Starting phenix.real_space_refine on Fri Apr 5 22:24:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8geh_29970/04_2024/8geh_29970_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8geh_29970/04_2024/8geh_29970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8geh_29970/04_2024/8geh_29970.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8geh_29970/04_2024/8geh_29970.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8geh_29970/04_2024/8geh_29970_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8geh_29970/04_2024/8geh_29970_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.021 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 11 5.16 5 C 3853 2.51 5 N 1069 2.21 5 O 1062 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5995 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 1812 Classifications: {'peptide': 301} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 198} Link IDs: {'PTRANS': 8, 'TRANS': 292} Chain breaks: 8 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 714 Unresolved non-hydrogen angles: 889 Unresolved non-hydrogen dihedrals: 578 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 15, 'ASP:plan': 19, 'PHE:plan': 5, 'GLU:plan': 23, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 438 Chain: "B" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2133 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 408 Unresolved non-hydrogen angles: 509 Unresolved non-hydrogen dihedrals: 309 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 24, 'ASN:plan1': 12, 'HIS:plan': 1, 'ASN%COO:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 244 Chain: "G" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 312 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "R" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 1723 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 160} Link IDs: {'PTRANS': 7, 'TRANS': 270} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 521 Unresolved non-hydrogen angles: 664 Unresolved non-hydrogen dihedrals: 409 Unresolved non-hydrogen chiralities: 71 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 236 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.12, per 1000 atoms: 0.69 Number of scatterers: 5995 At special positions: 0 Unit cell: (68.9, 98.58, 128.26, 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 11 16.00 O 1062 8.00 N 1069 7.00 C 3853 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.36 Conformation dependent library (CDL) restraints added in 1.4 seconds 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1826 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 8 sheets defined 44.9% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.767A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 53 through 60 Processing helix chain 'A' and resid 92 through 113 Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 144 through 147 No H-bonds generated for 'chain 'A' and resid 144 through 147' Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 196 through 199 No H-bonds generated for 'chain 'A' and resid 196 through 199' Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.655A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.757A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 392 removed outlier: 3.580A pdb=" N ARG A 380 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN A 384 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A 385 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 388 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A 389 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N TYR A 391 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.946A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 23 removed outlier: 3.591A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'R' and resid 32 through 60 removed outlier: 3.634A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 85 removed outlier: 4.158A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR R 73 " --> pdb=" O ASN R 69 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER R 74 " --> pdb=" O TYR R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 96 Processing helix chain 'R' and resid 103 through 136 removed outlier: 3.654A pdb=" N VAL R 117 " --> pdb=" O ASP R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 144 No H-bonds generated for 'chain 'R' and resid 141 through 144' Processing helix chain 'R' and resid 147 through 162 Processing helix chain 'R' and resid 