' and resid 1324 through 1345 Proline residue: R1331 - end of helix Processing helix chain 'F' and resid 43 through 46 Processing helix chain 'F' and resid 59 through 68 Processing helix chain 'F' and resid 81 through 84 Processing sheet with id=AA1, first strand: chain 'R' and resid 240 through 244 Processing sheet with id=AA2, first strand: chain 'R' and resid 395 through 396 Processing sheet with id=AA3, first strand: chain 'R' and resid 1054 through 1057 removed outlier: 6.191A pdb=" N LEU R1055 " --> pdb=" O LEU R1166 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU R1172 " --> pdb=" O LEU R1254 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE R1253 " --> pdb=" O ILE R1279 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE R1281 " --> pdb=" O ILE R1253 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ARG R1255 " --> pdb=" O ILE R1281 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 1120 through 1122 removed outlier: 5.758A pdb=" N TYR R1089 " --> pdb=" O PHE R1121 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR R1062 " --> pdb=" O LEU R1090 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 1210 through 1211 removed outlier: 6.974A pdb=" N ASP R1210 " --> pdb=" O TYR R1236 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 5 through 11 removed outlier: 6.323A pdb=" N ILE F 7 " --> pdb=" O THR F 78 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N THR F 78 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N THR F 9 " --> pdb=" O LYS F 76 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LYS F 76 " --> pdb=" O THR F 9 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL F 26 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU F 109 " --> pdb=" O THR F 24 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR F 24 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP F 40 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 5 through 11 removed outlier: 6.323A pdb=" N ILE F 7 " --> pdb=" O THR F 78 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N THR F 78 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N THR F 9 " --> pdb=" O LYS F 76 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LYS F 76 " --> pdb=" O THR F 9 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL F 26 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU F 109 " --> pdb=" O THR F 24 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR F 24 " --> pdb=" O LEU F 109 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1155 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: 1.18 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2332 1.34 - 1.46: 1766 1.46 - 1.58: 3398 1.58 - 1.70: 1 1.70 - 1.82: 72 Bond restraints: 7569 Sorted by residual: bond pdb=" C9 FK5 F2001 " pdb=" O4 FK5 F2001 " ideal model delta sigma weight residual 1.206 1.409 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C1 FK5 F2001 " pdb=" O2 FK5 F2001 " ideal model delta sigma weight residual 1.211 1.410 -0.199 2.00e-02 2.50e+03 9.91e+01 bond pdb=" C22 FK5 F2001 " pdb=" O9 FK5 F2001 " ideal model delta sigma weight residual 1.215 1.410 -0.195 2.00e-02 2.50e+03 9.52e+01 bond pdb=" C8 FK5 F2001 " pdb=" O3 FK5 F2001 " ideal model delta sigma weight residual 1.232 1.409 -0.177 2.00e-02 2.50e+03 7.83e+01 bond pdb=" C8 FK5 F2001 " pdb=" C9 FK5 F2001 " ideal model delta sigma weight residual 1.537 1.395 0.142 2.00e-02 2.50e+03 5.03e+01 ... (remaining 7564 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 9884 1.74 - 3.49: 293 3.49 - 5.23: 56 5.23 - 6.98: 13 6.98 - 8.72: 5 Bond angle restraints: 10251 Sorted by residual: angle pdb=" CA PRO R 342 " pdb=" N PRO R 342 " pdb=" CD PRO R 342 " ideal model delta sigma weight residual 112.00 104.37 7.63 1.40e+00 5.10e-01 2.97e+01 angle pdb=" N LYS R 463 " pdb=" CA LYS R 463 " pdb=" C LYS R 463 " ideal model delta sigma weight residual 114.39 108.59 5.80 1.45e+00 4.76e-01 1.60e+01 angle pdb=" N VAL R1290 " pdb=" CA VAL R1290 " pdb=" C VAL R1290 " ideal model delta sigma weight residual 113.71 110.04 3.67 9.50e-01 1.11e+00 1.49e+01 angle pdb=" CA ARG R 302 " pdb=" CB ARG R 302 " pdb=" CG ARG R 302 " ideal model delta sigma weight residual 114.10 120.45 -6.35 2.00e+00 2.50e-01 1.01e+01 angle pdb=" C2 FK5 F2001 " pdb=" C1 FK5 F2001 " pdb=" O1 FK5 F2001 " ideal model delta sigma weight residual 112.57 120.96 -8.39 3.00e+00 1.11e-01 7.82e+00 ... (remaining 10246 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.48: 4524 35.48 - 70.96: 51 70.96 - 106.44: 9 106.44 - 141.92: 0 141.92 - 177.40: 4 Dihedral angle restraints: 4588 sinusoidal: 1914 harmonic: 2674 Sorted by residual: dihedral pdb=" O5 FK5 F2001 " pdb=" C14 FK5 F2001 " pdb=" C15 FK5 F2001 " pdb=" O8 FK5 F2001 " ideal model delta sinusoidal sigma weight residual -11.37 166.03 -177.40 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C13 FK5 F2001 " pdb=" C14 FK5 F2001 " pdb=" C15 FK5 F2001 " pdb=" O8 FK5 F2001 " ideal model delta sinusoidal sigma weight residual 108.57 -76.15 -175.28 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C16 FK5 F2001 " pdb=" C14 FK5 F2001 " pdb=" C15 FK5 F2001 " pdb=" O5 FK5 F2001 " ideal model delta sinusoidal sigma weight residual 243.79 71.79 172.00 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 4585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1005 0.064 - 0.128: 130 0.128 - 0.192: 10 0.192 - 0.257: 2 0.257 - 0.321: 1 Chirality restraints: 1148 Sorted by residual: chirality pdb=" CG LEU R1026 " pdb=" CB LEU R1026 " pdb=" CD1 LEU R1026 " pdb=" CD2 LEU