Starting phenix.real_space_refine on Thu Mar 14 20:19:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj5_34833/03_2024/8hj5_34833_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj5_34833/03_2024/8hj5_34833.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj5_34833/03_2024/8hj5_34833_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj5_34833/03_2024/8hj5_34833_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj5_34833/03_2024/8hj5_34833_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj5_34833/03_2024/8hj5_34833.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj5_34833/03_2024/8hj5_34833.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj5_34833/03_2024/8hj5_34833_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj5_34833/03_2024/8hj5_34833_updated.pdb" } resolution = 3.0 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= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 6157 2.51 5 N 1658 2.21 5 O 1797 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 230": "OD1" <-> "OD2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A ASP 299": "OD1" <-> "OD2" Residue "A TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 346": "OD1" <-> "OD2" Residue "B ASP 226": "OD1" <-> "OD2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 109": "OD1" <-> "OD2" Residue "C TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 224": "OD1" <-> "OD2" Residue "E ASP 109": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9678 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1913 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 1 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2591 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "D" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 394 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "C" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1781 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "F" Number of atoms: 2001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2001 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 7, 'TRANS': 244} Chain breaks: 1 Chain: "E" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'U2U': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.62, per 1000 atoms: 0.58 Number of scatterers: 9678 At special positions: 0 Unit cell: (87.55, 133.45, 125.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1797 8.00 N 1658 7.00 C 6157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 160 " - pdb=" SG CYS C 230 " distance=2.04 Simple disulfide: pdb=" SG CYS F 161 " - pdb=" SG CYS F 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 2.0 seconds 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2294 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 15 sheets defined 28.7% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 10 through 32 Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 234 through 245 Processing helix chain 'A' and resid 262 through 270 Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 281 through 285 removed outlier: 3.956A pdb=" N ALA A 284 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG A 285 " --> pdb=" O GLU A 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 285' Processing helix chain 'A' and resid 300 through 319 removed outlier: 3.656A pdb=" N ARG A 304 " --> pdb=" O PRO A 300 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 358 removed outlier: 3.786A pdb=" N ILE A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 46 removed outlier: 3.539A pdb=" N CYS B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 54 No H-bonds generated for 'chain 'B' and resid 51 through 54' Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'D' and resid 14 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'F' and resid 29 through 51 Processing helix chain 'F' and resid 60 through 87 removed outlier: 3.666A pdb=" N PHE F 87 " --> pdb=" O SER F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 125 Proline residue: F 100 - end of helix removed outlier: 3.937A pdb=" N PHE F 107 " --> pdb=" O MET F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 131 removed outlier: 3.624A pdb=" N ARG F 131 " --> pdb=" O PRO F 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 127 through 131' Processing helix chain 'F' and resid 138 through 159 Processing helix chain 'F' and resid 172 through 204 Processing helix chain 'F' and resid 212 through 239 Proline residue: F 231 - end of helix Processing helix chain 'F' and resid 252 through 276 Proline residue: F 269 - end of helix removed outlier: 3.890A pdb=" N TYR F 272 " --> pdb=" O ASN F 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'A' and resid 254 through 260 removed outlier: 3.781A pdb=" N ALA A 221 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL A 202 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 70 through 72 removed outlier: 3.642A pdb=" N VAL B 348 " --> pdb=" O TRP B 360 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 79 through 84 removed outlier: 6.857A pdb=" N ALA B 94 " --> pdb=" O