166 through 171 Processing helix chain 'R' and resid 182 through 186 removed outlier: 3.657A pdb=" N ALA R 186 " --> pdb=" O ILE R 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 182 through 186' Processing helix chain 'R' and resid 197 through 207 removed outlier: 3.597A pdb=" N ILE R 201 " --> pdb=" O GLN R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 236 removed outlier: 3.615A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 293 removed outlier: 3.523A pdb=" N ILE R 277 " --> pdb=" O LYS R 273 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE R 278 " --> pdb=" O THR R 274 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP R 286 " --> pdb=" O PHE R 282 " (cutoff:3.500A) Proline residue: R 288 - end of helix Processing helix chain 'R' and resid 295 through 298 No H-bonds generated for 'chain 'R' and resid 295 through 298' Processing helix chain 'R' and resid 305 through 325 removed outlier: 3.631A pdb=" N ILE R 309 " --> pdb=" O LYS R 305 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 330 through 339 Processing sheet with id= A, first strand: chain 'A' and resid 286 through 292 removed outlier: 3.575A pdb=" N PHE A 290 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 44 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 49 through 52 Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.808A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.692A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.470A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 208 through 212 removed outlier: 3.573A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.336A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 276 through 278 removed outlier: 5.692A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 942 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.97 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2024 1.34 - 1.46: 1381 1.46 - 1.57: 2692 1.57 - 1.69: 0 1.69 - 1.81: 14 Bond restraints: 6111 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.450 -0.053 2.00e-02 2.50e+03 6.99e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.572 -0.049 2.00e-02 2.50e+03 6.10e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.442 -0.048 2.00e-02 2.50e+03 5.72e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.564 -0.044 2.00e-02 2.50e+03 4.91e+00 bond pdb=" CAI G1I R 501 " pdb=" NAN G1I R 501 " ideal model delta sigma weight residual 1.451 1.487 -0.036 2.00e-02 2.50e+03 3.30e+00 ... (remaining 6106 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.83: 110 106.83 - 113.63: 3421 113.63 - 120.43: 2188 120.43 - 127.24: 2650 127.24 - 134.04: 67 Bond angle restraints: 8436 Sorted by residual: angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.20 109.44 3.76 9.60e-01 1.09e+00 1.53e+01 angle pdb=" N GLY B 202 " pdb=" CA GLY B 202 " pdb=" C GLY B 202 " ideal model delta sigma weight residual 111.46 114.89 -3.43 1.75e+00 3.27e-01 3.83e+00 angle pdb=" C VAL A 214 " pdb=" N ASP A 215 " pdb=" CA ASP A 215 " ideal model delta sigma weight residual 121.54 125.12 -3.58 1.91e+00 2.74e-01 3.51e+00 angle pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " pdb=" CAI G1I R 501 " ideal model delta sigma weight residual 110.89 116.32 -5.43 3.00e+00 1.11e-01 3.27e+00 angle pdb=" CA ILE B 270 " pdb=" C ILE B 270 " pdb=" N CYS B 271 " ideal model delta sigma weight residual 118.71 116.64 2.07 1.15e+00 7.56e-01 3.24e+00 ... (remaining 8431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.91: 3159 10.91 - 21.82: 157 21.82 - 32.74: 77 32.74 - 43.65: 36 43.65 - 54.56: 9 Dihedral angle restraints: 3438 sinusoidal: 644 harmonic: 2794 Sorted by residual: dihedral pdb=" CA HIS B 183 " pdb=" C HIS B 183 " pdb=" N THR B 184 " pdb=" CA THR B 184 " ideal model delta harmonic sigma weight residual 180.00 -164.10 -15.90 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA ARG A 380 " pdb=" CB ARG A 380 " pdb=" CG ARG A 380 " pdb=" CD ARG A 380 " ideal model delta sinusoidal sigma weight residual -60.00 -109.66 49.66 3 1.50e+01 4.44e-03 8.80e+00 dihedral pdb=" CA ARG B 49 " pdb=" CB ARG B 49 " pdb=" CG ARG B 49 " pdb=" CD ARG B 49 " ideal model delta sinusoidal sigma weight residual 180.00 132.13 47.87 3 1.50e+01 4.44e-03 8.56e+00 ... (remaining 3435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 730 0.034 - 0.068: 233 0.068 - 0.102: 68 0.102 - 0.136: 18 0.136 - 0.171: 2 Chirality restraints: 1051 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.57 -0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CA ILE A 288 " pdb=" N ILE A 288 " pdb=" C ILE A 288 " pdb=" CB ILE A 288 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE B 157 " pdb=" N ILE B 157 " pdb=" C ILE B 157 " pdb=" CB ILE B 157 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.65e-01 ... (remaining 1048 not shown) Planarity restraints: 1096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 167 " -0.021 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO R 168 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.017 5.00e-02 4.00e+02 2.57e-02 1.05e+00 pdb=" N PRO B 236 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " 0.005 2.00e-02 2.50e+03 1.00e-02 1.00e+00 pdb=" C THR B 87 " -0.017 2.00e-02 2.50e+03 pdb=" O THR B 87 " 0.006 2.00e-02 2.50e+03 pdb=" N ASN B 88 " 0.006 2.00e-02 2.50e+03 ... (remaining 1093 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1660 2.80 - 3.33: 5850 3.33 - 3.85: 9439 3.85 - 4.38: 9827 4.38 - 4.90: 17284 Nonbonded interactions: 44060 Sorted by model distance: nonbonded pdb=" O LEU A 282 " pdb=" NE2 HIS A 357 " model vdw 2.276 2.520 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.289 2.440 nonbonded pdb=" ND1 HIS B 142 " pdb=" OG SER B 161 " model vdw 2.331 2.520 nonbonded pdb=" NE1 TRP A 277 " pdb=" O SER A 349 " model vdw 2.352 2.520 nonbonded pdb=" NH2 ARG B 49 " pdb=" O PHE G 61 " model vdw 2.357 2.520 ... (remaining 44055 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: 7.770 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: 2.260 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 21.840 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6111 Z= 0.184 Angle : 0.433 5.428 8436 Z= 0.241 Chirality : 0.039 0.171 1051 Planarity : 0.002 0.032 1096 Dihedral : 10.847 54.562 1612 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: 1.54 (0.28), residues: 930 helix: 2.42 (0.24), residues: 415 sheet: 0.67 (0.44), residues: 163 loop : -0.52 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 297 HIS 0.004 0.001 HIS B 183 PHE 0.011 0.001 PHE B 199 TYR 0.014 0.001 TYR R 141 ARG 0.004 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.751 Fit side-chains REVERT: A 380 ARG cc_start: 0.8813 (tmm-80) cc_final: 0.8369 (ttm170) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1450 time to fit residues: 12.3350 Evaluate side-chains 44 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6111 Z= 0.165 Angle : 0.421 4.886 8436 Z= 0.241 Chirality : 0.039 0.149 1051 Planarity : 0.003 0.030 1096 Dihedral : 3.713 14.450 1000 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.31 % Allowed : 8.81 % Favored : 90.88 % 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: 1.74 (0.28), residues: 930 helix: 2.73 (0.24), residues: 423 sheet: 0.53 (0.42), residues: 176 loop : -0.61 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 297 HIS 0.005 0.001 HIS B 225 PHE 0.008 0.001 PHE B 199 TYR 0.013 0.001 TYR R 199 ARG 0.003 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.685 Fit side-chains REVERT: B 17 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8471 (tm-30) REVERT: B 188 MET cc_start: 0.8810 (mmt) cc_final: 0.8512 (mmm) outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 0.1170 time to fit residues: 8.9968 Evaluate side-chains 44 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 0.0670 chunk 71 optimal weight: 0.3980 chunk 58 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6111 Z= 0.125 Angle : 0.384 4.967 8436 Z= 0.215 Chirality : 0.038 0.139 1051 Planarity : 0.002 0.029 1096 Dihedral : 3.535 16.181 1000 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.94 % Allowed : 13.52 % Favored : 85.53 % 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: 2.01 (0.28), residues: 930 helix: 3.08 (0.24), residues: 418 sheet: 0.47 (0.41), residues: 185 loop : -0.50 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 297 HIS 0.002 0.001 HIS B 225 PHE 0.007 0.001 PHE B 199 TYR 0.014 0.001 TYR R 199 ARG 0.003 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.731 Fit side-chains REVERT: B 17 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8413 (tm-30) REVERT: R 82 MET cc_start: 0.8298 (tmm) cc_final: 0.7940 (tmm) outliers start: 3 outliers final: 2 residues processed: 53 average time/residue: 0.1225 time to fit residues: 10.0682 Evaluate side-chains 46 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.0970 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 9 optimal weight: 0.0980 chunk 