R1026 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA TRP R1110 " pdb=" N TRP R1110 " pdb=" C TRP R1110 " pdb=" CB TRP R1110 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C10 FK5 F2001 " pdb=" C11 FK5 F2001 " pdb=" C9 FK5 F2001 " pdb=" O5 FK5 F2001 " both_signs ideal model delta sigma weight residual False 2.69 2.47 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1145 not shown) Planarity restraints: 1295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C18 FK5 F2001 " -0.077 2.00e-02 2.50e+03 8.40e-02 8.83e+01 pdb=" C19 FK5 F2001 " 0.026 2.00e-02 2.50e+03 pdb=" C20 FK5 F2001 " 0.131 2.00e-02 2.50e+03 pdb=" C21 FK5 F2001 " -0.104 2.00e-02 2.50e+03 pdb=" C37 FK5 F2001 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 459 " -0.021 2.00e-02 2.50e+03 4.13e-02 1.70e+01 pdb=" C VAL R 459 " 0.071 2.00e-02 2.50e+03 pdb=" O VAL R 459 " -0.027 2.00e-02 2.50e+03 pdb=" N ASP R 460 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 341 " 0.056 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO R 342 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO R 342 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO R 342 " 0.044 5.00e-02 4.00e+02 ... (remaining 1292 not shown) Histogram of nonbonded interaction distances: 1.21 - 1.95: 1 1.95 - 2.69: 134 2.69 - 3.43: 10865 3.43 - 4.16: 17554 4.16 - 4.90: 31509 Nonbonded interactions: 60063 Sorted by model distance: nonbonded pdb="FE FE R1505 " pdb="ZN ZN R1506 " model vdw 1.213 1.450 nonbonded pdb=" OD1 ASN R1126 " pdb="ZN ZN R1506 " model vdw 1.960 2.230 nonbonded pdb=" OD2 ASP R1094 " pdb="ZN ZN R1506 " model vdw 1.991 2.230 nonbonded pdb=" O GLY R 146 " pdb=" OG SER R 184 " model vdw 2.192 3.040 nonbonded pdb=" OD2 ASP R1094 " pdb="FE FE R1505 " model vdw 2.192 2.260 ... (remaining 60058 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.940 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6180 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 : 0.007 0.203 7573 Z= 0.322 Angle : 0.742 8.722 10256 Z= 0.401 Chirality : 0.045 0.321 1148 Planarity : 0.006 0.084 1294 Dihedral : 14.533 177.398 2858 Min Nonbonded Distance : 1.213 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.25 % Allowed : 0.25 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.94 (0.29), residues: 907 helix: 1.08 (0.24), residues: 471 sheet: 0.85 (0.60), residues: 66 loop : 0.14 (0.36), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 302 TYR 0.022 0.001 TYR R 127 PHE 0.028 0.002 PHE R 240 TRP 0.045 0.002 TRP R1110 HIS 0.005 0.001 HIS R1025 Details of bonding type rmsd covalent geometry : bond 0.00660 ( 7569) covalent geometry : angle 0.74140 (10251) SS BOND : bond 0.00239 ( 1) SS BOND : angle 1.49333 ( 2) hydrogen bonds : bond 0.13699 ( 390) hydrogen bonds : angle 6.40323 ( 1155) metal coordination : bond 0.00354 ( 2) link_ASP_CG-ANY_N : bond 0.00040 ( 1) link_ASP_CG-ANY_N : angle 0.70291 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 196 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 VAL cc_start: 0.8024 (t) cc_final: 0.7701 (p) REVERT: R 197 ILE cc_start: 0.7358 (mt) cc_final: 0.7050 (tt) REVERT: R 359 VAL cc_start: 0.3646 (t) cc_final: 0.1787 (m) REVERT: R 1115 LEU cc_start: 0.7815 (tp) cc_final: 0.7461 (tp) REVERT: R 1143 LYS cc_start: 0.7315 (tptp) cc_final: 0.7020 (tptp) REVERT: R 1163 LEU cc_start: 0.7564 (mt) cc_final: 0.7293 (mp) REVERT: R 1190 LYS cc_start: 0.7647 (mtmm) cc_final: 0.7328 (mtmm) REVERT: R 1305 MET cc_start: 0.3538 (tpt) cc_final: 0.3233 (tpt) REVERT: F 37 LYS cc_start: 0.8085 (ttpt) cc_final: 0.7791 (ttpp) REVERT: A 12 PHE cc_start: 0.6741 (m-10) cc_final: 0.6528 (m-10) outliers start: 2 outliers final: 2 residues processed: 198 average time/residue: 0.1058 time to fit residues: 26.5557 Evaluate side-chains 174 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 172 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 459 VAL Chi-restraints excluded: chain A residue 9 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.0470 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1260 GLN R1343 ASN ** F 23 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 = 0.4434 r_free = 0.4434 target = 0.187216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.170176 restraints weight = 10885.077| |-----------------------------------------------------------------------------| r_work (start): 0.4252 rms_B_bonded: 2.39 r_work: 0.4135 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7573 Z= 0.150 Angle : 0.620 8.701 10256 Z= 0.324 Chirality : 0.042 0.158 1148 Planarity : 0.005 0.054 1294 Dihedral : 13.195 175.244 1096 Min Nonbonded Distance : 1.208 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.49 % Allowed : 8.34 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.00 (0.29), residues: 907 helix: 1.16 (0.24), residues: 487 sheet: 0.84 (0.62), residues: 65 loop : 0.06 (0.36), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 302 TYR 0.023 0.002 TYR R 127 PHE 0.018 0.002 PHE R 385 TRP 0.024 0.001 TRP R1110 HIS 0.007 0.001 HIS R1257 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 7569) covalent geometry : angle 0.61920 (10251) SS BOND : bond 0.00105 ( 1) SS BOND : angle 1.23172 ( 2) hydrogen bonds : bond 0.04286 ( 390) hydrogen bonds : angle 4.91149 ( 1155) metal coordination : bond 0.00283 ( 2) link_ASP_CG-ANY_N : bond 0.00052 ( 1) link_ASP_CG-ANY_N : angle 1.10291 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 VAL cc_start: 0.8061 (t) cc_final: 0.7745 (p) REVERT: R 133 ARG cc_start: 0.7401 (ttm110) cc_final: 