Starting phenix.real_space_refine on Mon May 12 00:13:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kdf_62274/05_2025/9kdf_62274.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kdf_62274/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9kdf_62274/05_2025/9kdf_62274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kdf_62274/05_2025/9kdf_62274.map" model { file = "/net/cci-nas-00/data/ceres_data/9kdf_62274/05_2025/9kdf_62274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kdf_62274/05_2025/9kdf_62274.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.51, per 1000 atoms: 0.61 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: 2.29 Conformation dependent library (CDL) restraints added in 857.8 milliseconds 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: 0.81 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: 2.28 Time building geometry restraints manager: 2.54 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: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.830 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.640 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.045 0.002 TRP R1110 HIS 0.005 0.001 HIS R1025 PHE 0.028 0.002 PHE R 240 TYR 0.022 0.001 TYR R 127 ARG 0.007 0.000 ARG R 302 Details of bonding type rmsd hydrogen bonds : bond 0.13699 ( 390) hydrogen bonds : angle 6.40323 ( 1155) link_ASP_CG-ANY_N : bond 0.00040 ( 1) link_ASP_CG-ANY_N : angle 0.70291 ( 3) metal coordination : bond 0.00354 ( 2) SS BOND : bond 0.00239 ( 1) SS BOND : angle 1.49333 ( 2) covalent geometry : bond 0.00660 ( 7569) covalent geometry : angle 0.74140 (10251) *********************** 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 : 0.803 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: 0.1788 (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: 0.7022 (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: 0.7794 (ttpp) REVERT: A 12 PHE cc_start: 0.6741 (m-10) cc_final: 0.6527 (m-10) outliers start: 2 outliers final: 2 residues processed: 198 average time/residue: 0.2475 time to fit residues: 61.8145 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 : 0.814 ------------------------------------------------------------------------------- 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 75 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 0.0050 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 0.0970 chunk 42 optimal weight: 0.2980 chunk 52 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 overall best weight: 0.3592 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** R1343 ASN ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.188855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.172049 restraints weight = 10776.370| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 2.36 r_work: 0.4156 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 0.1590 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= 0.133 Angle : 0.605 8.449 10256 Z= 0.317 Chirality : 0.041 0.159 1148 Planarity : 0.005 0.053 1294 Dihedral : 13.134 174.184 1096 Min Nonbonded Distance : 1.257 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.37 % Allowed : 8.72 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.29), residues: 907 helix: 1.21 (0.24), residues: 487 sheet: 0.87 (0.61), residues: 65 loop : 0.11 (0.37), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R1110 HIS 0.005 0.001 HIS R1257 PHE 0.018 0.002 PHE R 385 TYR 0.023 0.001 TYR R 127 ARG 0.008 0.000 ARG R 302 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 390) hydrogen bonds : angle 4.91005 ( 1155) link_ASP_CG-ANY_N : bond 0.00007 ( 1) link_ASP_CG-ANY_N : angle 1.04979 ( 3) metal coordination : bond 0.00217 ( 2) SS BOND : bond 0.00079 ( 1) SS BOND : angle 1.16029 ( 2) covalent geometry : bond 0.00301 ( 7569) covalent geometry : angle 0.60501 (10251) *********************** 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 187 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 176 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 VAL cc_start: 0.8064 (t) cc_final: 0.7756 (p) REVERT: R 133 ARG cc_start: 0.7308 (ttm110) cc_final: 0.6992 (mtm180) REVERT: R 165 GLU cc_start: 0.7290 (mp0) cc_final: 0.6689 (mp0) REVERT: R 197 ILE cc_start: 0.7549 (mt) cc_final: 0.7235 (tt) REVERT: R 291 PHE cc_start: 0.7930 (t80) cc_final: 0.7679 (t80) REVERT: R 302 ARG cc_start: 0.7574 (pmt170) cc_final: 0.7347 (pmt170) REVERT: R 314 LYS cc_start: 0.8047 (mtmt) cc_final: 0.7665 (mtmm) REVERT: R 359 VAL cc_start: 0.3652 (t) cc_final: 0.1496 (m) REVERT: R 417 GLN cc_start: 0.6772 (pt0) cc_final: 0.6545 (pt0) REVERT: R 490 ARG cc_start: 0.7139 (tpt170) cc_final: 0.6910 (tpp-160) REVERT: R 1028 LYS cc_start: 0.7804 (mttt) cc_final: 0.7480 (mtmm) REVERT: R 1101 PHE cc_start: 0.6526 (m-80) cc_final: 0.6321 (m-80) REVERT: R 1110 TRP cc_start: 0.5097 (m-10) cc_final: 0.4634 (m-10) REVERT: R 1143 LYS cc_start: 0.7310 (tptp) cc_final: 0.7092 (tppt) REVERT: R 1167 MET cc_start: 0.5760 (tmm) cc_final: 0.4631 (tmm) REVERT: R 1171 PHE cc_start: 0.6756 (m-80) cc_final: 0.5807 (m-80) REVERT: R 1305 MET cc_start: 0.3789 (tpt) cc_final: 0.3442 (tpt) REVERT: R 1317 TYR cc_start: 0.7626 (t80) cc_final: 0.7126 (t80) REVERT: F 37 LYS cc_start: 0.8330 (ttpt) cc_final: 0.8012 (ttpp) outliers start: 11 outliers final: 8 residues processed: 178 average time/residue: 0.2282 time to fit residues: 52.7675 Evaluate side-chains 173 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 165 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 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 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 65 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 0.2980 chunk 62 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 412 ASN R1053 ASN ** R1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1260 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 = 0.4425 r_free = 0.4425 target = 0.185209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.167049 restraints weight = 10934.380| |-----------------------------------------------------------------------------| r_work (start): 0.4249 rms_B_bonded: 2.57 r_work: 0.4125 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7573 Z= 0.135 Angle : 0.578 8.178 10256 Z= 0.301 Chirality : 0.041 0.150 1148 Planarity : 0.004 0.048 1294 Dihedral : 13.101 177.518 1095 Min Nonbonded Distance : 1.202 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.24 % Allowed : 11.46 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.29), residues: 907 helix: 1.37 (0.24), residues: 479 sheet: 0.82 (0.62), residues: 65 loop : 0.06 (0.36), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R1110 HIS 0.005 0.001 HIS R1257 PHE 0.025 0.002 PHE R 510 TYR 0.025 0.001 TYR R 127 ARG 0.005 0.000 ARG R 201 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 390) hydrogen bonds : angle 4.67386 ( 1155) link_ASP_CG-ANY_N : bond 0.00039 ( 1) link_ASP_CG-ANY_N : angle 0.87049 ( 3) metal coordination : bond 0.00309 ( 2) SS BOND : bond 0.00040 ( 1) SS BOND : angle 0.71707 ( 2) covalent geometry : bond 0.00307 ( 7569) covalent geometry : angle 0.57830 (10251) *********************** 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 185 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 VAL cc_start: 0.8024 (t) cc_final: 0.7692 (p) REVERT: R 133 ARG cc_start: 0.7458 (ttm110) cc_final: 0.7106 (mtm180) REVERT: R 165 GLU cc_start: 0.7469 (mp0) cc_final: 0.7043 (mp0) REVERT: R 197 ILE cc_start: 0.7395 (mt) cc_final: 0.7019 (tt) REVERT: R 236 GLU cc_start: 0.6546 (tm-30) cc_final: 0.5853 (tm-30) REVERT: R 240 PHE cc_start: 0.7107 (m-10) cc_final: 0.6528 (m-10) REVERT: R 296 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6714 (mtp) REVERT: R 302 ARG cc_start: 0.7684 (pmt170) cc_final: 0.7326 (pmt170) REVERT: R 314 LYS cc_start: 0.8101 (mtmt) cc_final: 0.7756 (mtmm) REVERT: R 359 VAL cc_start: 0.3574 (t) cc_final: 0.1465 (m) REVERT: R 490 ARG cc_start: 0.7268 (tpt170) cc_final: 0.6794 (tpp-160) REVERT: R 494 LEU cc_start: 0.7783 (mt) cc_final: 0.7351 (mt) REVERT: R 1110 TRP cc_start: 0.5190 (m-10) cc_final: 0.4726 (m-10) REVERT: R 1139 LYS cc_start: 0.8028 (ttmt) cc_final: 0.7828 (ttmt) REVERT: R 1143 LYS cc_start: 0.7436 (tptp) cc_final: 0.7142 (tptp) REVERT: R 1163 LEU cc_start: 0.7722 (mt) cc_final: 0.7506 (mp) REVERT: R 1167 MET cc_start: 0.5837 (tmm) cc_final: 0.5360 (tmm) REVERT: R 1267 TYR cc_start: 0.6026 (m-80) cc_final: 0.5797 (m-10) REVERT: R 1305 MET cc_start: 0.3911 (tpt) cc_final: 0.3566 (tpt) outliers start: 18 outliers final: 15 residues processed: 171 average time/residue: 0.2195 time to fit residues: 49.1601 Evaluate side-chains 175 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 110 LEU 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 Chi-restraints excluded: chain F residue 50 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 11 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4399 r_free = 0.4399 target = 0.182654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.164192 restraints weight = 10819.093| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 2.57 r_work: 0.4088 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7573 Z= 0.169 Angle : 0.602 7.930 10256 Z= 0.315 Chirality : 0.042 0.149 1148 Planarity : 0.005 0.048 1294 Dihedral : 13.193 179.659 1093 Min Nonbonded Distance : 1.131 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.74 % Allowed : 13.82 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.29), residues: 907 helix: 1.26 (0.24), residues: 480 sheet: 0.75 (0.61), residues: 71 loop : 0.07 (0.37), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R1328 HIS 0.003 0.001 HIS R1257 PHE 0.025 0.002 PHE R 510 TYR 0.023 0.001 TYR R 127 ARG 0.009 0.001 ARG R 199 Details of bonding type rmsd hydrogen bonds : bond 0.04149 ( 390) hydrogen bonds : angle 4.66730 ( 1155) link_ASP_CG-ANY_N : bond 0.00024 ( 1) link_ASP_CG-ANY_N : angle 0.93146 ( 3) metal coordination : bond 0.00495 ( 2) SS BOND : bond 0.00136 ( 1) SS BOND : angle 0.50647 ( 2) covalent geometry : bond 0.00384 ( 7569) covalent geometry : angle 0.60202 (10251) *********************** 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 188 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 VAL cc_start: 0.8049 (t) cc_final: 0.7728 (p) REVERT: R 133 ARG cc_start: 0.7611 (ttm110) cc_final: 0.7172 (mtm180) REVERT: R 165 GLU cc_start: 0.7419 (mp0) cc_final: 0.6897 (mp0) REVERT: R 197 ILE cc_start: 0.7603 (mt) cc_final: 0.7269 (tt) REVERT: R 199 ARG cc_start: 0.7109 (ttm-80) cc_final: 0.6612 (mmm-85) REVERT: R 236 GLU cc_start: 0.6587 (tm-30) cc_final: 0.6061 (tm-30) REVERT: R 240 PHE cc_start: 0.7381 (m-10) cc_final: 0.6944 (m-10) REVERT: R 296 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6842 (mtp) REVERT: R 314 LYS cc_start: 0.8068 (mtmt) cc_final: 0.7623 (mtmm) REVERT: R 359 VAL cc_start: 0.3730 (t) cc_final: 0.1671 (m) REVERT: R 406 LYS cc_start: 0.8080 (tppt) cc_final: 0.7742 (tppt) REVERT: R 490 ARG cc_start: 0.7298 (tpt170) cc_final: 0.6785 (tpt170) REVERT: R 494 LEU cc_start: 0.7765 (mt) cc_final: 0.7492 (mt) REVERT: R 1110 TRP cc_start: 0.5361 (m-10) cc_final: 0.4675 (m-10) REVERT: R 1115 LEU cc_start: 0.8005 (tp) cc_final: 0.7770 (tp) REVERT: R 1139 LYS cc_start: 0.8022 (ttmt) cc_final: 0.7814 (ttmt) REVERT: R 1143 LYS cc_start: 0.7550 (tptp) cc_final: 0.7246 (tptp) REVERT: R 1171 PHE cc_start: 0.6980 (m-80) cc_final: 0.6153 (m-80) REVERT: R 1194 PHE cc_start: 0.6983 (m-80) cc_final: 0.6517 (m-80) REVERT: R 1267 TYR cc_start: 0.6012 (m-80) cc_final: 0.5771 (m-10) REVERT: R 1305 MET cc_start: 0.4055 (tpt) cc_final: 0.3742 (tpt) REVERT: R 1317 TYR cc_start: 0.7629 (t80) cc_final: 0.7366 (t80) REVERT: F 32 MET cc_start: 0.7864 (mtm) cc_final: 0.7639 (mtm) REVERT: F 55 LYS cc_start: 0.7632 (mmtt) cc_final: 0.7285 (mmtt) outliers start: 22 outliers final: 17 residues processed: 172 average time/residue: 0.2125 time to fit residues: 47.6669 Evaluate side-chains 177 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 ILE Chi-restraints excluded: chain R residue 125 ILE 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 20 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 76 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 = 0.4415 r_free = 0.4415 target = 0.184375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.166023 restraints weight = 10743.678| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 2.57 r_work: 0.4095 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.2395 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= 0.130 Angle : 0.574 8.361 10256 Z= 0.297 Chirality : 0.041 0.194 1148 Planarity : 0.004 0.044 1294 Dihedral : 13.126 179.775 1093 Min Nonbonded Distance : 1.201 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.74 % Allowed : 15.