Starting phenix.real_space_refine on Tue Feb 13 18:51:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6h_31480/02_2024/7f6h_31480_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6h_31480/02_2024/7f6h_31480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6h_31480/02_2024/7f6h_31480.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6h_31480/02_2024/7f6h_31480.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6h_31480/02_2024/7f6h_31480_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6h_31480/02_2024/7f6h_31480_updated.pdb" } resolution = 2.9 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= 0.000 sd= 0.004 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 57 5.16 5 C 4701 2.51 5 N 1243 2.21 5 O 1341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 93": "OE1" <-> "OE2" Residue "A PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A ARG 267": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ARG 38": "NH1" <-> "NH2" Residue "B ARG 60": "NH1" <-> "NH2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B ARG 247": "NH1" <-> "NH2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C ARG 197": "NH1" <-> "NH2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "C ARG 283": "NH1" <-> "NH2" Residue "D ARG 27": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7342 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2448 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 9, 'TRANS': 295} Chain: "L" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 75 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 3, 'TRANS': 5} Chain: "B" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1873 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 220} Chain breaks: 1 Chain: "C" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2530 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 324} Chain: "D" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 360 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 4, 'TRANS': 42} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.49, per 1000 atoms: 0.61 Number of scatterers: 7342 At special positions: 0 Unit cell: (101.4, 93.288, 123.708, 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 57 16.00 O 1341 8.00 N 1243 7.00 C 4701 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 304 " distance=2.03 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 211 " distance=2.04 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: 2.81 Conformation dependent library (CDL) restraints added in 1.3 seconds 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1738 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 8 sheets defined 41.2% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 52 through 84 removed outlier: 3.681A pdb=" N THR A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) Proline residue: A 61 - end of helix Processing helix chain 'A' and resid 91 through 118 Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 127 through 159 Processing helix chain 'A' and resid 171 through 195 Proline residue: A 191 - end of helix Processing helix chain 'A' and resid 218 through 229 Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 266 through 298 Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 304 through 332 removed outlier: 4.512A pdb=" N PHE A 319 " --> pdb=" O GLN A 315 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS A 326 " --> pdb=" O TYR A 322 " (cutoff:3.500A) Proline residue: A 329 - end of helix Processing helix chain 'A' and resid 337 through 350 Processing helix chain 'B' and resid 15 through 38 removed outlier: 4.345A pdb=" N ARG B 38 " --> pdb=" O ARG B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 62 Processing helix chain 'B' and resid 213 through 220 removed outlier: 5.327A pdb=" N HIS B 218 " --> pdb=" O ARG B 214 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N CYS B 219 " --> pdb=" O LYS B 215 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE B 220 " --> pdb=" O TRP B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 236 removed outlier: 3.644A pdb=" N TYR B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP B 236 " --> pdb=" O SER B 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 232 through 236' Processing helix chain 'B' and resid 247 through 260 Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'B' and resid 276 through 284 removed outlier: 4.580A pdb=" N MET B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 316 removed outlier: 3.803A pdb=" N LEU B 316 " --> pdb=" O MET B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 355 Processing helix chain 'C' and resid 12 through 24 Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'D' and