TYR B 80 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N MET B 82 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL B 92 " --> pdb=" O MET B 82 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N TRP B 84 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU B 90 " --> pdb=" O TRP B 84 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 91 " --> pdb=" O TRP B 103 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS B 99 " --> pdb=" O SER B 95 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP B 104 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LYS B 110 " --> pdb=" O ASP B 104 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 121 through 126 removed outlier: 6.925A pdb=" N GLY B 136 " --> pdb=" O MET B 122 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS B 124 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA B 134 " --> pdb=" O CYS B 124 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N TYR B 126 " --> pdb=" O TYR B 132 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N TYR B 132 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY B 137 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ILE B 141 " --> pdb=" O GLY B 137 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ASN B 146 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL B 156 " --> pdb=" O ASN B 146 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 199 through 202 removed outlier: 4.178A pdb=" N THR B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 208 through 213 removed outlier: 6.959A pdb=" N GLY B 223 " --> pdb=" O MET B 209 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU B 211 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL B 221 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE B 220 " --> pdb=" O TRP B 232 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 250 through 255 removed outlier: 6.831A pdb=" N GLY B 265 " --> pdb=" O ASN B 251 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE B 253 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA B 263 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N PHE B 255 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ALA B 261 " --> pdb=" O PHE B 255 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET B 283 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASP B 275 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLU B 281 " --> pdb=" O ASP B 275 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 297 through 299 Processing sheet with id= I, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.662A pdb=" N VAL C 5 " --> pdb=" O SER C 23 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 10 through 12 removed outlier: 5.502A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 147 through 149 removed outlier: 7.030A pdb=" N LYS C 245 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR C 228 " --> pdb=" O THR C 244 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU C 179 " --> pdb=" O LEU C 188 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LEU C 188 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 156 through 161 Processing sheet with id= M, first strand: chain 'E' and resid 3 through 5 removed outlier: 3.567A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 17 through 20 Processing sheet with id= O, first strand: chain 'E' and resid 122 through 124 removed outlier: 5.978A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER E 59 " --> pdb=" O ASP E 50 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1170 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: 2.65 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3122 1.34 - 1.46: 2473 1.46 - 1.58: 4200 1.58 - 1.70: 1 1.70 - 1.82: 91 Bond restraints: 9887 Sorted by residual: bond pdb=" N LEU F 51 " pdb=" CA LEU F 51 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.33e-02 5.65e+03 5.39e+00 bond pdb=" N ASN D 59 " pdb=" CA ASN D 59 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.41e-02 5.03e+03 4.56e+00 bond pdb=" C18 U2U F 501 " pdb=" C19 U2U F 501 " ideal model delta sigma weight residual 1.413 1.372 0.041 2.00e-02 2.50e+03 4.26e+00 bond pdb=" C21 U2U F 501 " pdb=" N2 U2U F 501 " ideal model delta sigma weight residual 1.360 1.322 0.038 2.00e-02 2.50e+03 3.69e+00 bond pdb=" CB GLU D 58 " pdb=" CG GLU D 58 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.53e+00 ... (remaining 9882 not shown) Histogram of bond angle deviations from ideal: 100.14 - 106.94: 229 106.94 - 113.73: 5434 113.73 - 120.52: 3843 120.52 - 127.32: 3792 127.32 - 134.11: 104 Bond angle restraints: 13402 Sorted by residual: angle pdb=" C17 U2U F 501 " pdb=" C22 U2U F 501 " pdb=" N3 U2U F 501 " ideal model delta sigma weight residual 147.58 117.79 29.79 3.00e+00 1.11e-01 9.86e+01 angle pdb=" N2 U2U F 501 " pdb=" C22 U2U F 501 " pdb=" N3 U2U F 501 " ideal model delta sigma weight residual 92.15 119.48 -27.33 3.00e+00 1.11e-01 8.30e+01 angle pdb=" C19 U2U F 501 " pdb=" C14 U2U F 501 " pdb=" O4 U2U F 501 " ideal model delta sigma weight residual 140.79 