41 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 82 optimal weight: 0.0770 chunk 24 optimal weight: 0.6980 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.027 6111 Z= 0.103 Angle : 0.373 5.027 8436 Z= 0.210 Chirality : 0.038 0.137 1051 Planarity : 0.002 0.030 1096 Dihedral : 3.382 13.601 1000 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.26 % Allowed : 15.72 % Favored : 83.02 % 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: 2.03 (0.28), residues: 930 helix: 3.09 (0.24), residues: 420 sheet: 0.43 (0.41), residues: 180 loop : -0.47 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 297 HIS 0.002 0.001 HIS B 142 PHE 0.006 0.001 PHE B 199 TYR 0.011 0.001 TYR R 199 ARG 0.003 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 1.060 Fit side-chains REVERT: B 17 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8475 (tm-30) REVERT: B 82 TRP cc_start: 0.8212 (m100) cc_final: 0.7945 (m-10) REVERT: R 82 MET cc_start: 0.8248 (tmm) cc_final: 0.7857 (tmm) outliers start: 4 outliers final: 4 residues processed: 53 average time/residue: 0.1425 time to fit residues: 11.7797 Evaluate side-chains 49 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6111 Z= 0.257 Angle : 0.452 5.290 8436 Z= 0.252 Chirality : 0.039 0.158 1051 Planarity : 0.003 0.027 1096 Dihedral : 3.872 13.102 1000 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.83 % Allowed : 17.30 % Favored : 79.87 % 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: 1.91 (0.28), residues: 930 helix: 3.04 (0.25), residues: 418 sheet: 0.22 (0.39), residues: 185 loop : -0.49 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 297 HIS 0.004 0.001 HIS B 225 PHE 0.013 0.001 PHE B 199 TYR 0.019 0.001 TYR R 199 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.710 Fit side-chains REVERT: B 17 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8432 (tm-30) REVERT: R 82 MET cc_start: 0.8343 (tmm) cc_final: 0.7896 (tmm) outliers start: 9 outliers final: 6 residues processed: 50 average time/residue: 0.1160 time to fit residues: 9.1494 Evaluate side-chains 48 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain R residue 281 THR Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 91 optimal weight: 0.3980 chunk 76 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6111 Z= 0.188 Angle : 0.411 5.107 8436 Z= 0.230 Chirality : 0.039 0.145 1051 Planarity : 0.002 0.027 1096 Dihedral : 3.804 17.533 1000 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.83 % Allowed : 18.87 % Favored : 78.30 % 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: 1.84 (0.28), residues: 930 helix: 3.00 (0.25), residues: 418 sheet: 0.14 (0.39), residues: 185 loop : -0.52 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 297 HIS 0.004 0.001 HIS B 183 PHE 0.011 0.001 PHE B 199 TYR 0.023 0.001 TYR R 141 ARG 0.001 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.706 Fit side-chains REVERT: B 17 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8430 (tm-30) REVERT: R 82 MET cc_start: 0.8316 (tmm) cc_final: 0.7860 (tmm) outliers start: 9 outliers final: 5 residues processed: 50 average time/residue: 0.1194 time to fit residues: 9.4088 Evaluate side-chains 48 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6111 Z= 0.254 Angle : 0.458 5.222 8436 Z= 0.257 Chirality : 0.039 0.151 1051 Planarity : 0.003 0.027 1096 Dihedral : 4.060 19.001 1000 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.14 % Allowed : 18.87 % Favored : 77.99 % 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: 1.73 (0.28), residues: 930 helix: 2.94 (0.25), residues: 417 sheet: 0.02 (0.39), residues: 175 loop : -0.55 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 297 HIS 0.003 0.001 HIS B 225 PHE 0.013 0.001 PHE B 199 TYR 0.021 0.001 TYR R 141 ARG 0.002 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.667 Fit side-chains REVERT: B 17 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8397 (tm-30) REVERT: B 297 TRP cc_start: 0.8255 (OUTLIER) cc_final: 0.7930 (m-10) REVERT: R 82 MET cc_start: 0.8352 (tmm) cc_final: 0.7877 (tmm) outliers start: 10 outliers final: 4 residues processed: 49 average time/residue: 0.1170 time to fit residues: 9.0680 Evaluate side-chains 47 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 83 optimal weight: 0.0050 chunk 87 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6111 Z= 0.159 Angle : 0.424 7.511 8436 Z= 0.233 Chirality : 0.038 0.141 1051 Planarity : 0.003 0.027 1096 Dihedral : 3.803 