resid 16 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing sheet with id= A, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.809A pdb=" N VAL B 269 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N HIS B 327 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU B 271 " --> pdb=" O HIS B 327 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER B 225 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE B 200 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU B 42 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ARG B 202 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU B 44 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL B 204 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N GLY B 46 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE B 190 " --> pdb=" O ASP B 205 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.860A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.863A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.685A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 221 through 223 removed outlier: 4.039A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.744A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.663A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 46 through 52 removed outlier: 3.599A pdb=" N ARG C 46 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN C 340 " --> pdb=" O ARG C 46 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER C 331 " --> pdb=" O PHE C 335 " (cutoff:3.500A) 340 hydrogen bonds defined for protein. 1005 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: 2.17 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2304 1.34 - 1.46: 1658 1.46 - 1.58: 3450 1.58 - 1.71: 0 1.71 - 1.83: 84 Bond restraints: 7496 Sorted by residual: bond pdb=" C10 CLR A 501 " pdb=" C5 CLR A 501 " ideal model delta sigma weight residual 1.519 1.383 0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" C10 CLR A 502 " pdb=" C5 CLR A 502 " ideal model delta sigma weight residual 1.519 1.387 0.132 2.00e-02 2.50e+03 4.37e+01 bond pdb=" C4 CLR A 501 " pdb=" C5 CLR A 501 " ideal model delta sigma weight residual 1.506 1.381 0.125 2.00e-02 2.50e+03 3.93e+01 bond pdb=" C4 CLR A 502 " pdb=" C5 CLR A 502 " ideal model delta sigma weight residual 1.506 1.383 0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" C6 CLR A 501 " pdb=" C7 CLR A 501 " ideal model delta sigma weight residual 1.492 1.390 0.102 2.00e-02 2.50e+03 2.62e+01 ... (remaining 7491 not shown) Histogram of bond angle deviations from ideal: 96.52 - 104.07: 93 104.07 - 111.62: 3440 111.62 - 119.17: 2848 119.17 - 126.72: 3678 126.72 - 134.27: 112 Bond angle restraints: 10171 Sorted by residual: angle pdb=" N PRO A 61 " pdb=" CA PRO A 61 " pdb=" C PRO A 61 " ideal model delta sigma weight residual 110.70 118.46 -7.76 1.22e+00 6.72e-01 4.04e+01 angle pdb=" N LEU B 358 " pdb=" CA LEU B 358 " pdb=" C LEU B 358 " ideal model delta sigma weight residual 113.41 106.93 6.48 1.22e+00 6.72e-01 2.83e+01 angle pdb=" CA PRO A 61 " pdb=" C PRO A 61 " pdb=" N PRO A 62 " ideal model delta sigma weight residual 117.93 124.19 -6.26 1.20e+00 6.94e-01 2.72e+01 angle pdb=" C ILE C 81 " pdb=" N TRP C 82 " pdb=" CA TRP C 82 " ideal model delta sigma weight residual 122.64 129.12 -6.48 1.70e+00 3.46e-01 1.45e+01 angle pdb=" CA ASN C 36 " pdb=" C ASN C 36 " pdb=" O ASN C 36 " ideal model delta sigma weight residual 122.63 117.75 4.88 1.29e+00 6.01e-01 1.43e+01 ... (remaining 10166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.95: 4329 23.95 - 47.90: 215 47.90 - 71.86: 14 71.86 - 95.81: 13 95.81 - 119.76: 2 Dihedral angle restraints: 4573 sinusoidal: 1898 harmonic: 2675 Sorted by residual: dihedral pdb=" CB CYS A 47 " pdb=" SG CYS A 47 " pdb=" SG CYS A 304 " pdb=" CB CYS A 304 " ideal model delta sinusoidal sigma weight residual 93.00 137.05 -44.05 1 1.00e+01 1.00e-02 2.70e+01 dihedral pdb=" CA THR A 209 " pdb=" C THR A 209 " pdb=" N ALA A 210 " pdb=" CA ALA A 210 " ideal model delta harmonic sigma weight residual -180.00 -156.62 -23.38 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" C10 CLR A 502 " pdb=" C1 CLR A 502 " pdb=" C2 CLR A 502 " pdb=" C3 CLR A 502 " ideal model delta sinusoidal sigma weight residual -56.83 62.93 -119.76 1 3.00e+01 1.11e-03 1.60e+01 ... (remaining 4570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1035 0.097 - 0.193: 114 0.193 - 0.290: 12 0.290 - 0.386: 7 0.386 - 0.483: 2 Chirality restraints: 1170 Sorted by residual: chirality pdb=" C14 CLR A 502 " pdb=" C13 CLR A 502 " pdb=" C15 CLR A 502 " pdb=" C8 CLR A 502 " both_signs ideal model delta sigma weight residual False -2.32 -2.80 0.48 2.00e-01 