117.64 23.15 3.00e+00 1.11e-01 5.95e+01 angle pdb=" C15 U2U F 501 " pdb=" C14 U2U F 501 " pdb=" O4 U2U F 501 " ideal model delta sigma weight residual 99.20 121.10 -21.90 3.00e+00 1.11e-01 5.33e+01 angle pdb=" C12 U2U F 501 " pdb=" C13 U2U F 501 " pdb=" O4 U2U F 501 " ideal model delta sigma weight residual 101.58 121.38 -19.80 3.00e+00 1.11e-01 4.36e+01 ... (remaining 13397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 5131 17.28 - 34.56: 555 34.56 - 51.84: 125 51.84 - 69.13: 19 69.13 - 86.41: 6 Dihedral angle restraints: 5836 sinusoidal: 2275 harmonic: 3561 Sorted by residual: dihedral pdb=" CB CYS E 99 " pdb=" SG CYS E 99 " pdb=" SG CYS E 107 " pdb=" CB CYS E 107 " ideal model delta sinusoidal sigma weight residual -86.00 -140.04 54.04 1 1.00e+01 1.00e-02 3.96e+01 dihedral pdb=" CA CYS E 107 " pdb=" C CYS E 107 " pdb=" N PHE E 108 " pdb=" CA PHE E 108 " ideal model delta harmonic sigma weight residual -180.00 -156.93 -23.07 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA GLU A 208 " pdb=" C GLU A 208 " pdb=" N ARG A 209 " pdb=" CA ARG A 209 " ideal model delta harmonic sigma weight residual 180.00 159.18 20.82 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 5833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 822 0.028 - 0.056: 435 0.056 - 0.084: 143 0.084 - 0.112: 80 0.112 - 0.140: 32 Chirality restraints: 1512 Sorted by residual: chirality pdb=" CA ILE C 190 " pdb=" N ILE C 190 " pdb=" C ILE C 190 " pdb=" CB ILE C 190 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA LEU F 51 " pdb=" N LEU F 51 " pdb=" C LEU F 51 " pdb=" CB LEU F 51 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ASP B 333 " pdb=" N ASP B 333 " pdb=" C ASP B 333 " pdb=" CB ASP B 333 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 1509 not shown) Planarity restraints: 1691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU F 152 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" C LEU F 152 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU F 152 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG F 153 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 271 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.48e+00 pdb=" C ILE F 271 " -0.032 2.00e-02 2.50e+03 pdb=" O ILE F 271 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR F 272 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE F 209 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO F 210 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO F 210 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 210 " 0.025 5.00e-02 4.00e+02 ... (remaining 1688 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1982 2.78 - 3.31: 8682 3.31 - 3.84: 15305 3.84 - 4.37: 17937 4.37 - 4.90: 32665 Nonbonded interactions: 76571 Sorted by model distance: nonbonded pdb=" OH TYR F 99 " pdb=" OE2 GLU F 157 " model vdw 2.244 2.440 nonbonded pdb=" OD1 ASP C 224 " pdb=" OH TYR C 228 " model vdw 2.262 2.440 nonbonded pdb=" OE2 GLU A 298 " pdb=" OG1 THR A 303 " model vdw 2.265 2.440 nonbonded pdb=" O SER E 85 " pdb=" OG SER E 85 " model vdw 2.270 2.440 nonbonded pdb=" OD1 ASP B 184 " pdb=" OG1 THR B 186 " model vdw 2.277 2.440 ... (remaining 76566 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.190 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.660 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9887 Z= 0.223 Angle : 0.855 29.790 13402 Z= 0.405 Chirality : 0.043 0.140 1512 Planarity : 0.004 0.044 1691 Dihedral : 14.819 86.406 3530 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.19 % Allowed : 18.68 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.98 (0.24), residues: 1214 helix: 1.26 (0.27), residues: 370 sheet: -1.21 (0.27), residues: 347 loop : -1.65 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 103 HIS 0.005 0.001 HIS A 325 PHE 0.015 0.001 PHE F 104 TYR 0.014 0.001 TYR A 31 ARG 0.007 0.000 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 117 time to evaluate : 1.056 Fit side-chains REVERT: B 283 MET cc_start: 0.7954 (ttm) cc_final: 0.7654 (ttm) REVERT: D 21 MET cc_start: 0.7123 (ttp) cc_final: 0.6835 (ttp) REVERT: D 46 LYS cc_start: 0.7833 (tttm) cc_final: 0.7619 (pptt) REVERT: D 59 ASN cc_start: 0.7599 (OUTLIER) cc_final: 0.7200 (t0) outliers start: 2 outliers final: 1 residues processed: 119 average time/residue: 1.2365 time to fit residues: 157.8806 Evaluate side-chains 114 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain D residue 59 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 0.0370 chunk 57 optimal weight: 0.0870 chunk 70 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 overall best weight: 0.9638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 ASN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.0543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9887 Z= 0.192 Angle : 0.581 10.895 13402 Z= 0.295 Chirality : 0.042 0.136 1512 Planarity : 0.003 0.040 1691 Dihedral : 5.678 71.342 1349 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.77 % Allowed : 16.79 