0.7052 (mtm180) REVERT: R 165 GLU cc_start: 0.7313 (mp0) cc_final: 0.6830 (mp0) REVERT: R 197 ILE cc_start: 0.7600 (mt) cc_final: 0.7297 (tt) REVERT: R 291 PHE cc_start: 0.7897 (t80) cc_final: 0.7678 (t80) REVERT: R 302 ARG cc_start: 0.7567 (pmt170) cc_final: 0.7338 (pmt170) REVERT: R 359 VAL cc_start: 0.3755 (t) cc_final: 0.1592 (m) REVERT: R 417 GLN cc_start: 0.6803 (pt0) cc_final: 0.6584 (pt0) REVERT: R 490 ARG cc_start: 0.7180 (tpt170) cc_final: 0.6667 (tpp-160) REVERT: R 494 LEU cc_start: 0.7604 (mt) cc_final: 0.7207 (mt) REVERT: R 1143 LYS cc_start: 0.7339 (tptp) cc_final: 0.7074 (tptp) REVERT: R 1167 MET cc_start: 0.5821 (tmm) cc_final: 0.4650 (tmm) REVERT: R 1171 PHE cc_start: 0.6788 (m-80) cc_final: 0.5808 (m-80) REVERT: R 1294 LYS cc_start: 0.7771 (ttmt) cc_final: 0.7497 (ttmm) REVERT: R 1305 MET cc_start: 0.3878 (tpt) cc_final: 0.3505 (tpt) REVERT: F 37 LYS cc_start: 0.8355 (ttpt) cc_final: 0.8027 (ttpp) outliers start: 12 outliers final: 9 residues processed: 177 average time/residue: 0.0927 time to fit residues: 21.2656 Evaluate side-chains 171 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 162 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 372 SER Chi-restraints excluded: chain R residue 416 THR Chi-restraints excluded: chain R residue 423 ASP Chi-restraints excluded: chain R residue 515 ASP Chi-restraints excluded: chain R residue 1029 GLU Chi-restraints excluded: chain R residue 1131 HIS Chi-restraints excluded: chain R residue 1210 ASP Chi-restraints excluded: chain A residue 9 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 44 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R1053 ASN ** R1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.182868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.164408 restraints weight = 10799.435| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 2.57 r_work: 0.4092 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7573 Z= 0.167 Angle : 0.629 11.328 10256 Z= 0.323 Chirality : 0.043 0.157 1148 Planarity : 0.005 0.049 1294 Dihedral : 13.163 178.503 1095 Min Nonbonded Distance : 1.148 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.99 % Allowed : 12.70 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.96 (0.29), residues: 907 helix: 1.21 (0.24), residues: 485 sheet: 0.76 (0.61), residues: 71 loop : -0.08 (0.37), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 201 TYR 0.026 0.002 TYR R 127 PHE 0.030 0.002 PHE R1136 TRP 0.012 0.001 TRP R1110 HIS 0.004 0.001 HIS R1257 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 7569) covalent geometry : angle 0.62890 (10251) SS BOND : bond 0.00120 ( 1) SS BOND : angle 0.68390 ( 2) hydrogen bonds : bond 0.04205 ( 390) hydrogen bonds : angle 4.77038 ( 1155) metal coordination : bond 0.00515 ( 2) link_ASP_CG-ANY_N : bond 0.00018 ( 1) link_ASP_CG-ANY_N : angle 0.91330 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 VAL cc_start: 0.8030 (t) cc_final: 0.7714 (p) REVERT: R 133 ARG cc_start: 0.7589 (ttm110) cc_final: 0.7210 (mtm180) REVERT: R 165 GLU cc_start: 0.7461 (mp0) cc_final: 0.7091 (mp0) REVERT: R 240 PHE cc_start: 0.7244 (m-10) cc_final: 0.6905 (m-10) REVERT: R 296 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6761 (mtp) REVERT: R 302 ARG cc_start: 0.7677 (pmt170) cc_final: 0.7330 (pmt170) REVERT: R 314 LYS cc_start: 0.8153 (mtmt) cc_final: 0.7743 (mtmm) REVERT: R 359 VAL cc_start: 0.3670 (t) cc_final: 0.1555 (m) REVERT: R 406 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7757 (tppt) REVERT: R 490 ARG cc_start: 0.7289 (tpt170) cc_final: 0.6768 (tpt170) REVERT: R 494 LEU cc_start: 0.7793 (mt) cc_final: 0.7509 (mt) REVERT: R 1139 LYS cc_start: 0.8027 (ttmt) cc_final: 0.7821 (ttmt) REVERT: R 1143 LYS cc_start: 0.7528 (tptp) cc_final: 0.7229 (tptp) REVERT: R 1155 MET cc_start: 0.5987 (ttt) cc_final: 0.5765 (ttt) REVERT: R 1167 MET cc_start: 0.5966 (tmm) cc_final: 0.5427 (tmm) REVERT: R 1267 TYR cc_start: 0.6053 (m-80) cc_final: 0.5805 (m-10) REVERT: R 1294 LYS cc_start: 0.7754 (ttmt) cc_final: 0.7480 (ttmm) REVERT: R 1305 MET cc_start: 0.4008 (tpt) cc_final: 0.3657 (tpt) REVERT: R 1317 TYR cc_start: 0.7606 (t80) cc_final: 0.7279 (t80) outliers start: 16 outliers final: 12 residues processed: 169 average time/residue: 0.0933 time to fit residues: 20.6185 Evaluate side-chains 173 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 296 MET Chi-restraints excluded: chain R residue 372 SER Chi-restraints excluded: chain R residue 406 LYS Chi-restraints excluded: chain R residue 416 THR Chi-restraints excluded: chain R residue 423 ASP Chi-restraints excluded: chain R residue 464 GLN Chi-restraints excluded: chain R residue 515 ASP Chi-restraints excluded: chain R residue 1029 GLU Chi-restraints excluded: chain R residue 1131 HIS Chi-restraints excluded: chain R residue 1210 ASP Chi-restraints excluded: chain R residue 1315 HIS Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 67 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 87 optimal weight: 0.0010 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 345 GLN R1053 ASN ** R1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1260 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.184169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.165710 restraints weight = 10936.824| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 2.61 r_work: 0.4105 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7573 Z= 0.132 Angle : 0.585 8.925 10256 Z= 0.301 Chirality : 0.041 0.165 1148 Planarity : 