2.50e+01 5.83e+00 chirality pdb=" C14 CLR A 501 " pdb=" C13 CLR A 501 " pdb=" C15 CLR A 501 " pdb=" C8 CLR A 501 " both_signs ideal model delta sigma weight residual False -2.32 -2.75 0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" C10 CLR A 502 " pdb=" C1 CLR A 502 " pdb=" C5 CLR A 502 " pdb=" C9 CLR A 502 " both_signs ideal model delta sigma weight residual False -2.85 -2.46 -0.38 2.00e-01 2.50e+01 3.70e+00 ... (remaining 1167 not shown) Planarity restraints: 1273 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS C 218 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.68e+00 pdb=" C CYS C 218 " -0.048 2.00e-02 2.50e+03 pdb=" O CYS C 218 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG C 219 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 105 " 0.012 2.00e-02 2.50e+03 1.44e-02 4.16e+00 pdb=" CG TYR C 105 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR C 105 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR C 105 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR C 105 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR C 105 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR C 105 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 105 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 140 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.18e+00 pdb=" C ALA C 140 " -0.031 2.00e-02 2.50e+03 pdb=" O ALA C 140 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY C 141 " 0.011 2.00e-02 2.50e+03 ... (remaining 1270 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1521 2.78 - 3.31: 6892 3.31 - 3.84: 11748 3.84 - 4.37: 14621 4.37 - 4.90: 25231 Nonbonded interactions: 60013 Sorted by model distance: nonbonded pdb=" O ARG C 68 " pdb=" OG SER C 84 " model vdw 2.246 2.440 nonbonded pdb=" O MET A 320 " pdb=" OG SER A 323 " model vdw 2.314 2.440 nonbonded pdb=" NH2 ARG A 196 " pdb=" O GLY L 4 " model vdw 2.332 2.520 nonbonded pdb=" NZ LYS A 260 " pdb=" OD2 ASP B 346 " model vdw 2.345 2.520 nonbonded pdb=" OE2 GLU B 17 " pdb=" NH2 ARG B 20 " model vdw 2.363 2.520 ... (remaining 60008 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: 0.650 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: 3.180 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 23.660 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 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 : 0.011 0.136 7496 Z= 0.725 Angle : 0.990 9.952 10171 Z= 0.608 Chirality : 0.069 0.483 1170 Planarity : 0.004 0.042 1273 Dihedral : 14.048 119.760 2829 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.87 % Allowed : 1.74 % Favored : 97.39 % 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: -0.14 (0.26), residues: 905 helix: 1.16 (0.25), residues: 390 sheet: 0.06 (0.38), residues: 175 loop : -1.67 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP C 82 HIS 0.014 0.003 HIS C 225 PHE 0.022 0.003 PHE A 319 TYR 0.033 0.003 TYR C 105 ARG 0.014 0.001 ARG C 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 0.773 Fit side-chains REVERT: A 184 CYS cc_start: 0.7103 (m) cc_final: 0.6494 (m) REVERT: B 32 ASP cc_start: 0.7491 (m-30) cc_final: 0.7289 (m-30) REVERT: C 217 MET cc_start: 0.7725 (ptm) cc_final: 0.7471 (ptm) REVERT: C 322 ASP cc_start: 0.7862 (m-30) cc_final: 0.7586 (m-30) outliers start: 7 outliers final: 2 residues processed: 125 average time/residue: 1.1310 time to fit residues: 149.9797 Evaluate side-chains 95 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 230 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 80 optimal weight: 0.2980 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 206 HIS A 246 GLN ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 ASN C 88 ASN C 220 GLN C 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7496 Z= 0.205 Angle : 0.540 9.187 10171 Z= 0.286 Chirality : 0.042 0.133 1170 Planarity : 0.004 0.039 1273 Dihedral : 4.962 28.116 1126 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.23 % Allowed : 9.31 % Favored : 88.46 % 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 (0.27), residues: 905 helix: 1.93 (0.25), residues: 390 sheet: -0.33 (0.36), residues: 194 loop : -1.34 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 82 HIS 0.004 0.001 HIS C 54 PHE 0.015 0.001 PHE C 199 TYR 0.016 0.001 TYR A 215 ARG 0.003 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 0.857 Fit side-chains REVERT: B 259 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7537 (pt) REVERT: C 217 MET cc_start: 0.8113 (ptm) cc_final: 0.7874 (ptm) REVERT: C 322 ASP cc_start: 0.7779 (m-30) cc_final: 0.7507 (m-30) outliers start: 18 outliers final: 9 residues processed: 110 average time/residue: 1.1194 time to fit residues: 