Starting phenix.real_space_refine on Sat Apr 6 16:39:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsp_36626/04_2024/8jsp_36626_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsp_36626/04_2024/8jsp_36626.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsp_36626/04_2024/8jsp_36626_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsp_36626/04_2024/8jsp_36626_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsp_36626/04_2024/8jsp_36626_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsp_36626/04_2024/8jsp_36626.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsp_36626/04_2024/8jsp_36626.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsp_36626/04_2024/8jsp_36626_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsp_36626/04_2024/8jsp_36626_updated.pdb" } resolution = 3.65 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5480 2.51 5 N 1470 2.21 5 O 1586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 308": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 330": "OE1" <-> "OE2" Residue "R GLU 340": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8599 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1743 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Chain: "B" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2516 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 322} Chain: "E" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1717 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "G" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 347 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 4, 'TRANS': 40} Chain: "R" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2264 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 12, 'TRANS': 273} Chain breaks: 1 Chain: "R" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UJL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.02, per 1000 atoms: 0.58 Number of scatterers: 8599 At special positions: 0 Unit cell: (103.96, 115.92, 129.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1586 8.00 N 1470 7.00 C 5480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.07 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " 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: 3.25 Conformation dependent library (CDL) restraints added in 1.7 seconds 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2058 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 14 sheets defined 35.0% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 removed outlier: 3.860A pdb=" N ALA A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.055A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 243 through 254 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.394A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 350 removed outlier: 3.933A pdb=" N LYS A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.323A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (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 helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'G' and resid 19 through 23 Processing helix chain 'G' and resid 30 through 47 removed outlier: 5.010A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'R' and resid 36 through 63 removed outlier: 3.686A pdb=" N VAL R 58 " --> pdb=" O ASN R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 98 Proline residue: R 91 - end of helix Processing helix chain 'R' and resid 106 through 122 Processing helix chain 'R' and resid 125 through 139 Processing helix chain 'R' and resid 141 through 146 Processing helix chain 'R' and resid 151 through 173 Proline residue: R 170 - end of helix Processing helix chain 'R' and resid 193 through 227 removed outlier: 4.060A pdb=" N THR R 200 " --> pdb=" O THR R 196 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ILE R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) Proline residue: R 207 - end of helix removed outlier: 3.661A pdb=" N ILE R 226 " --> pdb=" O ALA R 222 " (cutoff:3.500A) Processing