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.29), residues: 907 helix: 1.45 (0.24), residues: 482 sheet: 0.93 (0.61), residues: 71 loop : 0.17 (0.37), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R1328 HIS 0.003 0.000 HIS R1257 PHE 0.022 0.002 PHE R 510 TYR 0.021 0.001 TYR R 127 ARG 0.006 0.000 ARG R 199 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 390) hydrogen bonds : angle 4.53173 ( 1155) link_ASP_CG-ANY_N : bond 0.00073 ( 1) link_ASP_CG-ANY_N : angle 0.77216 ( 3) metal coordination : bond 0.00402 ( 2) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.47270 ( 2) covalent geometry : bond 0.00295 ( 7569) covalent geometry : angle 0.57355 (10251) *********************** 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 183 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 VAL cc_start: 0.8018 (t) cc_final: 0.7697 (p) REVERT: R 133 ARG cc_start: 0.7590 (ttm110) cc_final: 0.7221 (mtm180) REVERT: R 165 GLU cc_start: 0.7394 (mp0) cc_final: 0.6900 (mp0) REVERT: R 197 ILE cc_start: 0.7559 (mt) cc_final: 0.7208 (tt) REVERT: R 236 GLU cc_start: 0.6471 (tm-30) cc_final: 0.6184 (tm-30) REVERT: R 240 PHE cc_start: 0.7352 (m-10) cc_final: 0.6992 (m-10) REVERT: R 314 LYS cc_start: 0.8024 (mtmt) cc_final: 0.7577 (mtmm) REVERT: R 359 VAL cc_start: 0.3493 (t) cc_final: 0.1396 (m) REVERT: R 490 ARG cc_start: 0.7294 (tpt170) cc_final: 0.6823 (tpp-160) REVERT: R 494 LEU cc_start: 0.7819 (mt) cc_final: 0.7388 (mt) REVERT: R 525 ASN cc_start: 0.7548 (OUTLIER) cc_final: 0.7245 (t0) REVERT: R 1115 LEU cc_start: 0.8042 (tp) cc_final: 0.7791 (tp) REVERT: R 1139 LYS cc_start: 0.8002 (ttmt) cc_final: 0.7783 (ttmt) REVERT: R 1143 LYS cc_start: 0.7514 (tptp) cc_final: 0.7244 (tptp) REVERT: R 1167 MET cc_start: 0.5916 (tmm) cc_final: 0.5108 (tmm) REVERT: R 1171 PHE cc_start: 0.6913 (m-80) cc_final: 0.5838 (m-80) REVERT: R 1194 PHE cc_start: 0.6965 (m-80) cc_final: 0.6537 (m-80) REVERT: R 1261 ASP cc_start: 0.6852 (t0) cc_final: 0.6606 (t0) REVERT: R 1267 TYR cc_start: 0.5990 (m-80) cc_final: 0.5721 (m-10) REVERT: R 1305 MET cc_start: 0.4019 (tpt) cc_final: 0.3724 (tpt) REVERT: R 1317 TYR cc_start: 0.7546 (t80) cc_final: 0.7287 (t80) REVERT: F 32 MET cc_start: 0.7849 (mtm) cc_final: 0.7600 (mtm) REVERT: F 55 LYS cc_start: 0.7611 (mmtt) cc_final: 0.7239 (mmtt) outliers start: 22 outliers final: 16 residues processed: 169 average time/residue: 0.2176 time to fit residues: 48.1964 Evaluate side-chains 177 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 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 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 1210 ASP Chi-restraints excluded: chain R residue 1297 VAL 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 31 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 73 optimal weight: 0.0980 chunk 46 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 345 GLN R 412 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 = 0.4394 r_free = 0.4394 target = 0.182275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.163642 restraints weight = 10775.805| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 2.58 r_work: 0.4064 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7573 Z= 0.171 Angle : 0.608 8.863 10256 Z= 0.315 Chirality : 0.042 0.146 1148 Planarity : 0.004 0.048 1294 Dihedral : 13.198 179.959 1093 Min Nonbonded Distance : 1.118 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.36 % Allowed : 15.69 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.29), residues: 907 helix: 1.35 (0.24), residues: 481 sheet: 0.94 (0.62), residues: 67 loop : 0.02 (0.36), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R1328 HIS 0.003 0.001 HIS R1257 PHE 0.020 0.002 PHE R 291 TYR 0.021 0.001 TYR R 127 ARG 0.006 0.001 ARG R 201 Details of bonding type rmsd hydrogen bonds : bond 0.04058 ( 390) hydrogen bonds : angle 4.58407 ( 1155) link_ASP_CG-ANY_N : bond 0.00063 ( 1) link_ASP_CG-ANY_N : angle 0.90168 ( 3) metal coordination : bond 0.00530 ( 2) SS BOND : bond 0.00078 ( 1) SS BOND : angle 0.34372 ( 2) covalent geometry : bond 0.00389 ( 7569) covalent geometry : angle 0.60784 (10251) *********************** 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 191 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 VAL cc_start: 0.8025 (t) cc_final: 0.7693 (p) REVERT: R 133 ARG cc_start: 0.7681 (ttm110) cc_final: 0.7289 (mtm180) REVERT: R 165 GLU cc_start: 0.7425 (mp0) cc_final: 0.6878 (mp0) REVERT: R 197 ILE cc_start: 0.7447 (mt) cc_final: 0.7136 (tt) REVERT: R 236 GLU cc_start: 0.6460 (OUTLIER) cc_final: 0.5967 (tm-30) REVERT: R 240 PHE cc_start: 0.7509 (m-10) cc_final: 0.7007 (m-10) REVERT: R 314 LYS cc_start: 0.8087 (mtmt) cc_final: 0.7632 (mtmm) REVERT: R 359 VAL cc_start: 0.3590 (t) cc_final: 0.1487 (m) REVERT: R 490 ARG cc_start: 0.7291 (tpt170) cc_final: 0.6757 (tpt170) REVERT: R 494 LEU cc_start: 0.7926 (mt) cc_final: 0.7618 (mt) REVERT: R 525 ASN cc_start: 0.7595 (OUTLIER) cc_final: 0.7303 (t0) REVERT: R 1115 LEU cc_start: 0.8066 (tp) cc_final: 0.7819 (tp) REVERT: R 1139 LYS cc_start: 0.8051 (ttmt) cc_final: 0.7825 (ttmt) REVERT: R 1143 LYS cc_start: 0.7595 (tptp) cc_final: 0.7300 (tptp) REVERT: R 1167 MET cc_start: 0.6063 (tmm) cc_final: 0.5073 (tmm) REVERT: R 1171 PHE cc_start: 0.6994 (m-80) cc_final: 0.5846 (m-80) REVERT: R 1194 PHE cc_start: 0.7030 (m-80) cc_final: 0.6573 (m-80) REVERT: R 1261 ASP cc_start: 0.6891 (t0) cc_final: 0.6645 (t0) REVERT: R 1267 TYR cc_start: 0.6019 (m-80) cc_final: 0.5690 (m-10) REVERT: F 32 MET cc_start: 0.7845 (mtm) cc_final: 0.7586 (mtm) REVERT: F 55 LYS cc_start: 0.7724 (mmtt) cc_final: 0.7363 (mmtt) outliers start: 27 outliers final: 22 residues processed: 174 average time/residue: 0.2398 time to fit residues: 55.3364 Evaluate side-chains 184 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 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 1057 ILE 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 20 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** R1343 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.183444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.164789 restraints weight = 10712.967| |-----------------------------------------------------------------------------| r_work (start): 0.4215 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: 0.6556 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7573 Z= 0.151 Angle : 0.614 9.977 10256 Z= 0.314 Chirality : 0.041 0.146 1148 Planarity : 0.005 0.055 1294 Dihedral : 13.209 179.996 1093 Min Nonbonded Distance : 1.140 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.36 % Allowed : 16.81 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.29), residues: 907 helix: 1.43 (0.24), residues: 481 sheet: 1.12 (0.65), residues: 65 loop : 0.05 (0.36), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R1110 HIS 0.004 0.001 HIS R 452 PHE 0.023 0.002 PHE R 291 TYR 0.021 0.001 TYR R 127 ARG 0.010 0.001 ARG R 199 Details of bonding type rmsd hydrogen bonds : bond 0.03870 ( 390) hydrogen bonds : angle 4.54645 ( 1155) link_ASP_CG-ANY_N : bond 0.00063 ( 1) link_ASP_CG-ANY_N : angle 0.89432 ( 3) metal coordination : bond 0.00432 ( 2) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.42783 ( 2) covalent geometry : bond 0.00345 ( 7569) covalent geometry : angle 0.61352 (10251) *********************** 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 192 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 VAL cc_start: 0.8037 (t) cc_final: 0.7697 (p) REVERT: R 133 ARG cc_start: 0.7653 (ttm110) cc_final: 0.7177 (mtm180) REVERT: R 165 GLU cc_start: 0.7378 (mp0) cc_final: 0.6855 (mp0) REVERT: R 197 ILE cc_start: 0.7578 (mt) cc_final: 0.7260 (tt) REVERT: R 236 GLU cc_start: 0.6418 (OUTLIER) cc_final: 0.5921 (tm-30) REVERT: R 240 PHE cc_start: 0.7610 (m-10) cc_final: 0.7094 (m-10) REVERT: R 314 LYS cc_start: 0.8037 (mtmt) cc_final: 0.7591 (mtmm) REVERT: R 359 VAL cc_start: 0.3555 (t) cc_final: 0.1453 (m) REVERT: R 378 GLU cc_start: 0.6100 (tp30) cc_final: 0.5745 (tp30) REVERT: R 406 LYS cc_start: 0.8021 (tppt) cc_final: 0.7689 (tppt) REVERT: R 490 ARG cc_start: 0.7278 (tpt170) cc_final: 0.6736 (tpt170) REVERT: R 494 LEU