130.8473 Evaluate side-chains 102 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 331 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 87 optimal weight: 0.1980 chunk 72 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 263 GLN A 315 GLN ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN D 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7496 Z= 0.179 Angle : 0.502 8.780 10171 Z= 0.265 Chirality : 0.041 0.132 1170 Planarity : 0.003 0.039 1273 Dihedral : 4.447 29.566 1125 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.73 % Allowed : 12.28 % Favored : 84.99 % 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 (0.27), residues: 905 helix: 2.20 (0.26), residues: 391 sheet: -0.23 (0.36), residues: 195 loop : -1.29 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.004 0.001 HIS C 54 PHE 0.014 0.001 PHE C 234 TYR 0.008 0.001 TYR D 40 ARG 0.004 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 0.878 Fit side-chains REVERT: A 330 LEU cc_start: 0.8471 (tp) cc_final: 0.8255 (mt) REVERT: C 217 MET cc_start: 0.8039 (ptm) cc_final: 0.7762 (ptm) REVERT: C 311 HIS cc_start: 0.7822 (OUTLIER) cc_final: 0.5821 (m90) REVERT: C 322 ASP cc_start: 0.7722 (m-30) cc_final: 0.7447 (m-30) outliers start: 22 outliers final: 5 residues processed: 112 average time/residue: 1.0404 time to fit residues: 124.4413 Evaluate side-chains 98 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain C residue 311 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 48 optimal weight: 0.0060 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 263 GLN ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 HIS C 340 ASN D 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7496 Z= 0.192 Angle : 0.508 8.778 10171 Z= 0.266 Chirality : 0.041 0.134 1170 Planarity : 0.003 0.040 1273 Dihedral : 4.377 30.489 1125 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.73 % Allowed : 13.90 % Favored : 83.37 % 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: 0.81 (0.28), residues: 905 helix: 2.32 (0.26), residues: 390 sheet: -0.28 (0.37), residues: 192 loop : -1.20 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.004 0.001 HIS C 54 PHE 0.013 0.001 PHE C 199 TYR 0.014 0.001 TYR A 215 ARG 0.003 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 0.867 Fit side-chains REVERT: A 207 ASN cc_start: 0.7760 (OUTLIER) cc_final: 0.7514 (m-40) REVERT: B 32 ASP cc_start: 0.7141 (m-30) cc_final: 0.6839 (m-30) REVERT: C 47 THR cc_start: 0.8867 (OUTLIER) cc_final: 0.8637 (m) REVERT: C 322 ASP cc_start: 0.7715 (m-30) cc_final: 0.7449 (m-30) outliers start: 22 outliers final: 9 residues processed: 112 average time/residue: 1.0293 time to fit residues: 123.2499 Evaluate side-chains 104 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 312 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.3980 chunk 64 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.2980 chunk 77 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 0.0970 chunk 17 optimal weight: 0.5980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 263 GLN ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN C 340 ASN D 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7496 Z= 0.147 Angle : 0.485 8.134 10171 Z= 0.251 Chirality : 0.040 0.129 1170 Planarity : 0.003 0.039 1273 Dihedral : 4.108 29.538 1125 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.61 % Allowed : 15.14 % Favored : 82.26 % 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: 0.97 (0.28), residues: 905 helix: 2.48 (0.26), residues: 391 sheet: -0.18 (0.37), residues: 192 loop : -1.18 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.003 0.001 HIS C 54 PHE 0.013 0.001 PHE C 199 TYR 0.011 0.001 TYR A 215 ARG 0.004 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 0.862 Fit side-chains REVERT: B 203 MET cc_start: 0.8735 (mtt) cc_final: 0.8527 (mtt) REVERT: C 45 MET cc_start: 0.8365 (mtt) cc_final: 0.8004 (mtt) REVERT: C 47 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8658 (m) REVERT: C 215 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7608 (pp20) REVERT: C 256 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6894 (mtm180) REVERT: C 322 ASP cc_start: 0.7716 (m-30) cc_final: 0.7452 (m-30) outliers start: 21 outliers final: 11 residues processed: 116 average time/residue: 1.0451 time to fit residues: 129.2237 Evaluate side-chains 109 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 312 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 0.0670 chunk 86 optimal weight: 0.0770 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.0280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 263 GLN B 246 ASN C 340 ASN D 