helix chain 'R' and resid 325 through 356 removed outlier: 3.741A pdb=" N THR R 343 " --> pdb=" O ARG R 339 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL R 344 " --> pdb=" O GLU R 340 " (cutoff:3.500A) Processing helix chain 'R' and resid 359 through 367 Processing helix chain 'R' and resid 370 through 372 No H-bonds generated for 'chain 'R' and resid 370 through 372' Processing helix chain 'R' and resid 379 through 400 removed outlier: 3.785A pdb=" N ILE R 384 " --> pdb=" O LEU R 380 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLY R 389 " --> pdb=" O ILE R 385 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR R 390 " --> pdb=" O ASN R 386 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER R 393 " --> pdb=" O GLY R 389 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU R 394 " --> pdb=" O TYR R 390 " (cutoff:3.500A) Proline residue: R 397 - end of helix removed outlier: 3.692A pdb=" N TYR R 400 " --> pdb=" O ASN R 396 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 414 Processing sheet with id= A, first strand: chain 'A' and resid 196 through 200 removed outlier: 6.873A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ALA A 220 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU A 39 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ILE A 222 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N SER A 263 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N PHE A 223 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE A 265 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N VAL A 225 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N PHE A 267 " --> pdb=" O VAL A 225 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.811A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 178 through 180 removed outlier: 3.565A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 221 through 223 removed outlier: 4.257A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 251 through 254 Processing sheet with id= F, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.896A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.894A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 294 through 297 Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.679A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 17 through 20 removed outlier: 3.511A pdb=" N MET E 83 " --> pdb=" O ARG E 18 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE E 80 " --> pdb=" O SER E 71 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER E 71 " --> pdb=" O PHE E 80 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 115 through 117 removed outlier: 4.197A pdb=" N LEU E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA E 92 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TRP E 36 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR E 50 " --> pdb=" O TYR E 59 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR E 59 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 140 through 142 removed outlier: 4.008A pdb=" N THR E 141 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG E 160 " --> pdb=" O THR E 141 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER E 206 " --> pdb=" O THR E 213 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.614A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 226 through 231 removed outlier: 3.904A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 324 hydrogen bonds defined for protein. 