cc_start: 0.7884 (mt) cc_final: 0.7578 (mt) REVERT: R 525 ASN cc_start: 0.7625 (OUTLIER) cc_final: 0.7339 (t0) REVERT: R 1115 LEU cc_start: 0.8060 (tp) cc_final: 0.7794 (tp) REVERT: R 1143 LYS cc_start: 0.7597 (tptp) cc_final: 0.7301 (tptp) REVERT: R 1167 MET cc_start: 0.5983 (tmm) cc_final: 0.5125 (tmm) REVERT: R 1171 PHE cc_start: 0.6982 (m-80) cc_final: 0.5977 (m-80) REVERT: R 1194 PHE cc_start: 0.7023 (m-80) cc_final: 0.6578 (m-80) REVERT: R 1260 GLN cc_start: 0.6702 (mp-120) cc_final: 0.6482 (mp10) REVERT: R 1261 ASP cc_start: 0.6881 (t0) cc_final: 0.6629 (t0) REVERT: R 1267 TYR cc_start: 0.5996 (m-80) cc_final: 0.5686 (m-10) REVERT: F 32 MET cc_start: 0.7831 (mtm) cc_final: 0.7554 (mtm) REVERT: F 55 LYS cc_start: 0.7715 (mmtt) cc_final: 0.7352 (mmtt) REVERT: A 12 PHE cc_start: 0.6817 (m-10) cc_final: 0.6440 (m-10) outliers start: 27 outliers final: 22 residues processed: 175 average time/residue: 0.2201 time to fit residues: 50.4003 Evaluate side-chains 185 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 236 GLU 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 1057 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 43 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.4390 r_free = 0.4390 target = 0.182107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.163561 restraints weight = 10745.370| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 2.57 r_work: 0.4070 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7573 Z= 0.179 Angle : 0.648 10.104 10256 Z= 0.330 Chirality : 0.043 0.146 1148 Planarity : 0.004 0.048 1294 Dihedral : 13.245 179.478 1093 Min Nonbonded Distance : 1.112 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.74 % Allowed : 17.06 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.29), residues: 907 helix: 1.30 (0.24), residues: 488 sheet: 0.97 (0.65), residues: 65 loop : -0.11 (0.36), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R1328 HIS 0.002 0.001 HIS R 452 PHE 0.021 0.002 PHE R1136 TYR 0.020 0.001 TYR R 127 ARG 0.008 0.001 ARG R1031 Details of bonding type rmsd hydrogen bonds : bond 0.04118 ( 390) hydrogen bonds : angle 4.59913 ( 1155) link_ASP_CG-ANY_N : bond 0.00080 ( 1) link_ASP_CG-ANY_N : angle 0.92939 ( 3) metal coordination : bond 0.00552 ( 2) SS BOND : bond 0.00069 ( 1) SS BOND : angle 0.39761 ( 2) covalent geometry : bond 0.00409 ( 7569) covalent geometry : angle 0.64762 (10251) *********************** 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 192 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 VAL cc_start: 0.8030 (t) cc_final: 0.7697 (p) REVERT: R 133 ARG cc_start: 0.7725 (ttm110) cc_final: 0.7201 (mtm180) REVERT: R 165 GLU cc_start: 0.7463 (mp0) cc_final: 0.6896 (mp0) REVERT: R 197 ILE cc_start: 0.7488 (mt) cc_final: 0.7200 (tt) REVERT: R 236 GLU cc_start: 0.6460 (OUTLIER) cc_final: 0.5957 (tm-30) REVERT: R 240 PHE cc_start: 0.7677 (m-10) cc_final: 0.7147 (m-80) REVERT: R 314 LYS cc_start: 0.8071 (mtmt) cc_final: 0.7689 (mtmm) REVERT: R 318 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8085 (ttpm) REVERT: R 359 VAL cc_start: 0.3753 (t) cc_final: 0.1689 (m) REVERT: R 378 GLU cc_start: 0.6142 (tp30) cc_final: 0.5786 (tp30) REVERT: R 406 LYS cc_start: 0.8042 (tppt) cc_final: 0.7701 (tppt) REVERT: R 490 ARG cc_start: 0.7278 (tpt170) cc_final: 0.6791 (tpt170) REVERT: R 494 LEU cc_start: 0.7887 (mt) cc_final: 0.7594 (mt) REVERT: R 525 ASN cc_start: 0.7643 (OUTLIER) cc_final: 0.7375 (t0) REVERT: R 1115 LEU cc_start: 0.8071 (tp) cc_final: 0.7806 (tp) REVERT: R 1171 PHE cc_start: 0.7025 (m-80) cc_final: 0.6788 (m-80) REVERT: R 1194 PHE cc_start: 0.7060 (m-80) cc_final: 0.6601 (m-80) REVERT: R 1261 ASP cc_start: 0.6911 (t0) cc_final: 0.6662 (t0) REVERT: R 1267 TYR cc_start: 0.6022 (m-80) cc_final: 0.5746 (m-10) REVERT: F 32 MET cc_start: 0.7851 (mtm) cc_final: 0.7561 (mtm) REVERT: F 37 LYS cc_start: 0.8358 (ttpt) cc_final: 0.8080 (ttpp) REVERT: F 55 LYS cc_start: 0.7775 (mmtt) cc_final: 0.7422 (mmtt) outliers start: 30 outliers final: 23 residues processed: 173 average time/residue: 0.2239 time to fit residues: 50.5475 Evaluate side-chains 185 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 228 VAL 