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.64 (0.24), residues: 1214 helix: 1.73 (0.27), residues: 364 sheet: -1.07 (0.28), residues: 348 loop : -1.53 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 103 HIS 0.004 0.001 HIS A 325 PHE 0.017 0.001 PHE F 104 TYR 0.014 0.001 TYR A 31 ARG 0.004 0.000 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 121 time to evaluate : 1.298 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.6849 (mt0) cc_final: 0.6165 (mp10) REVERT: B 151 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8156 (mp0) REVERT: D 46 LYS cc_start: 0.7856 (tttm) cc_final: 0.7616 (pptt) REVERT: D 59 ASN cc_start: 0.7717 (OUTLIER) cc_final: 0.7177 (t0) REVERT: F 56 MET cc_start: 0.5365 (ppp) cc_final: 0.5148 (ppp) outliers start: 40 outliers final: 19 residues processed: 145 average time/residue: 1.0441 time to fit residues: 164.1579 Evaluate side-chains 133 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain D residue 59 ASN Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 30 optimal weight: 0.5980 chunk 110 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 67 ASN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 9887 Z= 0.375 Angle : 0.674 10.553 13402 Z= 0.346 Chirality : 0.045 0.194 1512 Planarity : 0.004 0.046 1691 Dihedral : 5.782 67.585 1349 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.72 % Allowed : 17.74 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.79 (0.24), residues: 1214 helix: 1.42 (0.26), residues: 366 sheet: -1.05 (0.28), residues: 348 loop : -1.57 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 147 HIS 0.007 0.001 HIS A 325 PHE 0.021 0.002 PHE F 104 TYR 0.018 0.002 TYR C 191 ARG 0.004 0.000 ARG F 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 113 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.7084 (mt0) cc_final: 0.6335 (mp10) REVERT: A 311 LYS cc_start: 0.6597 (tttm) cc_final: 0.6331 (tttp) REVERT: B 151 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8200 (mp0) REVERT: D 46 LYS cc_start: 0.7910 (tttm) cc_final: 0.7632 (pptt) REVERT: D 48 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7890 (p0) REVERT: D 59 ASN cc_start: 0.7844 (OUTLIER) cc_final: 0.7257 (t0) REVERT: F 56 MET cc_start: 0.5484 (ppp) cc_final: 0.5185 (ppp) outliers start: 50 outliers final: 25 residues processed: 144 average time/residue: 1.1140 time to fit residues: 172.7952 Evaluate side-chains 138 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 110 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 59 ASN Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 110 optimal weight: 0.0170 chunk 116 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 67 ASN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9887 Z= 0.157 Angle : 0.557 10.445 13402 Z= 0.282 Chirality : 0.041 0.144 1512 Planarity : 0.003 0.043 1691 Dihedral : 5.239 62.562 1349 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.68 % Allowed : 18.58 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.46 (0.24), residues: 1214 helix: 1.83 (0.27), residues: 364 sheet: -0.85 (0.28), residues: 338 loop : -1.48 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 103 HIS 0.003 0.001 HIS C 35 PHE 0.020 0.001 PHE F 104 TYR 0.012 0.001 TYR A 31 ARG 0.003 0.000 ARG B 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 119 time to evaluate : 1.173 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.6657 (mt0) cc_final: 0.6021 (mp10) REVERT: B 151 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8158 (mp0) REVERT: D 46 LYS cc_start: 0.7904 (tttm) cc_final: 0.7625 (pptt) REVERT: D 59 ASN cc_start: 0.7676 (OUTLIER) cc_final: 0.7016 (t0) REVERT: F 56 MET cc_start: 0.5363 (OUTLIER) cc_final: 0.5109 (ppp) outliers start: 39 outliers final: 18 residues processed: 142 average time/residue: 1.0703 time to fit residues: 164.5329 Evaluate side-chains 133 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain D residue 59 ASN Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 ASN B 361 ASN D 59 ASN F 67 ASN E 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9887 Z= 0.213 Angle : 0.591 10.500 13402 Z= 0.299 Chirality : 0.042 0.140 1512 Planarity : 0.004 0.040 1691 Dihedral : 5.183 60.261 1349 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.87 % Allowed : 20.00 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.45 (0.24), residues: 1214 helix: 1.81 (0.27), residues: 365 sheet: -0.92 (0.28), residues: 343 loop : -1.40 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 147 HIS 0.004 0.001 HIS A 325 PHE 0.020 0.001 PHE F 104 TYR 0.015 0.001 TYR A 31 ARG 0.003 0.000 ARG B 155 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 113 time to evaluate : 1.138 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.6803 (mt0) cc_final: 0.6133 (mp10) REVERT: B 151 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8135 (mp0) REVERT: D 46 LYS cc_start: 0.7921 (tttm) cc_final: 0.7603 (pptt) REVERT: C 235 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8446 (pt0) REVERT: F 56 MET cc_start: 0.5369 (OUTLIER) cc_final: 