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7496 Z= 0.248 Angle : 0.552 9.431 10171 Z= 0.287 Chirality : 0.042 0.137 1170 Planarity : 0.004 0.039 1273 Dihedral : 4.378 32.619 1125 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.35 % Allowed : 15.76 % Favored : 80.89 % 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: 0.80 (0.28), residues: 905 helix: 2.28 (0.26), residues: 392 sheet: -0.27 (0.37), residues: 192 loop : -1.18 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.006 0.001 HIS C 54 PHE 0.014 0.002 PHE A 319 TYR 0.012 0.001 TYR C 59 ARG 0.003 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 90 time to evaluate : 0.895 Fit side-chains REVERT: A 322 TYR cc_start: 0.8095 (OUTLIER) cc_final: 0.7849 (m-80) REVERT: B 32 ASP cc_start: 0.7121 (m-30) cc_final: 0.6869 (m-30) REVERT: B 57 LYS cc_start: 0.6899 (OUTLIER) cc_final: 0.6478 (ttmt) REVERT: B 203 MET cc_start: 0.8759 (mtt) cc_final: 0.8521 (mtt) REVERT: C 47 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8619 (m) REVERT: C 217 MET cc_start: 0.7836 (ptm) cc_final: 0.7595 (ptm) REVERT: C 256 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.7129 (mtm110) REVERT: C 322 ASP cc_start: 0.7729 (m-30) cc_final: 0.7445 (m-30) outliers start: 27 outliers final: 13 residues processed: 109 average time/residue: 1.0558 time to fit residues: 122.7202 Evaluate side-chains 108 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain D residue 21 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 263 GLN C 340 ASN D 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7496 Z= 0.219 Angle : 0.533 9.696 10171 Z= 0.277 Chirality : 0.042 0.197 1170 Planarity : 0.003 0.039 1273 Dihedral : 4.311 32.993 1125 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.72 % Allowed : 16.00 % Favored : 80.27 % 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: 0.82 (0.28), residues: 905 helix: 2.33 (0.26), residues: 391 sheet: -0.28 (0.37), residues: 192 loop : -1.20 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.004 0.001 HIS C 54 PHE 0.014 0.001 PHE B 255 TYR 0.016 0.001 TYR A 215 ARG 0.002 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 95 time to evaluate : 0.859 Fit side-chains REVERT: A 163 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.5920 (mpt) REVERT: A 192 MET cc_start: 0.7496 (mmm) cc_final: 0.7269 (mmp) REVERT: A 322 TYR cc_start: 0.8012 (OUTLIER) cc_final: 0.7802 (m-80) REVERT: B 203 MET cc_start: 0.8768 (mtt) cc_final: 0.8563 (mtt) REVERT: C 47 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8626 (m) REVERT: C 70 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8052 (OUTLIER) REVERT: C 256 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.7163 (mtm110) REVERT: C 311 HIS cc_start: 0.7774 (OUTLIER) cc_final: 0.5948 (m90) REVERT: C 322 ASP cc_start: 0.7741 (m-30) cc_final: 0.7458 (m-30) outliers start: 30 outliers final: 16 residues processed: 116 average time/residue: 1.0914 time to fit residues: 134.6251 Evaluate side-chains 114 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 21 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 263 GLN C 340 ASN D 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7496 Z= 0.187 Angle : 0.521 9.341 10171 Z= 0.270 Chirality : 0.041 0.165 1170 Planarity : 0.003 0.039 1273 Dihedral : 4.225 31.971 1125 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.97 % Allowed : 15.63 % Favored : 80.40 % 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: 0.90 (0.28), residues: 905 helix: 2.42 (0.26), residues: 391 sheet: -0.24 (0.37), residues: 192 loop : -1.19 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.003 0.001 HIS C 54 PHE 0.013 0.001 PHE B 255 TYR 0.013 0.001 TYR C 59 ARG 0.003 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 94 time to evaluate : 0.893 Fit side-chains REVERT: A 163 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.5660 (mpt) REVERT: A 192 MET cc_start: 0.7465 (mmm) cc_final: 0.7223 (mmp) REVERT: A 322 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.7729 (m-80) REVERT: B 32 ASP cc_start: 0.7103 (m-30) cc_final: 0.6883 (m-30) REVERT: B 57 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.6403 (ttmt) REVERT: B 203 MET cc_start: 0.8765 (mtt) cc_final: 0.8539 (mtt) REVERT: B 259 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7580 (pt) REVERT: C 47 THR cc_start: 0.8869 (OUTLIER) cc_final: 0.8625 (m) REVERT: C 70 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7968 (pt) REVERT: C 234 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8024 (m-80) REVERT: C 322 ASP cc_start: 0.7726 (m-30) cc_final: 0.7457 (m-30) outliers start: 32 outliers final: 17 residues processed: 115 average time/residue: 