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 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 1057 ILE 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 74 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.0040 chunk 41 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 = 0.4407 r_free = 0.4407 target = 0.183847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.165198 restraints weight = 10779.698| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 2.59 r_work: 0.4103 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7573 Z= 0.144 Angle : 0.645 11.174 10256 Z= 0.326 Chirality : 0.041 0.148 1148 Planarity : 0.004 0.044 1294 Dihedral : 13.213 179.847 1093 Min Nonbonded Distance : 1.166 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.99 % Allowed : 17.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.29), residues: 907 helix: 1.48 (0.24), residues: 481 sheet: 0.89 (0.63), residues: 65 loop : 0.01 (0.36), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R1110 HIS 0.002 0.001 HIS R1257 PHE 0.023 0.002 PHE R1136 TYR 0.020 0.001 TYR R 127 ARG 0.009 0.001 ARG R1031 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 390) hydrogen bonds : angle 4.50767 ( 1155) link_ASP_CG-ANY_N : bond 0.00074 ( 1) link_ASP_CG-ANY_N : angle 0.85920 ( 3) metal coordination : bond 0.00304 ( 2) SS BOND : bond 0.00064 ( 1) SS BOND : angle 0.44058 ( 2) covalent geometry : bond 0.00332 ( 7569) covalent geometry : angle 0.64447 (10251) *********************** 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 194 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 VAL cc_start: 0.8054 (t) cc_final: 0.7708 (p) REVERT: R 133 ARG cc_start: 0.7581 (ttm110) cc_final: 0.7119 (mtm180) REVERT: R 197 ILE cc_start: 0.7472 (mt) cc_final: 0.7164 (tt) REVERT: R 236 GLU cc_start: 0.6408 (OUTLIER) cc_final: 0.5813 (tm-30) REVERT: R 240 PHE cc_start: 0.7513 (m-10) cc_final: 0.7047 (m-80) REVERT: R 314 LYS cc_start: 0.8031 (mtmt) cc_final: 0.7584 (mtmm) REVERT: R 318 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7961 (ttpm) REVERT: R 359 VAL cc_start: 0.3506 (t) cc_final: 0.1386 (m) REVERT: R 378 GLU cc_start: 0.6124 (tp30) cc_final: 0.5692 (tp30) REVERT: R 406 LYS cc_start: 0.7991 (tppt) cc_final: 0.7648 (tppt) REVERT: R 490 ARG cc_start: 0.7287 (tpt170) cc_final: 0.6818 (tpt170) REVERT: R 494 LEU cc_start: 0.7898 (mt) cc_final: 0.7592 (mt) REVERT: R 525 ASN cc_start: 0.7632 (OUTLIER) cc_final: 0.7383 (t0) REVERT: R 1115 LEU cc_start: 0.8004 (tp) cc_final: 0.7764 (tp) REVERT: R 1167 MET cc_start: 0.6181 (ttt) cc_final: 0.5292 (tmm) REVERT: R 1194 PHE cc_start: 0.7092 (m-80) cc_final: 0.6632 (m-80) REVERT: R 1260 GLN cc_start: 0.6744 (mp10) cc_final: 0.6497 (mp10) REVERT: R 1261 ASP cc_start: 0.7229 (t0) cc_final: 0.6969 (t0) REVERT: R 1267 TYR cc_start: 0.6053 (m-80) cc_final: 0.5712 (m-10) REVERT: F 32 MET cc_start: 0.7810 (mtm) cc_final: 0.7537 (mtm) REVERT: F 55 LYS cc_start: 0.7742 (mmtt) cc_final: 0.7374 (mmtt) outliers start: 32 outliers final: 21 residues processed: 175 average time/residue: 0.2152 time to fit residues: 49.2204 Evaluate side-chains 185 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 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 450 ASP Chi-restraints excluded: chain R residue 464 GLN 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 1057 ILE 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 45 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 63 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 66 optimal weight: 0.2980 chunk 84 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** ** F 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.186280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.168814 restraints weight = 10802.781| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 2.38 r_work: 0.4116 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7573 Z= 0.141 Angle : 0.658 11.882 10256 Z= 0.330 Chirality : 0.041 0.149 1148 Planarity : 0.004 0.045 1294 Dihedral : 13.160 179.583 1093 Min Nonbonded Distance : 1.165 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.99 % Allowed : 18.