948 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: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1561 1.32 - 1.45: 2279 1.45 - 1.57: 4849 1.57 - 1.69: 0 1.69 - 1.82: 90 Bond restraints: 8779 Sorted by residual: bond pdb=" C6 UJL R 501 " pdb=" C7 UJL R 501 " ideal model delta sigma weight residual 1.607 1.425 0.182 2.00e-02 2.50e+03 8.30e+01 bond pdb=" C8 UJL R 501 " pdb=" S1 UJL R 501 " ideal model delta sigma weight residual 1.546 1.715 -0.169 2.00e-02 2.50e+03 7.12e+01 bond pdb=" C9 UJL R 501 " pdb=" S1 UJL R 501 " ideal model delta sigma weight residual 1.566 1.728 -0.162 2.00e-02 2.50e+03 6.53e+01 bond pdb=" C7 UJL R 501 " pdb=" C8 UJL R 501 " ideal model delta sigma weight residual 1.443 1.355 0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C VAL R 89 " pdb=" O VAL R 89 " ideal model delta sigma weight residual 1.236 1.279 -0.043 1.19e-02 7.06e+03 1.31e+01 ... (remaining 8774 not shown) Histogram of bond angle deviations from ideal: 90.96 - 99.57: 5 99.57 - 108.19: 329 108.19 - 116.80: 5775 116.80 - 125.42: 5643 125.42 - 134.03: 141 Bond angle restraints: 11893 Sorted by residual: angle pdb=" C GLU E 234 " pdb=" N TYR E 235 " pdb=" CA TYR E 235 " ideal model delta sigma weight residual 122.89 113.22 9.67 1.12e+00 7.97e-01 7.45e+01 angle pdb=" C8 UJL R 501 " pdb=" S1 UJL R 501 " pdb=" C9 UJL R 501 " ideal model delta sigma weight residual 107.54 90.96 16.58 3.00e+00 1.11e-01 3.05e+01 angle pdb=" N VAL R 85 " pdb=" CA VAL R 85 " pdb=" CB VAL R 85 " ideal model delta sigma weight residual 110.62 116.10 -5.48 1.05e+00 9.07e-01 2.72e+01 angle pdb=" C CYS B 121 " pdb=" CA CYS B 121 " pdb=" CB CYS B 121 " ideal model delta sigma weight residual 111.23 118.17 -6.94 1.42e+00 4.96e-01 2.39e+01 angle pdb=" CA VAL R 85 " pdb=" C VAL R 85 " pdb=" O VAL R 85 " ideal model delta sigma weight residual 121.41 116.94 4.47 1.04e+00 9.25e-01 1.85e+01 ... (remaining 11888 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 4682 17.31 - 34.62: 435 34.62 - 51.93: 78 51.93 - 69.24: 13 69.24 - 86.55: 9 Dihedral angle restraints: 5217 sinusoidal: 2025 harmonic: 3192 Sorted by residual: dihedral pdb=" CA LEU B 79 " pdb=" C LEU B 79 " pdb=" N ILE B 80 " pdb=" CA ILE B 80 " ideal model delta harmonic sigma weight residual -180.00 -158.54 -21.46 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA TYR E 235 " pdb=" C TYR E 235 " pdb=" N PRO E 236 " pdb=" CA PRO E 236 " ideal model delta harmonic sigma weight residual 180.00 159.20 20.80 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ASP B 118 " pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta harmonic sigma weight residual -180.00 -159.37 -20.63 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 5214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 923 0.045 - 0.089: 318 0.089 - 0.134: 94 0.134 - 0.179: 16 0.179 - 0.223: 2 Chirality restraints: 1353 Sorted by residual: chirality pdb=" CB THR A 327 " pdb=" CA THR A 327 " pdb=" OG1 THR A 327 " pdb=" CG2 THR A 327 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB VAL R 85 " pdb=" CA VAL R 85 " pdb=" CG1 VAL R 85 " pdb=" CG2 VAL R 85 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.99e-01 chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 1350 not shown) Planarity restraints: 1497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 120 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.01e+00 pdb=" C ILE B 120 " -0.046 2.00e-02 2.50e+03 pdb=" O ILE B 120 " 0.018 2.00e-02 2.50e+03 pdb=" N CYS B 121 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 407 " 0.022 2.00e-02 2.50e+03 1.86e-02 6.03e+00 pdb=" CG PHE R 407 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE R 407 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE R 407 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE R 407 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE R 407 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE R 407 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP R 140 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO R 141 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO R 141 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO R 141 " 0.032 5.00e-02 4.00e+02 ... (remaining 1494 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 993 2.74 - 3.28: 8706 3.28 - 3.82: 13755 3.82 - 4.36: 15669 4.36 - 4.90: 27119 Nonbonded interactions: 66242 Sorted by model distance: nonbonded pdb=" NE1 TRP E 47 " pdb=" O ALA E 49 " model vdw 2.204 2.520 nonbonded pdb=" OG SER A 293 " pdb=" OE1 GLU A 298 " model vdw 2.211 2.440 nonbonded pdb=" O ARG E 98 " pdb=" OG SER E 99 " model vdw 2.234 2.440 nonbonded pdb=" O ILE B 37 " pdb=" NZ LYS B 301 " model vdw 2.237 2.520 nonbonded pdb=" O ASP E 90 " pdb=" OH TYR E 94 " model vdw 2.239 2.440 ... (remaining 66237 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.190 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 26.840 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 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 0.182 8779 Z= 0.470 Angle : 0.830 16.579 11893 Z= 0.468 Chirality : 0.049 0.223 1353 Planarity : 0.005 0.058 1497 Dihedral : 14.073 86.552 3147 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.86 % Allowed : 0.86 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.89 (0.25), residues: 1084 helix: 0.72 (0.26), residues: 383 sheet: -0.93 (0.34), residues: 239 loop : -1.47 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 82 HIS 0.008 0.002 HIS B 91 PHE 0.042 0.003 PHE R 407 TYR 0.026 0.003 TYR R 96 ARG 0.004 0.001 ARG E 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 164 time to evaluate : 1.017 Fit side-chains REVERT: A 346 ASN cc_start: 0.7768 (m110) cc_final: 0.7446 (m-40) REVERT: E 93 MET cc_start: 0.7738 (mpp) cc_final: 0.6880 (mpp) REVERT: R 330 GLU cc_start: 0.8616 (tp30) cc_final: 0.8403 (tp30) REVERT: R 337 LEU cc_start: 0.8831 (mm) cc_final: 0.8514 (mm) outliers start: 8 outliers final: 3 residues processed: 172 average time/residue: 0.2108 time to fit residues: 50.2862 Evaluate side-chains 125 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 122 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 115 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 GLN ** R 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8779 Z= 0.177 Angle : 0.596 7.135 11893 Z= 0.310 Chirality : 0.042 0.184 1353 Planarity : 0.004 0.041 1497 Dihedral : 5.687 88.639 1206 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.27 % Allowed : 9.92 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.26), residues: 1084 helix: 1.37 (0.27), residues: 383 sheet: -0.88 (0.33), residues: 244 loop : -1.38 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.013 0.001 PHE B 292 TYR 0.028 0.002 TYR E 235 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 148 time to evaluate : 1.092 Fit side-chains REVERT: A 346 ASN cc_start: 0.7706 (m110) cc_final: 0.7249 (m110) REVERT: B 221 THR cc_start: 0.8678 (p) cc_final: 0.8430 (p) REVERT: B 266 HIS cc_start: 0.7534 (t-90) cc_final: 0.7112 (t-90) REVERT: E 34 MET cc_start: 0.6809 (mmm) cc_final: 0.6568 (tmm) REVERT: R 113 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7332 (mm) REVERT: R 333 ARG cc_start: 0.8580 (ptp-170) cc_final: 0.8209 (ptp-170) REVERT: R 334 LYS cc_start: 0.8490 (mtmm) cc_final: 0.8251 (mtmm) REVERT: R 335 MET cc_start: 0.7389 (ttp) cc_final: 0.7053 (ttm) outliers start: 21 outliers final: 15 residues processed: 163 average time/residue: 0.2121 time to fit residues: 47.6422 Evaluate side-chains 151 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 135 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 344 VAL Chi-restraints excluded: chain R residue 406 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 66 optimal weight: 0.0030 chunk 26 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 322 HIS B 183 HIS ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8779 Z= 0.149 Angle : 0.541 6.404 11893 Z= 0.284 Chirality : 0.041 0.162 1353 Planarity : 0.003 0.043 1497 Dihedral : 5.045 87.622 1206 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.37 % Allowed : 14.13 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.18 (0.26), residues: 1084 helix: 1.68 (0.28), residues: 383 sheet: -0.75 (0.32), residues: 254 loop : -1.31 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS B 91 PHE 0.010 0.001 PHE E 68 TYR 0.031 0.001 TYR E 235 ARG 0.002 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 153 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 