Starting phenix.real_space_refine on Sat Apr 6 03:29:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvu_32858/04_2024/7wvu_32858_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvu_32858/04_2024/7wvu_32858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvu_32858/04_2024/7wvu_32858.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvu_32858/04_2024/7wvu_32858.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvu_32858/04_2024/7wvu_32858_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvu_32858/04_2024/7wvu_32858_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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 50 5.16 5 C 4405 2.51 5 N 1157 2.21 5 O 1250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 318": "OE1" <-> "OE2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6862 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2279 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 12, 'TRANS': 285} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1714 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2457 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 8, 'ASN:plan1': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 92 Chain: "C" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 382 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "L" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Classifications: {'peptide': 3} Modifications used: {'COO': 1} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 4.76, per 1000 atoms: 0.69 Number of scatterers: 6862 At special positions: 0 Unit cell: (113.905, 117.04, 80.465, 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 50 16.00 O 1250 8.00 N 1157 7.00 C 4405 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.4 seconds 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1710 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 8 sheets defined 44.3% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'R' and resid 22 through 52 Processing helix chain 'R' and resid 59 through 87 removed outlier: 3.514A pdb=" N PHE R 74 " --> pdb=" O ALA R 70 " (cutoff:3.500A) Proline residue: R 79 - end of helix removed outlier: 3.644A pdb=" N ARG R 84 " --> pdb=" O PHE R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 128 removed outlier: 3.808A pdb=" N ASP R 106 " --> pdb=" O PHE R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 135 Processing helix chain 'R' and resid 139 through 162 removed outlier: 3.659A pdb=" N ILE R 147 " --> pdb=" O LYS R 143 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY R 148 " --> pdb=" O LYS R 144 " (cutoff:3.500A) Proline residue: R 149 - end of helix Proline residue: R 159 - end of helix Processing helix chain 'R' and resid 187 through 210 Processing helix chain 'R' and resid 213 through 230 Processing helix chain 'R' and resid 238 through 266 Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 268 through 273 removed outlier: 3.914A pdb=" N GLN R 273 " --> pdb=" O ARG R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 301 removed outlier: 3.632A pdb=" N ASN R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER R 294 " --> pdb=" O ALA R 290 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 306 through 315 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.600A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 52 removed outlier: 4.070A pdb=" N CYS A 47 " --> pdb=" O GLU A 43 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 217 removed outlier: 4.582A pdb=" N GLY A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.768A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 308 removed outlier: 4.367A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 351 removed outlier: 3.663A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 3.659A pdb=" N THR B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 23 removed outlier: 3.631A pdb=" N ALA C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 removed outlier: 3.620A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 320 through 323 removed outlier: 3.674A pdb=" N TYR A 320 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 39 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 38 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.158A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.815A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.791A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 198 through 202 Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.624A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.356A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 318 through 320 340 hydrogen bonds defined for protein. 