18.896 1000 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.52 % Allowed : 19.81 % Favored : 77.67 % 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: 1.76 (0.28), residues: 930 helix: 2.97 (0.25), residues: 418 sheet: -0.02 (0.38), residues: 185 loop : -0.53 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 297 HIS 0.002 0.001 HIS B 183 PHE 0.010 0.001 PHE B 241 TYR 0.021 0.001 TYR R 141 ARG 0.001 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.709 Fit side-chains REVERT: B 17 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8333 (tm-30) REVERT: B 273 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8606 (mp) REVERT: R 82 MET cc_start: 0.8320 (tmm) cc_final: 0.7848 (tmm) outliers start: 8 outliers final: 4 residues processed: 54 average time/residue: 0.1194 time to fit residues: 10.1301 Evaluate side-chains 48 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.0570 chunk 87 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 56 optimal weight: 0.0670 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6111 Z= 0.142 Angle : 0.411 7.440 8436 Z= 0.225 Chirality : 0.038 0.142 1051 Planarity : 0.002 0.027 1096 Dihedral : 3.664 17.380 1000 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.89 % Allowed : 20.75 % Favored : 77.36 % 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: 1.81 (0.28), residues: 930 helix: 3.06 (0.25), residues: 419 sheet: -0.03 (0.38), residues: 185 loop : -0.57 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 297 HIS 0.002 0.001 HIS B 183 PHE 0.010 0.001 PHE B 199 TYR 0.019 0.001 TYR R 141 ARG 0.001 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.734 Fit side-chains REVERT: B 17 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8330 (tm-30) REVERT: B 273 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8624 (mp) REVERT: R 82 MET cc_start: 0.8301 (tmm) cc_final: 0.7831 (tmm) outliers start: 6 outliers final: 3 residues processed: 48 average time/residue: 0.1182 time to fit residues: 8.9787 Evaluate side-chains 49 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 0.0060 chunk 59 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 overall best weight: 1.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6111 Z= 0.291 Angle : 0.477 6.945 8436 Z= 0.265 Chirality : 0.040 0.149 1051 Planarity : 0.003 0.027 1096 Dihedral : 4.092 19.237 1000 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.89 % Allowed : 20.75 % Favored : 77.36 % 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: 1.60 (0.28), residues: 930 helix: 2.88 (0.25), residues: 418 sheet: -0.18 (0.39), residues: 175 loop : -0.61 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 297 HIS 0.003 0.001 HIS B 225 PHE 0.012 0.001 PHE B 199 TYR 0.018 0.001 TYR B 264 ARG 0.001 0.000 ARG B 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.660 Fit side-chains REVERT: B 17 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8322 (tm-30) REVERT: B 273 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8593 (mp) REVERT: R 82 MET cc_start: 0.8355 (tmm) cc_final: 0.7864 (tmm) outliers start: 6 outliers final: 4 residues processed: 47 average time/residue: 0.1151 time to fit residues: 8.6654 Evaluate side-chains 48 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 281 THR Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 75 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 9 optimal weight: 20.0000 chunk 13 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.083951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.072371 restraints weight = 22096.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.073670 restraints weight = 13438.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.074786 restraints weight = 9628.939| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6111 Z= 0.175 Angle : 0.426 7.131 8436 Z= 0.234 Chirality : 0.038 0.143 1051 Planarity : 0.003 0.027 1096 Dihedral : 3.891 21.045 1000 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.20 % Allowed : 20.75 % Favored : 77.04 % 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: 1.60 (0.28), residues: 930 helix: 2.91 (0.25), residues: 418 sheet: -0.26 (0.38), residues: 186 loop : -0.60 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 297 HIS 0.002 0.001 HIS B 183 PHE 0.010 0.001 PHE B 199 TYR 0.018 0.001 TYR R 141 ARG 0.001 0.000 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1324.02 seconds wall clock time: 25 minutes 4.10 seconds (1504.10 seconds total)