0.004 0.046 1294 Dihedral : 13.073 178.490 1093 Min Nonbonded Distance : 1.208 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.24 % Allowed : 15.19 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.17 (0.29), residues: 907 helix: 1.38 (0.24), residues: 487 sheet: 0.91 (0.62), residues: 65 loop : 0.02 (0.36), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R1031 TYR 0.022 0.001 TYR R 127 PHE 0.024 0.002 PHE R 510 TRP 0.015 0.001 TRP R1110 HIS 0.005 0.001 HIS R1257 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 7569) covalent geometry : angle 0.58481 (10251) SS BOND : bond 0.00019 ( 1) SS BOND : angle 0.51393 ( 2) hydrogen bonds : bond 0.03773 ( 390) hydrogen bonds : angle 4.58130 ( 1155) metal coordination : bond 0.00370 ( 2) link_ASP_CG-ANY_N : bond 0.00028 ( 1) link_ASP_CG-ANY_N : angle 0.79150 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 VAL cc_start: 0.8022 (t) cc_final: 0.7693 (p) REVERT: R 133 ARG cc_start: 0.7607 (ttm110) cc_final: 0.7219 (mtm180) REVERT: R 165 GLU cc_start: 0.7411 (mp0) cc_final: 0.6971 (mp0) REVERT: R 166 ASP cc_start: 0.7983 (m-30) cc_final: 0.7758 (m-30) REVERT: R 240 PHE cc_start: 0.7275 (m-10) cc_final: 0.6926 (m-10) REVERT: R 314 LYS cc_start: 0.8149 (mtmt) cc_final: 0.7765 (mtmm) REVERT: R 359 VAL cc_start: 0.3537 (t) cc_final: 0.1422 (m) REVERT: R 490 ARG cc_start: 0.7284 (tpt170) cc_final: 0.6694 (tmt-80) REVERT: R 494 LEU cc_start: 0.7794 (mt) cc_final: 0.6819 (mt) REVERT: R 525 ASN cc_start: 0.7502 (OUTLIER) cc_final: 0.7187 (t0) REVERT: R 1115 LEU cc_start: 0.8034 (tp) cc_final: 0.7771 (tp) REVERT: R 1139 LYS cc_start: 0.8013 (ttmt) cc_final: 0.7801 (ttmt) REVERT: R 1143 LYS cc_start: 0.7538 (tptp) cc_final: 0.7283 (tptp) REVERT: R 1171 PHE cc_start: 0.6913 (m-80) cc_final: 0.6049 (m-80) REVERT: R 1267 TYR cc_start: 0.6018 (m-80) cc_final: 0.5768 (m-10) REVERT: R 1305 MET cc_start: 0.3999 (tpt) cc_final: 0.3717 (tpt) REVERT: R 1317 TYR cc_start: 0.7567 (t80) cc_final: 0.7244 (t80) outliers start: 18 outliers final: 14 residues processed: 173 average time/residue: 0.0943 time to fit residues: 21.3961 Evaluate side-chains 173 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 408 MET Chi-restraints excluded: chain R residue 423 ASP Chi-restraints excluded: chain R residue 464 GLN Chi-restraints excluded: chain R residue 515 ASP Chi-restraints excluded: chain R residue 525 ASN Chi-restraints excluded: chain R residue 1029 GLU Chi-restraints excluded: chain R residue 1131 HIS Chi-restraints excluded: chain R residue 1210 ASP Chi-restraints excluded: chain R residue 1315 HIS Chi-restraints excluded: chain R residue 1340 MET Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 88 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 35 optimal weight: 0.0050 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R1053 ASN ** R1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1260 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.183106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.164722 restraints weight = 10894.225| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 2.58 r_work: 0.4086 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7573 Z= 0.150 Angle : 0.589 8.056 10256 Z= 0.304 Chirality : 0.041 0.145 1148 Planarity : 0.004 0.045 1294 Dihedral : 13.092 179.607 1093 Min Nonbonded Distance : 1.144 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.11 % Allowed : 14.94 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.22 (0.29), residues: 907 helix: 1.43 (0.24), residues: 487 sheet: 1.01 (0.65), residues: 65 loop : 0.01 (0.36), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R1031 TYR 0.021 0.001 TYR R 127 PHE 0.022 0.002 PHE R 510 TRP 0.014 0.001 TRP R1110 HIS 0.003 0.001 HIS R1257 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 7569) covalent geometry : angle 0.58902 (10251) SS BOND : bond 0.00072 ( 1) SS BOND : angle 0.41632 ( 2) hydrogen bonds : bond 0.03887 ( 390) hydrogen bonds : angle 4.56238 ( 1155) metal coordination : bond 0.00451 ( 2) link_ASP_CG-ANY_N : bond 0.00054 ( 1) link_ASP_CG-ANY_N : angle 0.85380 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 VAL cc_start: 0.8038 (t) cc_final: 0.7713 (p) REVERT: R 133 ARG cc_start: 0.7600 (ttm110) cc_final: 0.7236 (mtm180) REVERT: R 165 GLU cc_start: 0.7395 (mp0) cc_final: 0.6975 (mp0) REVERT: R 240 PHE cc_start: 0.7402 (m-10) cc_final: 0.7098 (m-10) REVERT: R 245 MET cc_start: 0.6263 (ptm) cc_final: 0.6038 (ptt) REVERT: R 314 LYS cc_start: 0.8163 (mtmt) cc_final: 0.7791 (mtmm) REVERT: R 359 VAL cc_start: 0.3574 (t) cc_final: 0.1452 (m) REVERT: R 406 LYS cc_start: 0.8057 (tppt) cc_final: 0.7714 (tppt) REVERT: R 490 ARG cc_start: 0.7264 (tpt170) cc_final: 0.6650 (tmt-80) REVERT: R 494 LEU cc_start: 0.7869 (mt) cc_final: 0.6930 (mt) REVERT: R 525 ASN cc_start: 0.7554 (OUTLIER) cc_final: 0.7254 (t0) REVERT: R 1115 LEU cc_start: 0.8034 (tp) cc_final: 0.7777 (tp) REVERT: R 1143 LYS cc_start: 0.7559 (tptp) cc_final: 0.7305 (tptp) REVERT: R 1167 MET cc_start: 0.5818 (tmm) cc_final: 0.5040 (tmm) REVERT: R 1171 PHE cc_start: 0.6893 (m-80) cc_final: 0.5885 (m-80) REVERT: R 1267 TYR cc_start: 0.6004 (m-80) cc_final: 0.5732 (m-10) REVERT: R 1305 MET cc_start: 0.4025 (tpt) cc_final: 0.3779 (tpt) REVERT: R 1317 TYR cc_start: 0.7541 (t80) cc_final: 0.7259 (t80) REVERT: F 37 LYS cc_start: 0.8353 (ttpt) cc_final: 0.8032 (ttpp) REVERT: F 55 LYS cc_start: 0.7657 (mmtt) cc_final: 0.7297 (mmtt) outliers start: 25 outliers final: 21 residues processed: 176 average time/residue: 