1.0368 time to fit residues: 127.2257 Evaluate side-chains 117 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 93 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 21 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 0.0970 chunk 24 optimal weight: 0.8980 chunk 72 optimal weight: 0.0970 chunk 75 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 263 GLN B 303 GLN C 266 HIS C 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7496 Z= 0.170 Angle : 0.521 8.980 10171 Z= 0.270 Chirality : 0.041 0.155 1170 Planarity : 0.003 0.038 1273 Dihedral : 4.133 30.993 1125 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.23 % Allowed : 16.50 % Favored : 80.27 % 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: 0.95 (0.28), residues: 905 helix: 2.47 (0.26), residues: 392 sheet: -0.25 (0.37), residues: 192 loop : -1.17 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.003 0.001 HIS C 54 PHE 0.013 0.001 PHE B 255 TYR 0.013 0.001 TYR A 215 ARG 0.003 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 93 time to evaluate : 0.806 Fit side-chains REVERT: A 192 MET cc_start: 0.7375 (mmm) cc_final: 0.7108 (mmp) REVERT: A 322 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.7687 (m-80) REVERT: B 32 ASP cc_start: 0.7107 (m-30) cc_final: 0.6877 (m-30) REVERT: B 57 LYS cc_start: 0.6859 (OUTLIER) cc_final: 0.6432 (ttmt) REVERT: B 203 MET cc_start: 0.8763 (mtt) cc_final: 0.8534 (mtt) REVERT: B 259 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7571 (pt) REVERT: C 47 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8615 (m) REVERT: C 70 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7893 (pt) REVERT: C 234 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8035 (m-80) REVERT: C 311 HIS cc_start: 0.7729 (OUTLIER) cc_final: 0.5902 (m90) REVERT: C 322 ASP cc_start: 0.7713 (m-30) cc_final: 0.7441 (m-30) outliers start: 26 outliers final: 15 residues processed: 111 average time/residue: 1.0278 time to fit residues: 121.7075 Evaluate side-chains 115 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 311 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 263 GLN C 259 GLN C 340 ASN D 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7496 Z= 0.334 Angle : 0.617 11.467 10171 Z= 0.320 Chirality : 0.045 0.141 1170 Planarity : 0.004 0.040 1273 Dihedral : 4.682 35.702 1125 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.60 % Allowed : 16.38 % Favored : 80.02 % 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: 0.67 (0.28), residues: 905 helix: 2.17 (0.26), residues: 388 sheet: -0.14 (0.38), residues: 180 loop : -1.32 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 82 HIS 0.006 0.001 HIS B 327 PHE 0.015 0.002 PHE A 319 TYR 0.011 0.002 TYR D 40 ARG 0.004 0.000 ARG A 155 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 89 time to evaluate : 0.869 Fit side-chains REVERT: B 32 ASP cc_start: 0.7053 (m-30) cc_final: 0.6811 (m-30) REVERT: B 57 LYS cc_start: 0.6919 (OUTLIER) cc_final: 0.6644 (ttmt) REVERT: B 259 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7576 (pt) REVERT: C 70 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8112 (pt) REVERT: C 234 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.7928 (m-80) REVERT: C 322 ASP cc_start: 0.7811 (m-30) cc_final: 0.7521 (m-30) outliers start: 29 outliers final: 16 residues processed: 110 average time/residue: 1.0194 time to fit residues: 120.0332 Evaluate side-chains 108 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 38 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 72 optimal weight: 0.0270 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 0.0970 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 263 GLN B 303 GLN C 340 ASN D 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.156897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.121578 restraints weight = 7783.461| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.50 r_work: 0.3241 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7496 Z= 0.165 Angle : 0.542 11.131 10171 Z= 0.281 Chirality : 0.041 0.142 1170 Planarity : 0.003 0.039 1273 Dihedral : 4.302 32.680 1125 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.85 % Allowed : 16.87 % Favored : 80.27 % 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: 0.87 (0.28), residues: 905 helix: 2.46 (0.26), residues: 387 sheet: -0.33 (0.37), residues: 197 loop : -1.22 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.002 0.001 HIS C 311 PHE 0.013 0.001 PHE B 255 TYR 0.011 0.001 TYR A 215 ARG 0.004 0.000 ARG A 196 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2934.65 seconds wall clock time: 52 minutes 57.13 seconds (3177.13 seconds total)