990 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: 1.87 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2206 1.34 - 1.46: 1622 1.46 - 1.58: 3108 1.58 - 1.70: 0 1.70 - 1.81: 70 Bond restraints: 7006 Sorted by residual: bond pdb=" SD FME L 1 " pdb=" CE FME L 1 " ideal model delta sigma weight residual 1.805 1.752 0.053 2.00e-02 2.50e+03 7.06e+00 bond pdb=" CG FME L 1 " pdb=" SD FME L 1 " ideal model delta sigma weight residual 1.817 1.772 0.045 2.00e-02 2.50e+03 5.03e+00 bond pdb=" N FME L 1 " pdb=" CN FME L 1 " ideal model delta sigma weight residual 1.335 1.375 -0.040 2.00e-02 2.50e+03 3.97e+00 bond pdb=" N FME L 1 " pdb=" CA FME L 1 " ideal model delta sigma weight residual 1.458 1.436 0.022 1.90e-02 2.77e+03 1.33e+00 bond pdb=" C ALA R 212 " pdb=" N PRO R 213 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.09e+00 ... (remaining 7001 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.09: 145 107.09 - 113.82: 4015 113.82 - 120.55: 2760 120.55 - 127.28: 2536 127.28 - 134.01: 74 Bond angle restraints: 9530 Sorted by residual: angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 121.54 127.78 -6.24 1.91e+00 2.74e-01 1.07e+01 angle pdb=" CA LEU R 39 " pdb=" CB LEU R 39 " pdb=" CG LEU R 39 " ideal model delta sigma weight residual 116.30 124.54 -8.24 3.50e+00 8.16e-02 5.54e+00 angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 121.54 125.96 -4.42 1.91e+00 2.74e-01 5.36e+00 angle pdb=" C PHE R 102 " pdb=" N THR R 103 " pdb=" CA THR R 103 " ideal model delta sigma weight residual 121.64 117.20 4.44 2.13e+00 2.20e-01 4.34e+00 angle pdb=" CB GLN A 333 " pdb=" CG GLN A 333 " pdb=" CD GLN A 333 " ideal model delta sigma weight residual 112.60 115.84 -3.24 1.70e+00 3.46e-01 3.63e+00 ... (remaining 9525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 3749 17.71 - 35.41: 280 35.41 - 53.12: 60 53.12 - 70.82: 6 70.82 - 88.52: 5 Dihedral angle restraints: 4100 sinusoidal: 1466 harmonic: 2634 Sorted by residual: dihedral pdb=" CB CYS R 98 " pdb=" SG CYS R 98 " pdb=" SG CYS R 176 " pdb=" CB CYS R 176 " ideal model delta sinusoidal sigma weight residual -86.00 -171.88 85.88 1 1.00e+01 1.00e-02 8.91e+01 dihedral pdb=" CG ARG B 150 " pdb=" CD ARG B 150 " pdb=" NE ARG B 150 " pdb=" CZ ARG B 150 " ideal model delta sinusoidal sigma weight residual -90.00 -130.97 40.97 2 1.50e+01 4.44e-03 9.17e+00 dihedral pdb=" CA ARG R 269 " pdb=" CB ARG R 269 " pdb=" CG ARG R 269 " pdb=" CD ARG R 269 " ideal model delta sinusoidal sigma weight residual 180.00 127.00 53.00 3 1.50e+01 4.44e-03 9.17e+00 ... (remaining 4097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 725 0.029 - 0.058: 262 0.058 - 0.087: 86 0.087 - 0.117: 47 0.117 - 0.146: 6 Chirality restraints: 1126 Sorted by residual: chirality pdb=" CB VAL R 164 " pdb=" CA VAL R 164 " pdb=" CG1 VAL R 164 " pdb=" CG2 VAL R 164 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ASN B 119 " pdb=" N ASN B 119 " pdb=" C ASN B 119 " pdb=" CB ASN B 119 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 1123 not shown) Planarity restraints: 1199 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.061 5.00e-02 4.00e+02 9.23e-02 1.36e+01 pdb=" N PRO B 236 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 148 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO R 149 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO R 149 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO R 149 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 287 " 0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO A 288 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " 0.021 5.00e-02 4.00e+02 ... (remaining 1196 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 938 2.76 - 3.29: 6768 3.29 - 3.83: 11647 3.83 - 4.36: 13043 4.36 - 4.90: 23369 Nonbonded interactions: 55765 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.221 2.440 nonbonded pdb=" OH TYR R 257 " pdb=" O LEU L 2 " model vdw 2.267 2.440 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.304 2.440 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.311 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.333 2.440 ... (remaining 55760 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: 0.720 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: 4.020 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.590 Find NCS groups from input model: 0.220 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 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 : 0.002 0.053 7006 Z= 0.139 Angle : 0.466 8.238 9530 Z= 0.252 Chirality : 0.038 0.146 1126 Planarity : 0.004 0.092 1199 Dihedral : 13.254 88.524 2387 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.98 (0.29), residues: 894 helix: 2.27 (0.26), residues: 397 sheet: 0.29 (0.43), residues: 155 loop : -1.17 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 49 HIS 0.001 0.000 HIS R 229 PHE 0.009 0.001 PHE B 151 TYR 0.005 0.001 TYR B 264 ARG 0.008 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.701 Fit side-chains REVERT: B 191 SER cc_start: 0.8220 (p) cc_final: 0.8020 (p) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1698 time to fit residues: 31.6248 Evaluate side-chains 111 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 0.0870 chunk 35 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 0.0770 chunk 79 optimal weight: 3.9990 overall best weight: 0.5916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 311 ASN ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7006 Z= 0.176 Angle : 0.486 6.852 9530 Z= 0.250 Chirality : 0.040 0.141 1126 Planarity : 0.004 0.064 1199 Dihedral : 4.321 80.610 963 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.28 % Allowed : 10.68 % Favored : 88.03 % 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: 1.10 (0.29), residues: 894 helix: 2.40 (0.26), residues: 400 sheet: 0.18 (0.41), residues: 160 loop : -1.11 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.000 HIS B 91 PHE 0.011 0.001 PHE A 250 TYR 0.010 0.001 TYR A 296 ARG 0.003 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 113 time to evaluate : 0.854 Fit side-chains REVERT: R 54 ARG cc_start: 0.7010 (mmm-85) cc_final: 0.6620 (mmt180) REVERT: A 309 ASP cc_start: 0.7308 (m-30) cc_final: 0.7075 (m-30) outliers start: 9 outliers final: 6 residues processed: 119 average time/residue: 0.1757 time to fit residues: 29.1988 Evaluate side-chains 106 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 156 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 ASN ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7006 Z= 0.212 Angle : 0.506 7.994 9530 Z= 0.259 Chirality : 0.040 0.148 1126 Planarity : 0.004 0.051 1199 Dihedral : 4.561 81.223 963 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.56 % Allowed : 11.40 % Favored : 86.04 % 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: 0.93 (0.29), residues: 894 helix: 2.20 (0.26), residues: 399 sheet: -0.00 (0.41), residues: 166 loop : -1.06 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 339 HIS 0.002 0.000 HIS B 225 PHE 0.014 0.001 PHE A 250 TYR 0.011 0.001 TYR R 257 ARG 0.003 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 0.829 Fit side-chains REVERT: R 54 ARG cc_start: 0.7154 (mmm-85) cc_final: 0.6427 (mmt180) REVERT: R 152 MET cc_start: 0.5931 (tpt) cc_final: 0.5628 (tpt) REVERT: A 9 ASP cc_start: 0.7499 (m-30) cc_final: 0.7269 (m-30) REVERT: A 309 ASP cc_start: 0.7557 (m-30) cc_final: 0.7333 (m-30) outliers start: 18 outliers final: 16 residues processed: 124 average time/residue: 0.1825 time to fit residues: 31.7135 Evaluate side-chains 123 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 339 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 0.0980 chunk 80 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 ASN ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7006 Z= 0.211 Angle : 0.494 7.209 9530 Z= 0.254 Chirality : 0.040 0.158 1126 Planarity : 0.004 0.049 1199 Dihedral : 4.589 79.814 963 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.13 % Allowed : 13.68 % Favored : 82.19 % 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: 0.96 (0.29), residues: 894 helix: 2.19 (0.26), residues: 391 sheet: -0.06 (0.41), residues: 168 loop : -0.86 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 339 HIS 0.006 0.001 HIS B 142 PHE 0.014 0.001 PHE R 210 TYR 0.010 0.001 TYR B 59 ARG 0.003 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 113 time to evaluate : 1.002 Fit side-chains REVERT: R 152 MET cc_start: 0.6188 (tpt) cc_final: 0.5938 (tpt) REVERT: A 9 ASP cc_start: 0.7486 (m-30) cc_final: 0.7236 (m-30) REVERT: B 228 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7445 (p0) REVERT: B 259 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.7010 (pm20) outliers start: 29 outliers final: 22 residues processed: 129 average time/residue: 0.2337 time to fit residues: 42.0162 Evaluate side-chains 134 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 110 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 339 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 58 optimal weight: 0.0050 chunk 0 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 76 optimal weight: 0.2980 chunk 21 optimal weight: 7.9990 chunk 28 optimal weight: 0.0000 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7006 Z= 0.148 Angle : 0.479 7.649 9530 Z= 0.242 Chirality : 0.039 0.135 1126 Planarity : 0.003 0.048 1199 Dihedral : 4.456 77.327 963 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.13 % Allowed : 15.81 % Favored : 81.05 % 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: 0.93 (0.29), residues: 894 helix: 2.13 (0.27), residues: 395 sheet: -0.09 (0.42), residues: 164 loop : -0.86 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 339 HIS 0.002 0.000 HIS B 54 PHE 0.008 0.001 PHE R 210 TYR 0.013 0.001 TYR A 296 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 0.792 Fit side-chains REVERT: R 152 MET cc_start: 0.6175 (tpt) cc_final: 0.5937 (tpt) REVERT: A 9 ASP cc_start: 0.7451 (m-30) cc_final: 0.7203 (m-30) REVERT: B 228 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7441 (p0) outliers start: 22 outliers final: 19 residues processed: 122 average time/residue: 0.1616 time to fit residues: 27.8505 Evaluate side-chains 125 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.3980 chunk 16 optimal weight: 0.0170 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 7 optimal weight: 0.0770 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 0.3980 chunk 82 optimal weight: 4.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 ASN ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7006 Z= 0.168 Angle : 0.475 7.765 9530 Z= 0.243 Chirality : 0.039 0.130 1126 Planarity : 0.003 0.047 1199 Dihedral : 4.455 77.561 963 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.70 % Allowed : 15.10 % Favored : 81.20 % 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: 0.88 (0.29), residues: 894 helix: 2.11 (0.27), residues: 395 sheet: -0.16 (0.41), residues: 164 loop : -0.89 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 339 HIS 0.002 0.000 HIS B 142 PHE 0.011 0.001 PHE R 210 TYR 0.013 0.001 TYR B 59 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 0.701 Fit side-chains REVERT: R 87 MET cc_start: 0.5868 (mtt) cc_final: 0.5664 (mtt) REVERT: R 152 MET cc_start: 0.6305 (tpt) cc_final: 0.6077 (tpt) REVERT: A 9 ASP cc_start: 0.7450 (m-30) cc_final: 0.7190 (m-30) REVERT: B 52 ARG cc_start: 0.8220 (ptp90) cc_final: 0.8013 (ptp90) REVERT: B 228 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7452 (p0) outliers start: 26 outliers final: 24 residues processed: 130 average time/residue: 0.1482 time to fit residues: 27.5772 Evaluate side-chains 132 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 62 optimal weight: 0.4980 chunk 71 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 33 optimal weight: 0.4980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7006 Z= 0.281 Angle : 0.550 8.059 9530 Z= 0.278 Chirality : 0.041 0.137 1126 Planarity : 0.004 0.047 1199 Dihedral : 4.734 80.771 963 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.56 % Allowed : 16.81 % Favored : 78.63 % 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: 0.60 (0.29), residues: 894 helix: 1.94 (0.26), residues: 396 sheet: -0.58 (0.39), residues: 170 loop : -0.96 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 339 HIS 0.002 0.001 HIS B 142 PHE 0.013 0.001 PHE R 210 TYR 0.014 0.002 TYR A 296 ARG 0.002 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 109 time to evaluate : 0.817 Fit side-chains REVERT: R 152 MET cc_start: 0.6556 (tpt) cc_final: 0.6319 (tpt) REVERT: A 9 ASP cc_start: 0.7468 (m-30) cc_final: 0.7211 (m-30) REVERT: B 223 THR cc_start: 0.7875 (OUTLIER) cc_final: 0.7612 (t) REVERT: B 228 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.7472 (p0) REVERT: B 259 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.7124 (pm20) outliers start: 32 outliers final: 24 residues processed: 133 average time/residue: 0.1529 time to fit residues: 28.9340 Evaluate side-chains 130 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 103 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 339 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 8.9990 chunk 25 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.0870 chunk 66 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 74 optimal weight: 0.0270 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 57 HIS ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 ASN ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7006 Z= 0.152 Angle : 0.495 8.294 9530 Z= 0.249 Chirality : 0.040 0.138 1126 Planarity : 0.003 0.046 1199 Dihedral : 4.510 76.687 963 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.13 % Allowed : 18.23 % Favored : 78.63 % 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 (0.29), residues: 894 helix: 1.98 (0.27), residues: 396 sheet: -0.45 (0.40), residues: 165 loop : -0.86 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 339 HIS 0.003 0.000 HIS B 54 PHE 0.011 0.001 PHE R 33 TYR 0.013 0.001 TYR A 296 ARG 0.004 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 0.752 Fit side-chains REVERT: A 9 ASP cc_start: 0.7415 (m-30) cc_final: 0.7159 (m-30) REVERT: B 223 THR cc_start: 0.7817 (OUTLIER) cc_final: 0.7564 (t) REVERT: B 228 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7464 (p0) REVERT: B 259 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.7148 (pm20) outliers start: 22 outliers final: 18 residues processed: 130 average time/residue: 0.1354 time to fit residues: 25.8331 Evaluate side-chains 129 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 339 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 74 optimal weight: 0.0470 chunk 78 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN A 311 ASN ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7006 Z= 0.192 Angle : 0.519 8.986 9530 Z= 0.259 Chirality : 0.040 0.158 1126 Planarity : 0.003 0.046 1199 Dihedral : 4.530 77.299 963 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.13 % Allowed : 17.52 % Favored : 78.35 % 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: 0.69 (0.29), residues: 894 helix: 1.97 (0.26), residues: 396 sheet: -0.53 (0.40), residues: 166 loop : -0.84 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 339 HIS 0.002 0.000 HIS B 54 PHE 0.011 0.001 PHE R 33 TYR 0.012 0.001 TYR A 296 ARG 0.004 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 107 time to evaluate : 0.782 Fit side-chains REVERT: A 9 ASP cc_start: 0.7411 (m-30) cc_final: 0.7203 (m-30) REVERT: A 198 MET cc_start: 0.7831 (mtt) cc_final: 0.7600 (mtt) REVERT: B 223 THR cc_start: 0.7842 (OUTLIER) cc_final: 0.7602 (t) REVERT: B 228 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.7468 (p0) REVERT: B 259 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.6199 (pm20) outliers start: 29 outliers final: 25 residues processed: 128 average time/residue: 0.1399 time to fit residues: 26.4288 Evaluate side-chains 134 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 106 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 339 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 10.0000 chunk 39 optimal weight: 0.1980 chunk 58 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 0.0040 chunk 42 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7006 Z= 0.163 Angle : 0.507 8.986 9530 Z= 0.253 Chirality : 0.040 0.142 1126 Planarity : 0.003 0.046 1199 Dihedral : 4.479 76.512 963 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.85 % Allowed : 17.52 % Favored : 78.63 % 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: 0.72 (0.29), residues: 894 helix: 1.98 (0.27), residues: 396 sheet: -0.51 (0.40), residues: 166 loop : -0.81 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 339 HIS 0.002 0.000 HIS B 54 PHE 0.010 0.001 PHE R 33 TYR 0.012 0.001 TYR A 296 ARG 0.004 0.000 ARG B 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 105 time to evaluate : 0.831 Fit side-chains REVERT: R 82 MET cc_start: 0.6607 (mmm) cc_final: 0.6324 (mmt) REVERT: A 9 ASP cc_start: 0.7399 (m-30) cc_final: 0.7190 (m-30) REVERT: A 198 MET cc_start: 0.7846 (mtt) cc_final: 0.7622 (mtt) REVERT: B 223 THR cc_start: 0.7861 (OUTLIER) cc_final: 0.7630 (t) REVERT: B 228 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7462 (p0) REVERT: B 259 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.7099 (pm20) outliers start: 27 outliers final: 23 residues processed: 123 average time/residue: 0.1380 time to fit residues: 25.0185 Evaluate side-chains 127 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 101 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 339 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.3980 chunk 64 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 chunk 69 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 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 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 ASN ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.170787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.134028 restraints weight = 7163.727| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.97 r_work: 0.3474 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7006 Z= 0.185 Angle : 0.511 8.937 9530 Z= 0.256 Chirality : 0.040 0.137 1126 Planarity : 0.003 0.046 1199 Dihedral : 4.506 76.800 963 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.27 % Allowed : 17.38 % Favored : 78.35 % 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: 0.69 (0.29), residues: 894 helix: 1.98 (0.26), residues: 396 sheet: -0.59 (0.42), residues: 154 loop : -0.82 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 339 HIS 0.002 0.000 HIS B 54 PHE 0.010 0.001 PHE R 33 TYR 0.011 0.001 TYR A 296 ARG 0.004 0.000 ARG B 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1932.75 seconds wall clock time: 36 minutes 0.28 seconds (2160.28 seconds total)