0.0977 time to fit residues: 22.5035 Evaluate side-chains 183 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 302 ARG Chi-restraints excluded: chain R residue 372 SER Chi-restraints excluded: chain R residue 408 MET Chi-restraints excluded: chain R residue 416 THR Chi-restraints excluded: chain R residue 423 ASP Chi-restraints excluded: chain R residue 464 GLN Chi-restraints excluded: chain R residue 515 ASP Chi-restraints excluded: chain R residue 524 LEU Chi-restraints excluded: chain R residue 525 ASN Chi-restraints excluded: chain R residue 1029 GLU Chi-restraints excluded: chain R residue 1131 HIS Chi-restraints excluded: chain R residue 1210 ASP Chi-restraints excluded: chain R residue 1297 VAL Chi-restraints excluded: chain R residue 1315 HIS Chi-restraints excluded: chain R residue 1340 MET Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 74 optimal weight: 7.9990 chunk 40 optimal weight: 0.0980 chunk 66 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 79 optimal weight: 0.0570 chunk 17 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 345 GLN ** R1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1260 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.184576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.166157 restraints weight = 10848.000| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 2.60 r_work: 0.4097 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7573 Z= 0.128 Angle : 0.586 8.904 10256 Z= 0.301 Chirality : 0.040 0.168 1148 Planarity : 0.004 0.047 1294 Dihedral : 13.018 178.342 1093 Min Nonbonded Distance : 1.202 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.36 % Allowed : 15.94 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.35 (0.29), residues: 907 helix: 1.55 (0.24), residues: 487 sheet: 0.94 (0.64), residues: 65 loop : 0.07 (0.36), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R1031 TYR 0.021 0.001 TYR R 127 PHE 0.023 0.002 PHE R 291 TRP 0.013 0.001 TRP R1110 HIS 0.004 0.000 HIS R1257 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7569) covalent geometry : angle 0.58644 (10251) SS BOND : bond 0.00013 ( 1) SS BOND : angle 0.35510 ( 2) hydrogen bonds : bond 0.03675 ( 390) hydrogen bonds : angle 4.46850 ( 1155) metal coordination : bond 0.00358 ( 2) link_ASP_CG-ANY_N : bond 0.00060 ( 1) link_ASP_CG-ANY_N : angle 0.74665 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 VAL cc_start: 0.8021 (t) cc_final: 0.7689 (p) REVERT: R 133 ARG cc_start: 0.7591 (ttm110) cc_final: 0.7122 (mtm180) REVERT: R 236 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.5821 (tm-30) REVERT: R 240 PHE cc_start: 0.7433 (m-10) cc_final: 0.6955 (m-10) REVERT: R 245 MET cc_start: 0.6259 (ptm) cc_final: 0.6032 (ptt) REVERT: R 314 LYS cc_start: 0.8143 (mtmt) cc_final: 0.7744 (mtmm) REVERT: R 318 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.8060 (ttpm) REVERT: R 359 VAL cc_start: 0.3401 (t) cc_final: 0.1318 (m) REVERT: R 406 LYS cc_start: 0.7991 (tppt) cc_final: 0.7659 (tppt) REVERT: R 490 ARG cc_start: 0.7258 (tpt170) cc_final: 0.6706 (tmt-80) REVERT: R 494 LEU cc_start: 0.7906 (mt) cc_final: 0.6962 (mt) REVERT: R 525 ASN cc_start: 0.7560 (OUTLIER) cc_final: 0.7277 (t0) REVERT: R 1101 PHE cc_start: 0.6976 (m-80) cc_final: 0.6688 (m-80) REVERT: R 1115 LEU cc_start: 0.8013 (tp) cc_final: 0.7752 (tp) REVERT: R 1139 LYS cc_start: 0.8005 (ttmt) cc_final: 0.7797 (mttt) REVERT: R 1143 LYS cc_start: 0.7609 (tptp) cc_final: 0.7341 (tptp) REVERT: R 1171 PHE cc_start: 0.6869 (m-80) cc_final: 0.5998 (m-80) REVERT: R 1261 ASP cc_start: 0.7157 (t0) cc_final: 0.6927 (t0) REVERT: R 1267 TYR cc_start: 0.6018 (m-80) cc_final: 0.5731 (m-10) REVERT: R 1305 MET cc_start: 0.4085 (tpt) cc_final: 0.3852 (tpt) REVERT: R 1317 TYR cc_start: 0.7543 (t80) cc_final: 0.7214 (t80) REVERT: F 55 LYS cc_start: 0.7652 (mmtt) cc_final: 0.7291 (mmtt) outliers start: 27 outliers final: 18 residues processed: 171 average time/residue: 0.0942 time to fit residues: 21.1213 Evaluate side-chains 180 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 236 GLU Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 302 ARG Chi-restraints excluded: chain R residue 318 LYS Chi-restraints excluded: chain R residue 372 SER Chi-restraints excluded: chain R residue 408 MET Chi-restraints excluded: chain R residue 464 GLN Chi-restraints excluded: chain R residue 515 ASP Chi-restraints excluded: chain R residue 524 LEU Chi-restraints excluded: chain R residue 525 ASN Chi-restraints excluded: chain R residue 1029 GLU Chi-restraints excluded: chain R residue 1131 HIS Chi-restraints excluded: chain R residue 1210 ASP Chi-restraints excluded: chain R residue 1297 VAL Chi-restraints excluded: chain R residue 1315 HIS Chi-restraints excluded: chain R residue 1340 MET Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 66 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1053 ASN ** R1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1260 GLN R1343 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.183248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.164547 restraints weight = 10855.656| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 2.60 r_work: 0.4074 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7573 Z= 0.153 Angle : 0.611 9.563 10256 Z= 0.313 Chirality : 0.041 0.145 1148 Planarity : 0.004 0.049 1294 Dihedral : 13.054 179.026 1093 Min Nonbonded Distance : 1.133 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.49 % Allowed : 17.68 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.28 (0.29), residues: 907 helix: 1.53 (0.24), residues: 487 sheet: 0.79 (0.62), residues: 67 loop : -0.00 (0.36), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R1031 TYR 0.020 0.001 TYR R 127 PHE 0.022 0.002 PHE R 291 TRP 0.008 0.001 TRP R1110 HIS 0.002 0.000 HIS R1257 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 7569) covalent geometry : angle 0.61057 (10251) SS BOND : bond 0.00015 ( 1) SS BOND : angle 0.48752 ( 2) hydrogen bonds : bond 0.03864 ( 390) hydrogen bonds : angle 4.51293 ( 1155) metal coordination : bond 0.00374 ( 2) link_ASP_CG-ANY_N : bond 0.00068 ( 1) link_ASP_CG-ANY_N : angle 0.91988 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 106 VAL cc_start: 0.8015 (t) cc_final: 0.7691 (p) REVERT: R 133 ARG cc_start: 0.7626 (ttm110) cc_final: 0.7154 (mtm180) REVERT: R 165 GLU cc_start: 0.7322 (mp0) cc_final: 0.6796 (mp0) REVERT: R 236 GLU cc_start: 0.6501 (OUTLIER) cc_final: 0.5847 (tm-30) REVERT: R 240 PHE cc_start: 0.7453 (m-10) cc_final: 0.6949 (m-80) REVERT: R 245 MET cc_start: 0.6282 (ptm) cc_final: 0.6056 (ptt) REVERT: R 286 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7407 (mt) REVERT: R 314 LYS cc_start: 0.8177 (mtmt) cc_final: 0.7761 (mtmm) REVERT: R 318 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8066 (ttpm) REVERT: R 359 VAL cc_start: 0.3450 (t) cc_final: 0.1367 (m) REVERT: R 406 LYS cc_start: 0.8019 (tppt) cc_final: 0.7506 (tptt) REVERT: R 490 ARG cc_start: 0.7275 (tpt170) cc_final: 0.6726 (tmt-80) REVERT: R 494 LEU cc_start: 0.7920 (mt) cc_final: 0.6994 (mt) REVERT: R 525 ASN cc_start: 0.7548 (OUTLIER) cc_final: 0.7276 (t0) REVERT: R 1115 LEU cc_start: 0.8003 (tp) cc_final: 0.7721 (tp) REVERT: R 1167 MET cc_start: 0.5854 (tmm) cc_final: 0.5137 (tmm) REVERT: R 1171 PHE cc_start: 0.6908 (m-80) cc_final: 0.5973 (m-80) REVERT: R 1217 ASN cc_start: 0.7748 (m110) cc_final: 0.7543 (m110) REVERT: R 1261 ASP cc_start: 0.6859 (t0) cc_final: 0.6633 (t0) REVERT: R 1267 TYR cc_start: 0.6041 (m-80) cc_final: 0.5726 (m-10) REVERT: F 55 LYS cc_start: 0.7703 (mmtt) cc_final: 0.7332 (mmtt) outliers start: 28 outliers final: 23 residues processed: 174 average time/residue: 0.0977 time to fit residues: 22.2231 Evaluate side-chains 187 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 236 GLU Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 302 ARG Chi-restraints excluded: chain R residue 318 LYS Chi-restraints excluded: chain R residue 372 SER Chi-restraints excluded: chain R residue 408 MET Chi-restraints excluded: chain R residue 416 THR Chi-restraints excluded: chain R residue 423 ASP Chi-restraints excluded: chain R residue 464 GLN Chi-restraints excluded: chain R residue 515 ASP Chi-restraints excluded: chain R residue 524 LEU Chi-restraints excluded: chain R residue 525 ASN Chi-restraints excluded: chain R residue 1029 GLU Chi-restraints excluded: chain R residue 1131 HIS Chi-restraints excluded: chain R residue 1210 ASP Chi-restraints excluded: chain R residue 1297 VAL Chi-restraints excluded: chain R residue 1315 HIS Chi-restraints excluded: chain R residue 1340 MET Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 50 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 64 optimal weight: 0.2980 chunk 22 optimal weight: 0.0170 chunk 30 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 chunk 83 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1260 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.185160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.166690 restraints weight = 10853.994| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 2.59 r_work: 0.4117 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7573 Z= 0.124 Angle : 0.595 10.587 10256 Z= 0.303 Chirality : 0.040 0.166 1148 Planarity : 0.004 0.046 1294 Dihedral : 12.902 175.282 1093 Min Nonbonded Distance : 1.206 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.74 % Allowed : 17.81 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.48 (0.29), residues: 907 helix: 1.70 (0.24), residues: 482 sheet: 1.03 (0.64), residues: 65 loop : 0.09 (0.36), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R1031 TYR 0.021 0.001 TYR R 127 PHE 0.024 0.001 PHE R 291 TRP 0.011 0.001 TRP R1110 HIS 0.003 0.000 HIS R1257 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 7569) covalent geometry : angle 0.59458 (10251) SS BOND : bond 0.00051 ( 1) SS BOND : angle 0.46705 ( 2) hydrogen bonds : bond 0.03560 ( 390) hydrogen bonds : angle 4.41286 ( 1155) metal coordination : bond 0.00329 ( 2) link_ASP_CG-ANY_N : bond 0.00068 ( 1) link_ASP_CG-ANY_N : angle 0.72221 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 VAL cc_start: 0.8018 (t) cc_final: 0.7679 (p) REVERT: R 133 ARG cc_start: 0.7464 (ttm110) cc_final: 0.7058 (mtm180) REVERT: R 236 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.5736 (tm-30) REVERT: R 240 PHE cc_start: 0.7455 (m-10) cc_final: 0.6917 (m-80) REVERT: R 245 MET cc_start: 0.6215 (ptm) cc_final: 0.6011 (ptt) REVERT: R 286 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7528 (mt) REVERT: R 314 LYS cc_start: 0.8140 (mtmt) cc_final: 0.7766 (mtmm) REVERT: R 318 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.8053 (ttpm) REVERT: R 359 VAL cc_start: 0.3356 (t) cc_final: 0.1288 (m) REVERT: R 378 GLU cc_start: 0.5969 (tp30) cc_final: 0.5672 (tp30) REVERT: R 406 LYS cc_start: 0.7973 (tppt) cc_final: 0.7481 (tptm) REVERT: R 490 ARG cc_start: 0.7287 (tpt170) cc_final: 0.6752 (tmt-80) REVERT: R 494 LEU cc_start: 0.7922 (mt) cc_final: 0.7023 (mt) REVERT: R 525 