247 MET cc_start: 0.6469 (mmm) cc_final: 0.6264 (mmm) REVERT: A 346 ASN cc_start: 0.7776 (m110) cc_final: 0.7241 (m110) REVERT: B 221 THR cc_start: 0.8623 (p) cc_final: 0.8401 (p) REVERT: B 228 ASP cc_start: 0.6056 (OUTLIER) cc_final: 0.5397 (m-30) REVERT: B 266 HIS cc_start: 0.7566 (t-90) cc_final: 0.7099 (t-170) REVERT: E 34 MET cc_start: 0.6591 (mmm) cc_final: 0.6284 (tmm) REVERT: E 110 PHE cc_start: 0.7279 (t80) cc_final: 0.6836 (m-80) REVERT: R 330 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7193 (tm-30) REVERT: R 333 ARG cc_start: 0.8605 (ptp-170) cc_final: 0.8339 (ptp-170) REVERT: R 334 LYS cc_start: 0.8338 (mtmm) cc_final: 0.7694 (mtmm) outliers start: 22 outliers final: 19 residues processed: 165 average time/residue: 0.2127 time to fit residues: 47.8213 Evaluate side-chains 160 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 139 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 330 GLU Chi-restraints excluded: chain R residue 406 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 0.0040 chunk 27 optimal weight: 0.9980 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 183 HIS ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8779 Z= 0.168 Angle : 0.541 6.457 11893 Z= 0.284 Chirality : 0.041 0.139 1353 Planarity : 0.003 0.045 1497 Dihedral : 4.923 89.033 1202 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.59 % Allowed : 16.07 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.27), residues: 1084 helix: 1.78 (0.28), residues: 383 sheet: -0.65 (0.33), residues: 253 loop : -1.30 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.006 0.001 HIS B 183 PHE 0.017 0.001 PHE E 68 TYR 0.029 0.001 TYR A 230 ARG 0.003 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 146 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.6607 (mmm) cc_final: 0.6404 (mmm) REVERT: A 346 ASN cc_start: 0.7795 (m110) cc_final: 0.7200 (m110) REVERT: B 48 ARG cc_start: 0.7788 (mmt180) cc_final: 0.7137 (mmm-85) REVERT: B 221 THR cc_start: 0.8658 (p) cc_final: 0.8418 (p) REVERT: B 266 HIS cc_start: 0.7586 (t-90) cc_final: 0.7229 (t70) REVERT: E 34 MET cc_start: 0.6571 (mmm) cc_final: 0.6250 (tmm) REVERT: E 110 PHE cc_start: 0.7269 (t80) cc_final: 0.6835 (m-80) REVERT: R 330 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7165 (tm-30) REVERT: R 333 ARG cc_start: 0.8598 (ptp-170) cc_final: 0.8287 (ptp-170) REVERT: R 334 LYS cc_start: 0.8304 (mtmm) cc_final: 0.7463 (mtmm) outliers start: 24 outliers final: 19 residues processed: 160 average time/residue: 0.2161 time to fit residues: 47.4875 Evaluate side-chains 156 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 330 GLU Chi-restraints excluded: chain R residue 406 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 0.0770 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8779 Z= 0.162 Angle : 0.534 6.774 11893 Z= 0.279 Chirality : 0.041 0.135 1353 Planarity : 0.003 0.047 1497 Dihedral : 4.740 89.012 1202 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.34 % Allowed : 16.18 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.02 (0.26), residues: 1084 helix: 1.84 (0.28), residues: 383 sheet: -0.62 (0.32), residues: 253 loop : -1.28 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 161 HIS 0.003 0.001 HIS B 91 PHE 0.015 0.001 PHE E 68 TYR 0.032 0.001 TYR E 235 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 140 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.6638 (mmm) cc_final: 0.6405 (mmm) REVERT: A 346 ASN cc_start: 0.7803 (m110) cc_final: 0.7167 (m110) REVERT: B 48 ARG cc_start: 0.7751 (mmt180) cc_final: 0.7159 (mmm-85) REVERT: B 221 THR cc_start: 0.8662 (p) cc_final: 0.8451 (p) REVERT: B 266 HIS cc_start: 0.7636 (t-90) cc_final: 0.7267 (t70) REVERT: E 34 MET cc_start: 0.6512 (mmm) cc_final: 0.6161 (tmm) REVERT: E 110 PHE cc_start: 0.7243 (t80) cc_final: 0.6826 (m-80) REVERT: E 228 TYR cc_start: 0.6189 (m-80) cc_final: 0.5812 (m-80) REVERT: R 330 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7180 (tm-30) REVERT: R 333 ARG cc_start: 0.8587 (ptp-170) cc_final: 0.8326 (ptp-170) REVERT: R 334 LYS cc_start: 0.8282 (mtmm) cc_final: 0.7591 (mtmm) outliers start: 31 outliers final: 23 residues processed: 161 average time/residue: 0.2117 time to fit residues: 47.2477 Evaluate side-chains 156 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 330 GLU Chi-restraints excluded: chain R residue 406 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 0.0970 chunk 93 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 183 HIS ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8779 Z= 0.249 Angle : 0.588 8.946 11893 Z= 0.308 Chirality : 0.042 0.154 1353 Planarity : 0.004 0.049 1497 Dihedral : 4.850 84.029 1201 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.88 % Allowed : 16.50 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.20 (0.27), residues: 1084 helix: 1.69 (0.28), residues: 383 sheet: -0.81 (0.32), residues: 262 loop : -1.32 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 297 HIS 0.005 0.001 HIS B 91 PHE 0.016 0.002 PHE B 234 TYR 0.029 0.002 TYR A 230 ARG 0.003 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 138 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.6583 (mtp) cc_final: 0.6007 (mtt) REVERT: A 247 MET cc_start: 0.6689 (mmm) cc_final: 0.6445 (mmm) REVERT: A 346 ASN cc_start: 0.7817 (m110) cc_final: 0.7160 (m110) REVERT: B 48 ARG cc_start: 0.7985 (mmt180) cc_final: 0.7358 (mmm-85) REVERT: B 221 THR cc_start: 0.8698 (p) cc_final: 0.8465 (p) REVERT: B 228 ASP cc_start: 0.6073 (OUTLIER) cc_final: 0.5402 (m-30) REVERT: B 266 HIS cc_start: 0.7725 (t-90) cc_final: 0.7268 (t-90) REVERT: E 34 MET cc_start: 0.6660 (mmm) cc_final: 0.6290 (tmm) REVERT: E 110 PHE cc_start: 0.7324 (t80) cc_final: 0.6932 (m-80) REVERT: E 228 TYR cc_start: 0.6266 (m-80) cc_final: 0.5680 (m-80) REVERT: R 65 ARG cc_start: 0.7160 (ttp-110) cc_final: 0.6509 (tpt90) REVERT: R 333 ARG cc_start: 0.8594 (ptp-170) cc_final: 0.8292 (ptp-170) REVERT: R 334 LYS cc_start: 0.8309 (mtmm) cc_final: 0.7858 (mtmm) outliers start: 36 outliers final: 30 residues processed: 162 average time/residue: 0.2050 time to fit residues: 45.8306 Evaluate side-chains 164 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 133 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 171 ASN Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 128 CYS Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 344 VAL Chi-restraints excluded: chain R residue 406 ASP Chi-restraints excluded: chain R residue 414 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 75 optimal weight: 0.0270 chunk 87 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 103 optimal weight: 0.1980 chunk 64 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 0.0870 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 ASN ** R 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8779 Z= 0.147 Angle : 0.550 9.290 11893 Z= 0.284 Chirality : 0.041 0.142 1353 Planarity : 0.003 0.046 1497 Dihedral : 4.698 88.514 1201 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.59 % Allowed : 18.45 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.01 (0.27), residues: 1084 helix: 1.86 (0.28), residues: 382 sheet: -0.55 (0.33), residues: 249 loop : -1.28 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.006 0.001 HIS B 183 PHE 0.014 0.001 PHE E 68 TYR 0.036 0.001 TYR E 235 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6536 (mtp) cc_final: 0.6008 (mtt) REVERT: A 25 GLU cc_start: 0.7436 (tm-30) cc_final: 0.7206 (tm-30) REVERT: A 247 MET cc_start: 0.6630 (mmm) cc_final: 0.6395 (mmm) REVERT: A 346 ASN cc_start: 0.7699 (m110) cc_final: 0.7032 (m110) REVERT: B 48 ARG cc_start: 0.7885 (mmt180) cc_final: 0.7321 (mmm-85) REVERT: B 221 THR cc_start: 0.8594 (p) cc_final: 0.8381 (p) REVERT: B 266 HIS cc_start: 0.7617 (t-90) cc_final: 0.7169 (t70) REVERT: E 34 MET cc_start: 0.6413 (mmm) cc_final: 0.6061 (tmm) REVERT: E 110 PHE cc_start: 0.7274 (t80) cc_final: 0.6941 (m-80) REVERT: E 228 TYR cc_start: 0.6198 (m-80) cc_final: 0.5550 (m-80) REVERT: R 65 ARG cc_start: 0.7160 (ttp-110) cc_final: 0.6446 (tpt90) REVERT: R 333 ARG cc_start: 0.8613 (ptp-170) cc_final: 0.8324 (ptp-170) REVERT: R 334 LYS cc_start: 0.8273 (mtmm) cc_final: 0.7853 (mtmm) outliers start: 24 outliers final: 20 residues processed: 159 average time/residue: 0.2223 time to fit residues: 48.6847 Evaluate side-chains 153 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 128 CYS Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 162 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 40.0000 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 93 optimal weight: 30.0000 chunk 98 optimal weight: 2.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 ASN ** R 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 8779 Z= 0.422 Angle : 0.729 10.653 11893 Z= 0.381 Chirality : 0.047 0.157 1353 Planarity : 0.005 0.053 1497 Dihedral : 5.214 73.820 1201 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.63 % Favored : 94.28 % Rotamer: Outliers : 3.78 % Allowed : 18.45 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.71 (0.26), residues: 1084 helix: 1.33 (0.28), residues: 376 sheet: -1.16 (0.31), residues: 260 loop : -1.58 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 36 HIS 0.009 0.002 HIS B 91 PHE 0.026 0.003 PHE B 234 TYR 0.037 0.003 TYR E 59 ARG 0.006 0.001 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 131 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6925 (mtp) cc_final: 0.6312 (mtt) REVERT: A 232 LEU cc_start: 0.5114 (OUTLIER) cc_final: 0.4719 (mp) REVERT: B 48 ARG cc_start: 0.7979 (mmt180) cc_final: 0.7373 (mmm-85) REVERT: B 228 ASP cc_start: 0.6313 (OUTLIER) cc_final: 0.5647 (m-30) REVERT: B 266 HIS cc_start: 0.7857 (t-90) cc_final: 0.7406 (t-90) REVERT: B 268 ASN cc_start: 0.8537 (m-40) cc_final: 0.8323 (t0) REVERT: E 34 MET cc_start: 0.6899 (mmm) cc_final: 0.6573 (tmm) REVERT: E 98 ARG cc_start: 0.7818 (ttp-170) cc_final: 0.7602 (ttp-170) REVERT: E 110 PHE cc_start: 0.7578 (t80) cc_final: 0.7163 (m-80) REVERT: E 228 TYR cc_start: 0.6689 (m-80) cc_final: 0.5681 (m-80) REVERT: R 65 ARG cc_start: 0.7135 (ttp-110) cc_final: 0.6693 (tpt90) REVERT: R 333 ARG cc_start: 0.8600 (ptp-170) cc_final: 0.8260 (ptp-170) REVERT: R 334 LYS cc_start: 0.8305 (mtmm) cc_final: 0.7875 (mtmm) outliers start: 35 outliers final: 30 residues processed: 154 average time/residue: 0.2217 time to fit residues: 46.8974 Evaluate side-chains 158 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 171 ASN Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 128 CYS Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 344 VAL Chi-restraints excluded: chain R residue 406 ASP Chi-restraints excluded: chain R residue 414 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 ASN ** R 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 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 : 0.003 0.034 8779 Z= 0.198 Angle : 0.601 8.250 11893 Z= 0.309 Chirality : 0.042 0.150 1353 Planarity : 0.003 0.049 1497 Dihedral : 4.884 83.329 1201 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.34 % Allowed : 19.20 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.47 (0.26), residues: 1084 helix: 1.71 (0.28), residues: 372 sheet: -1.12 (0.31), residues: 264 loop : -1.52 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 176 HIS 0.003 0.001 HIS B 91 PHE 0.020 0.002 PHE B 292 TYR 0.038 0.002 TYR E 235 ARG 0.004 0.000 ARG R 327 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 141 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.6815 (mtp) cc_final: 0.6188 (mtt) REVERT: A 25 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7265 (tm-30) REVERT: A 232 LEU cc_start: 0.5261 (OUTLIER) cc_final: 0.4852 (mp) REVERT: B 48 ARG cc_start: 0.7931 (mmt180) cc_final: 0.7359 (mmm-85) REVERT: B 228 ASP cc_start: 0.6150 (OUTLIER) cc_final: 0.5487 (m-30) REVERT: B 266 HIS cc_start: 