0.5105 (ppp) outliers start: 41 outliers final: 25 residues processed: 134 average time/residue: 1.1128 time to fit residues: 161.4931 Evaluate side-chains 140 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 112 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 68 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 ASN F 67 ASN E 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9887 Z= 0.324 Angle : 0.654 10.779 13402 Z= 0.334 Chirality : 0.044 0.152 1512 Planarity : 0.004 0.040 1691 Dihedral : 5.373 59.791 1347 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 5.19 % Allowed : 18.96 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.62 (0.24), residues: 1214 helix: 1.57 (0.27), residues: 365 sheet: -0.95 (0.28), residues: 350 loop : -1.46 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 147 HIS 0.006 0.001 HIS A 325 PHE 0.022 0.002 PHE F 104 TYR 0.017 0.002 TYR C 191 ARG 0.004 0.000 ARG B 155 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 108 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.7073 (mt0) cc_final: 0.6342 (mp10) REVERT: A 282 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6984 (mm-30) REVERT: A 324 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7010 (mtm180) REVERT: B 151 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8169 (mp0) REVERT: B 238 MET cc_start: 0.7209 (mmm) cc_final: 0.6667 (ttt) REVERT: D 46 LYS cc_start: 0.7990 (tttm) cc_final: 0.7651 (pptt) REVERT: D 48 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7871 (p0) REVERT: C 235 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8375 (pt0) REVERT: F 56 MET cc_start: 0.5626 (OUTLIER) cc_final: 0.5375 (ppp) REVERT: E 86 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7359 (mm) outliers start: 55 outliers final: 30 residues processed: 139 average time/residue: 1.1718 time to fit residues: 175.2971 Evaluate side-chains 143 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 106 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 67 ASN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9887 Z= 0.195 Angle : 0.596 10.581 13402 Z= 0.300 Chirality : 0.042 0.139 1512 Planarity : 0.003 0.039 1691 Dihedral : 5.131 58.219 1347 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.87 % Allowed : 20.75 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.46 (0.24), residues: 1214 helix: 1.80 (0.27), residues: 364 sheet: -0.86 (0.28), residues: 340 loop : -1.43 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 212 HIS 0.004 0.001 HIS A 325 PHE 0.021 0.001 PHE F 104 TYR 0.014 0.001 TYR A 31 ARG 0.004 0.000 ARG B 155 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 117 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.6777 (mt0) cc_final: 0.6111 (mp10) REVERT: A 299 ASP cc_start: 0.7475 (t70) cc_final: 0.7219 (t70) REVERT: B 151 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8166 (mp0) REVERT: B 238 MET cc_start: 0.6798 (mmm) cc_final: 0.6125 (ttt) REVERT: D 46 LYS cc_start: 0.7993 (tttm) cc_final: 0.7643 (pptt) REVERT: C 235 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8449 (pt0) REVERT: F 56 MET cc_start: 0.5401 (OUTLIER) cc_final: 0.5154 (ppp) REVERT: E 105 ARG cc_start: 0.6604 (OUTLIER) cc_final: 0.6284 (ptm160) outliers start: 41 outliers final: 25 residues processed: 142 average time/residue: 1.1283 time to fit residues: 172.6445 Evaluate side-chains 142 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 113 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 101 optimal weight: 0.3980 chunk 108 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 67 ASN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9887 Z= 0.320 Angle : 0.650 10.754 13402 Z= 0.331 Chirality : 0.044 0.143 1512 Planarity : 0.004 0.038 1691 Dihedral : 5.348 58.971 1347 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.72 % Allowed : 20.28 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.55 (0.24), residues: 1214 helix: 1.63 (0.26), residues: 365 sheet: -0.93 (0.28), residues: 351 loop : -1.41 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 147 HIS 0.006 0.001 HIS A 325 PHE 0.022 0.002 PHE F 104 TYR 0.017 0.002 TYR C 191 ARG 0.004 0.000 ARG B 155 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 111 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.7101 (mt0) cc_final: 0.6352 (mp10) REVERT: A 282 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6970 (mm-30) REVERT: A 324 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.6929 (mtm180) REVERT: B 151 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8186 (mp0) REVERT: B 238 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.6661 (ttt) REVERT: D 46 LYS cc_start: 0.8003 (tttm) cc_final: 0.7648 (pptt) REVERT: C 235 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8373 (pt0) REVERT: F 56 MET cc_start: 0.5403 (OUTLIER) cc_final: 0.5158 (ppp) REVERT: E 86 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7370 (mm) REVERT: E 105 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.6173 (ptm160) outliers start: 50 