ASN cc_start: 0.7496 (OUTLIER) cc_final: 0.7267 (t0) REVERT: R 1101 PHE cc_start: 0.6823 (m-80) cc_final: 0.6486 (m-80) REVERT: R 1167 MET cc_start: 0.5784 (tmm) cc_final: 0.5107 (tmm) REVERT: R 1171 PHE cc_start: 0.6871 (m-80) cc_final: 0.5947 (m-80) REVERT: R 1260 GLN cc_start: 0.6682 (mp-120) cc_final: 0.6408 (mp10) REVERT: R 1261 ASP cc_start: 0.7169 (t0) cc_final: 0.6920 (t0) REVERT: R 1267 TYR cc_start: 0.6045 (m-80) cc_final: 0.5735 (m-10) REVERT: F 55 LYS cc_start: 0.7663 (mmtt) cc_final: 0.7304 (mmtt) outliers start: 30 outliers final: 22 residues processed: 172 average time/residue: 0.0932 time to fit residues: 21.0817 Evaluate side-chains 183 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 236 GLU Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 302 ARG Chi-restraints excluded: chain R residue 318 LYS Chi-restraints excluded: chain R residue 372 SER Chi-restraints excluded: chain R residue 408 MET Chi-restraints excluded: chain R residue 416 THR Chi-restraints excluded: chain R residue 464 GLN Chi-restraints excluded: chain R residue 515 ASP Chi-restraints excluded: chain R residue 524 LEU Chi-restraints excluded: chain R residue 525 ASN Chi-restraints excluded: chain R residue 1029 GLU Chi-restraints excluded: chain R residue 1131 HIS Chi-restraints excluded: chain R residue 1210 ASP Chi-restraints excluded: chain R residue 1297 VAL Chi-restraints excluded: chain R residue 1305 MET Chi-restraints excluded: chain R residue 1315 HIS Chi-restraints excluded: chain R residue 1340 MET Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 44 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 13 optimal weight: 0.0070 chunk 49 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 22 optimal weight: 0.0060 chunk 46 optimal weight: 0.5980 overall best weight: 0.3414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R1053 ASN ** R1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.186313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.168073 restraints weight = 10781.344| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 2.54 r_work: 0.4133 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7573 Z= 0.121 Angle : 0.603 11.150 10256 Z= 0.307 Chirality : 0.040 0.158 1148 Planarity : 0.004 0.046 1294 Dihedral : 12.879 175.342 1093 Min Nonbonded Distance : 1.216 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.36 % Allowed : 18.31 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.29), residues: 907 helix: 1.70 (0.24), residues: 489 sheet: 0.92 (0.63), residues: 65 loop : 0.08 (0.36), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R1031 TYR 0.024 0.001 TYR R1238 PHE 0.025 0.001 PHE R 291 TRP 0.017 0.001 TRP R1110 HIS 0.003 0.000 HIS R1257 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7569) covalent geometry : angle 0.60271 (10251) SS BOND : bond 0.00000 ( 1) SS BOND : angle 0.45857 ( 2) hydrogen bonds : bond 0.03391 ( 390) hydrogen bonds : angle 4.41060 ( 1155) metal coordination : bond 0.00272 ( 2) link_ASP_CG-ANY_N : bond 0.00063 ( 1) link_ASP_CG-ANY_N : angle 0.71357 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 106 VAL cc_start: 0.8042 (t) cc_final: 0.7707 (p) REVERT: R 133 ARG cc_start: 0.7239 (ttm110) cc_final: 0.6954 (mtm180) REVERT: R 236 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.5744 (tm-30) REVERT: R 240 PHE cc_start: 0.7542 (m-10) cc_final: 0.7147 (m-10) REVERT: R 245 MET cc_start: 0.6214 (ptm) cc_final: 0.6003 (ptt) REVERT: R 314 LYS cc_start: 0.8090 (mtmt) cc_final: 0.7687 (mtmm) REVERT: R 318 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7985 (ttpm) REVERT: R 359 VAL cc_start: 0.3317 (t) cc_final: 0.1225 (m) REVERT: R 378 GLU cc_start: 0.5912 (tp30) cc_final: 0.5661 (tp30) REVERT: R 490 ARG cc_start: 0.7281 (tpt170) cc_final: 0.6816 (tmt-80) REVERT: R 494 LEU cc_start: 0.7871 (mt) cc_final: 0.6986 (mt) REVERT: R 525 ASN cc_start: 0.7512 (OUTLIER) cc_final: 0.7280 (t0) REVERT: R 1057 ILE cc_start: 0.7981 (mt) cc_final: 0.7628 (pt) REVERT: R 1098 ARG cc_start: 0.6143 (mmt-90) cc_final: 0.5437 (mmm-85) REVERT: R 1101 PHE cc_start: 0.6796 (m-80) cc_final: 0.6484 (m-80) REVERT: R 1167 MET cc_start: 0.5727 (tmm) cc_final: 0.5105 (tmm) REVERT: R 1171 PHE cc_start: 0.6797 (m-80) cc_final: 0.5979 (m-80) REVERT: R 1226 HIS cc_start: 0.7957 (t70) cc_final: 0.7605 (t70) REVERT: R 1261 ASP cc_start: 0.7120 (t0) cc_final: 0.6858 (t0) REVERT: R 1267 TYR cc_start: 0.5974 (m-80) cc_final: 0.5708 (m-10) REVERT: F 55 LYS cc_start: 0.7681 (mmtt) cc_final: 0.7334 (mmtt) REVERT: A 12 PHE cc_start: 0.6724 (m-10) cc_final: 0.6420 (m-10) outliers start: 27 outliers final: 22 residues processed: 170 average time/residue: 0.0946 time to fit residues: 21.1477 Evaluate side-chains 183 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 236 GLU Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 302 ARG Chi-restraints excluded: chain R residue 318 LYS Chi-restraints excluded: chain R residue 372 SER Chi-restraints excluded: chain R residue 408 MET Chi-restraints excluded: chain R residue 416 THR Chi-restraints excluded: chain R residue 464 GLN Chi-restraints excluded: chain R residue 515 ASP Chi-restraints excluded: chain R residue 524 LEU Chi-restraints excluded: chain R residue 525 ASN Chi-restraints excluded: chain R residue 1029 GLU Chi-restraints excluded: chain R residue 1131 HIS Chi-restraints excluded: chain R residue 1210 ASP Chi-restraints excluded: chain R residue 1297 VAL Chi-restraints excluded: chain R residue 1305 MET Chi-restraints excluded: chain R residue 1315 HIS Chi-restraints excluded: chain R residue 1340 MET Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.2980 chunk 36 optimal weight: 0.0030 chunk 65 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.187628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.169983 restraints weight = 10872.293| |-----------------------------------------------------------------------------| r_work (start): 0.4254 rms_B_bonded: 2.44 r_work: 0.4134 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7573 Z= 0.133 Angle : 0.623 11.925 10256 Z= 0.316 Chirality : 0.041 0.164 1148 Planarity : 0.005 0.054 1294 Dihedral : 12.897 176.519 1093 Min Nonbonded Distance : 1.183 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.36 % Allowed : 18.06 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.37 (0.29), residues: 907 helix: 1.62 (0.24), residues: 489 sheet: 0.72 (0.64), residues: 65 loop : 0.04 (0.36), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 199 TYR 0.019 0.001 TYR R 127 PHE 0.022 0.002 PHE R 291 TRP 0.014 0.001 TRP R1110 HIS 0.004 0.000 HIS R1257 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7569) covalent geometry : angle 0.62307 (10251) SS BOND : bond 0.00005 ( 1) SS BOND : angle 0.38326 ( 2) hydrogen bonds : bond 0.03573 ( 390) hydrogen bonds : angle 4.45829 ( 1155) metal coordination : bond 0.00375 ( 2) link_ASP_CG-ANY_N : bond 0.00087 ( 1) link_ASP_CG-ANY_N : angle 0.69108 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 106 VAL cc_start: 0.8067 (t) cc_final: 0.7723 (p) REVERT: R 133 ARG cc_start: 0.7235 (ttm110) cc_final: 0.6785 (mtm180) REVERT: R 165 GLU cc_start: 0.7169 (mp0) cc_final: 0.6648 (mp0) REVERT: R 236 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.5834 (tm-30) REVERT: R 240 PHE cc_start: 0.7483 (m-10) cc_final: 0.7104 (m-10) REVERT: R 314 LYS cc_start: 0.8105 (mtmt) cc_final: 0.7735 (mtmm) REVERT: R 318 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7968 (ttpm) REVERT: R 359 VAL cc_start: 0.3359 (t) cc_final: 0.1266 (m) REVERT: R 406 LYS cc_start: 0.7977 (tppt) cc_final: 0.7600 (tppt) REVERT: R 490 ARG cc_start: 0.7266 (tpt170) cc_final: 0.6790 (tmt-80) REVERT: R 494 LEU cc_start: 0.7803 (mt) cc_final: 0.6942 (mt) REVERT: R 525 ASN cc_start: 0.7489 (OUTLIER) cc_final: 0.7257 (t0) REVERT: R 1098 ARG cc_start: 0.6249 (mmt-90) cc_final: 0.5600 (mpt-90) REVERT: R 1101 PHE cc_start: 0.6802 (m-80) cc_final: 0.6486 (m-80) REVERT: R 1167 MET cc_start: 0.5822 (tmm) cc_final: 0.5187 (tmm) REVERT: R 1171 PHE cc_start: 0.6803 (m-80) cc_final: 0.5912 (m-80) REVERT: R 1261 ASP cc_start: 0.7104 (t0) cc_final: 0.6835 (t0) REVERT: R 1267 TYR cc_start: 0.5921 (m-80) cc_final: 0.5690 (m-10) REVERT: F 55 LYS cc_start: 0.7693 (mmtt) cc_final: 0.7356 (mmtt) outliers start: 27 outliers final: 22 residues processed: 169 average time/residue: 0.0958 time to fit residues: 21.3776 Evaluate side-chains 182 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 236 GLU Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 302 ARG Chi-restraints excluded: chain R residue 318 LYS Chi-restraints excluded: chain R residue 372 SER Chi-restraints excluded: chain R residue 408 MET Chi-restraints excluded: chain R residue 416 THR Chi-restraints excluded: chain R residue 464 GLN Chi-restraints excluded: chain R residue 515 ASP Chi-restraints excluded: chain R residue 524 LEU Chi-restraints excluded: chain R residue 525 ASN Chi-restraints excluded: chain R residue 1029 GLU Chi-restraints excluded: chain R residue 1131 HIS Chi-restraints excluded: chain R residue 1210 ASP Chi-restraints excluded: chain R residue 1297 VAL Chi-restraints excluded: chain R residue 1305 MET Chi-restraints excluded: chain R residue 1315 HIS Chi-restraints excluded: chain R residue 1340 MET Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 74 optimal weight: 4.9990 chunk 22 optimal weight: 0.0470 chunk 60 optimal weight: 0.0000 chunk 52 optimal weight: 1.9990 chunk 8 optimal weight: 0.0060 chunk 86 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.2298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1309 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 = 0.4463 r_free = 0.4463 target = 0.189534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.171824 restraints weight = 10838.312| |-----------------------------------------------------------------------------| r_work (start): 0.4275 rms_B_bonded: 2.46 r_work: 0.4153 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7573 Z= 0.117 Angle : 0.599 11.655 10256 Z= 0.305 Chirality : 0.040 0.156 1148 Planarity : 0.004 0.048 1294 Dihedral : 12.710 173.626 1093 Min Nonbonded Distance : 1.273 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.74 % Allowed : 19.05 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.29), residues: 907 helix: 1.77 (0.24), residues: 489 sheet: 0.65 (0.65), residues: 65 loop : 0.08 (0.36), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 199 TYR 0.019 0.001 TYR R 127 PHE 0.022 0.001 PHE R 291 TRP 0.017 0.001 TRP R1110 HIS 0.003 0.000 HIS R1257 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 7569) covalent geometry : angle 0.59933 (10251) SS BOND : bond 0.00066 ( 1) SS BOND : angle 0.45979 ( 2) hydrogen bonds : bond 0.03287 ( 390) hydrogen bonds : angle 4.37979 ( 1155) metal coordination : bond 0.00291 ( 2) link_ASP_CG-ANY_N : bond 0.00086 ( 1) link_ASP_CG-ANY_N : angle 0.63211 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1716.89 seconds wall clock time: 30 minutes 10.92 seconds (1810.92 seconds total)