0.7745 (t-90) cc_final: 0.7385 (t-90) REVERT: E 34 MET cc_start: 0.6581 (mmm) cc_final: 0.6232 (tmm) REVERT: E 110 PHE cc_start: 0.7364 (t80) cc_final: 0.7083 (m-80) REVERT: E 228 TYR cc_start: 0.6519 (m-80) cc_final: 0.5630 (m-80) REVERT: R 65 ARG cc_start: 0.7130 (ttp-110) cc_final: 0.6569 (tpt90) REVERT: R 333 ARG cc_start: 0.8608 (ptp-170) cc_final: 0.8317 (ptp-170) REVERT: R 334 LYS cc_start: 0.8283 (mtmm) cc_final: 0.7812 (mtmm) outliers start: 31 outliers final: 24 residues processed: 163 average time/residue: 0.2136 time to fit residues: 47.4303 Evaluate side-chains 161 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 135 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 47 TRP Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 406 ASP Chi-restraints excluded: chain R residue 414 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 106 optimal weight: 0.0970 chunk 98 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8779 Z= 0.183 Angle : 0.603 9.278 11893 Z= 0.309 Chirality : 0.041 0.189 1353 Planarity : 0.003 0.047 1497 Dihedral : 4.760 87.433 1201 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.91 % Allowed : 20.06 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.25 (0.26), residues: 1084 helix: 1.79 (0.28), residues: 376 sheet: -0.95 (0.32), residues: 252 loop : -1.36 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 176 HIS 0.003 0.001 HIS B 91 PHE 0.016 0.001 PHE B 292 TYR 0.038 0.002 TYR E 235 ARG 0.004 0.000 ARG R 327 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 140 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.6720 (mtp) cc_final: 0.6109 (mtt) REVERT: A 25 GLU cc_start: 0.7533 (tm-30) cc_final: 0.7297 (tm-30) REVERT: A 232 LEU cc_start: 0.5197 (OUTLIER) cc_final: 0.4763 (mp) REVERT: B 48 ARG cc_start: 0.7922 (mmt180) cc_final: 0.7381 (mmm-85) REVERT: B 228 ASP cc_start: 0.6123 (OUTLIER) cc_final: 0.5453 (m-30) REVERT: B 266 HIS cc_start: 0.7773 (t-90) cc_final: 0.7338 (t-90) REVERT: E 34 MET cc_start: 0.6450 (mmm) cc_final: 0.6102 (tmm) REVERT: E 110 PHE cc_start: 0.7339 (t80) cc_final: 0.7022 (m-80) REVERT: E 228 TYR cc_start: 0.6395 (m-80) cc_final: 0.5554 (m-80) REVERT: R 65 ARG cc_start: 0.7148 (ttp-110) cc_final: 0.6495 (tpt90) REVERT: R 333 ARG cc_start: 0.8587 (ptp-170) cc_final: 0.8272 (ptp-170) REVERT: R 334 LYS cc_start: 0.8271 (mtmm) cc_final: 0.7896 (mtmm) REVERT: R 335 MET cc_start: 0.6957 (ttp) cc_final: 0.6629 (ttm) outliers start: 27 outliers final: 22 residues processed: 160 average time/residue: 0.2246 time to fit residues: 48.5766 Evaluate side-chains 158 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 47 TRP Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 162 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 183 HIS ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 386 ASN ** 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 = 0.4539 r_free = 0.4539 target = 0.210844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.169486 restraints weight = 11075.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.167856 restraints weight = 8918.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.170461 restraints weight = 7272.448| |-----------------------------------------------------------------------------| r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8779 Z= 0.275 Angle : 0.639 8.657 11893 Z= 0.330 Chirality : 0.043 0.160 1353 Planarity : 0.004 0.049 1497 Dihedral : 4.896 81.509 1201 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.13 % Allowed : 19.96 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.26), residues: 1084 helix: 1.62 (0.28), residues: 368 sheet: -1.08 (0.31), residues: 265 loop : -1.57 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 36 HIS 0.006 0.001 HIS B 91 PHE 0.020 0.002 PHE B 292 TYR 0.036 0.002 TYR E 235 ARG 0.004 0.000 ARG A 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2016.18 seconds wall clock time: 37 minutes 41.95 seconds (2261.95 seconds total)