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.29), residues: 907 helix: 1.48 (0.24), residues: 489 sheet: 0.85 (0.63), residues: 65 loop : -0.03 (0.36), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R1110 HIS 0.003 0.000 HIS R1257 PHE 0.023 0.002 PHE R 291 TYR 0.020 0.001 TYR R 127 ARG 0.009 0.001 ARG R1031 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 390) hydrogen bonds : angle 4.52222 ( 1155) link_ASP_CG-ANY_N : bond 0.00098 ( 1) link_ASP_CG-ANY_N : angle 0.74951 ( 3) metal coordination : bond 0.00344 ( 2) SS BOND : bond 0.00051 ( 1) SS BOND : angle 0.41626 ( 2) covalent geometry : bond 0.00329 ( 7569) covalent geometry : angle 0.65781 (10251) ********************** 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 188 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 VAL cc_start: 0.8101 (t) cc_final: 0.7767 (p) REVERT: R 133 ARG cc_start: 0.7447 (ttm110) cc_final: 0.7050 (mtm180) REVERT: R 165 GLU cc_start: 0.7295 (mp0) cc_final: 0.6795 (mp0) REVERT: R 197 ILE cc_start: 0.7590 (mt) cc_final: 0.7315 (tt) REVERT: R 236 GLU cc_start: 0.6361 (OUTLIER) cc_final: 0.5773 (tm-30) REVERT: R 240 PHE cc_start: 0.7494 (m-10) cc_final: 0.7140 (m-10) REVERT: R 314 LYS cc_start: 0.7952 (mtmt) cc_final: 0.7553 (mtmm) REVERT: R 318 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7857 (ttpm) REVERT: R 359 VAL cc_start: 0.3526 (t) cc_final: 0.1386 (m) REVERT: R 378 GLU cc_start: 0.5845 (tp30) cc_final: 0.5514 (tp30) REVERT: R 406 LYS cc_start: 0.7952 (tppt) cc_final: 0.7623 (tppt) REVERT: R 490 ARG cc_start: 0.7212 (tpt170) cc_final: 0.6796 (tpt170) REVERT: R 494 LEU cc_start: 0.7785 (mt) cc_final: 0.7501 (mt) REVERT: R 525 ASN cc_start: 0.7601 (OUTLIER) cc_final: 0.7335 (t0) REVERT: R 1055 LEU cc_start: 0.8047 (mp) cc_final: 0.7836 (mt) REVERT: R 1104 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6990 (mm-30) REVERT: R 1115 LEU cc_start: 0.7970 (tp) cc_final: 0.7741 (tp) REVERT: R 1167 MET cc_start: 0.6156 (ttt) cc_final: 0.5057 (tmm) REVERT: R 1171 PHE cc_start: 0.6890 (m-80) cc_final: 0.5910 (m-80) REVERT: R 1261 ASP cc_start: 0.7165 (t0) cc_final: 0.6904 (t0) REVERT: R 1267 TYR cc_start: 0.5962 (m-80) cc_final: 0.5691 (m-10) REVERT: F 32 MET cc_start: 0.7628 (mtm) cc_final: 0.7386 (mtm) REVERT: F 55 LYS cc_start: 0.7700 (mmtt) cc_final: 0.7382 (mmtt) outliers start: 24 outliers final: 18 residues processed: 172 average time/residue: 0.2239 time to fit residues: 50.3738 Evaluate side-chains 181 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 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 408 MET Chi-restraints excluded: chain R residue 464 GLN 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 1057 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 42 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 6 optimal weight: 0.0570 chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 HIS ** 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 = 0.4421 r_free = 0.4421 target = 0.185632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.167970 restraints weight = 10745.399| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 2.40 r_work: 0.4111 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7573 Z= 0.147 Angle : 0.670 12.002 10256 Z= 0.336 Chirality : 0.042 0.149 1148 Planarity : 0.004 0.045 1294 Dihedral : 13.085 179.513 1093 Min Nonbonded Distance : 1.160 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.24 % Allowed : 18.80 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.29), residues: 907 helix: 1.49 (0.24), residues: 489 sheet: 0.81 (0.62), residues: 65 loop : -0.05 (0.37), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R1110 HIS 0.003 0.001 HIS R 452 PHE 0.022 0.002 PHE R 291 TYR 0.020 0.001 TYR R 127 ARG 0.008 0.001 ARG R1031 Details of bonding type rmsd hydrogen bonds : bond 0.03767 ( 390) hydrogen bonds : angle 4.54936 ( 1155) link_ASP_CG-ANY_N : bond 0.00091 ( 1) link_ASP_CG-ANY_N : angle 0.83863 ( 3) metal coordination : bond 0.00348 ( 2) SS BOND : bond 0.00079 ( 1) SS BOND : angle 0.37551 ( 2) covalent geometry : bond 0.00341 ( 7569) covalent geometry : angle 0.67043 (10251) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3527.84 seconds wall clock time: 61 minutes 54.63 seconds (3714.63 seconds total)