outliers final: 33 residues processed: 139 average time/residue: 1.2361 time to fit residues: 184.1230 Evaluate side-chains 149 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 108 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 33 optimal weight: 0.1980 chunk 98 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 67 ASN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9887 Z= 0.168 Angle : 0.586 10.561 13402 Z= 0.294 Chirality : 0.041 0.134 1512 Planarity : 0.003 0.038 1691 Dihedral : 5.049 57.282 1347 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.58 % Allowed : 21.60 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.29 (0.24), residues: 1214 helix: 2.01 (0.27), residues: 363 sheet: -0.75 (0.29), residues: 324 loop : -1.39 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 212 HIS 0.004 0.001 HIS C 35 PHE 0.019 0.001 PHE F 104 TYR 0.013 0.001 TYR A 31 ARG 0.004 0.000 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 114 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.6652 (mt0) cc_final: 0.6019 (mp10) REVERT: A 299 ASP cc_start: 0.7473 (t70) cc_final: 0.7212 (t70) REVERT: A 324 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6760 (mtm180) REVERT: B 151 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8167 (mp0) REVERT: B 238 MET cc_start: 0.6725 (OUTLIER) cc_final: 0.6103 (ttt) REVERT: D 46 LYS cc_start: 0.7961 (tttm) cc_final: 0.7542 (pptt) REVERT: D 48 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7779 (p0) REVERT: C 11 LEU cc_start: 0.8072 (mp) cc_final: 0.7762 (tp) REVERT: F 56 MET cc_start: 0.5218 (OUTLIER) cc_final: 0.4994 (ppp) REVERT: E 105 ARG cc_start: 0.6510 (OUTLIER) cc_final: 0.6105 (ptm160) outliers start: 38 outliers final: 24 residues processed: 138 average time/residue: 1.1486 time to fit residues: 170.8662 Evaluate side-chains 142 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 112 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 chunk 120 optimal weight: 2.9990 chunk 110 optimal weight: 0.0570 chunk 95 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 ASN F 67 ASN E 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9887 Z= 0.163 Angle : 0.578 10.662 13402 Z= 0.288 Chirality : 0.041 0.135 1512 Planarity : 0.003 0.037 1691 Dihedral : 4.925 56.490 1347 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.11 % Allowed : 22.17 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.14 (0.24), residues: 1214 helix: 2.14 (0.27), residues: 363 sheet: -0.71 (0.28), residues: 332 loop : -1.28 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 103 HIS 0.003 0.001 HIS C 35 PHE 0.019 0.001 PHE F 104 TYR 0.013 0.001 TYR A 31 ARG 0.005 0.000 ARG B 240 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 115 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.6641 (mt0) cc_final: 0.6033 (mp10) REVERT: A 299 ASP cc_start: 0.7451 (t70) cc_final: 0.7189 (t70) REVERT: A 324 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.6741 (mtm180) REVERT: B 151 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: B 238 MET cc_start: 0.6337 (OUTLIER) cc_final: 0.5682 (ttm) REVERT: D 46 LYS cc_start: 0.7956 (tttm) cc_final: 0.7533 (pptt) REVERT: D 48 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7736 (p0) REVERT: C 11 LEU cc_start: 0.8075 (mp) cc_final: 0.7871 (tp) REVERT: C 154 GLU cc_start: 0.6145 (OUTLIER) cc_final: 0.5776 (pm20) REVERT: E 105 ARG cc_start: 0.6434 (OUTLIER) cc_final: 0.6027 (ptm160) outliers start: 33 outliers final: 20 residues processed: 136 average time/residue: 1.1421 time to fit residues: 167.3999 Evaluate side-chains 137 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 111 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 105 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 0.0040 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 0.0570 chunk 98 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 84 optimal weight: 0.0870 chunk 5 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 overall best weight: 0.3888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 ASN D 18 GLN F 45 ASN F 67 ASN E 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.177094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.123703 restraints weight = 9950.908| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.39 r_work: 0.3347 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9887 Z= 0.135 Angle : 0.561 10.835 13402 Z= 0.278 Chirality : 0.041 0.136 1512 Planarity : 0.003 0.037 1691 Dihedral : 4.555 54.942 1345 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.55 % Allowed : 23.02 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.05 (0.24), residues: 1214 helix: 2.33 (0.27), residues: 363 sheet: -0.66 (0.29), residues: 321 loop : -1.31 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 103 HIS 0.003 0.001 HIS C 35 PHE 0.017 0.001 PHE F 104 TYR 0.019 0.001 TYR C 60 ARG 0.005 0.000 ARG B 240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3705.09 seconds wall clock time: 66 minutes 12.45 seconds (3972.45 seconds total)