Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 11:47:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvu_32858/10_2023/7wvu_32858_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvu_32858/10_2023/7wvu_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_32858/10_2023/7wvu_32858.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvu_32858/10_2023/7wvu_32858.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvu_32858/10_2023/7wvu_32858_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvu_32858/10_2023/7wvu_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-1.21rc1-5097/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: 4.26, per 1000 atoms: 0.62 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: 2.97 Conformation dependent library (CDL) restraints added in 1.1 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: 1.09 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: 2.24 Time building geometry restraints manager: 3.20 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: 0.980 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: 4.050 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 23.260 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.340 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.825 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1708 time to fit residues: 31.8677 Evaluate side-chains 111 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.768 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0575 ------------------------------------------------------------------------------- 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: 0.7111 moved from start: 0.1360 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= 0.180 Angle : 0.491 6.679 9530 Z= 0.252 Chirality : 0.040 0.139 1126 Planarity : 0.004 0.064 1199 Dihedral : 4.359 80.523 963 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.14 % Allowed : 10.97 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.29), residues: 894 helix: 2.37 (0.26), residues: 400 sheet: 0.18 (0.41), residues: 160 loop : -1.09 (0.32), residues: 334 *********************** 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 124 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 0.796 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 121 average time/residue: 0.1688 time to fit residues: 28.4493 Evaluate side-chains 106 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 0.821 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0756 time to fit residues: 1.6264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7006 Z= 0.256 Angle : 0.533 6.852 9530 Z= 0.276 Chirality : 0.041 0.151 1126 Planarity : 0.004 0.054 1199 Dihedral : 4.779 82.923 963 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.71 % Allowed : 12.96 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.28), residues: 894 helix: 2.08 (0.27), residues: 392 sheet: -0.03 (0.40), residues: 168 loop : -1.06 (0.32), residues: 334 *********************** 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 135 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 0.932 Fit side-chains outliers start: 19 outliers final: 15 residues processed: 125 average time/residue: 0.1503 time to fit residues: 26.9726 Evaluate side-chains 119 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 0.758 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0668 time to fit residues: 2.8381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 53 optimal weight: 0.0770 chunk 80 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- 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 119 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7006 Z= 0.202 Angle : 0.499 7.407 9530 Z= 0.257 Chirality : 0.040 0.136 1126 Planarity : 0.004 0.049 1199 Dihedral : 4.610 78.948 963 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.71 % Allowed : 15.38 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.29), residues: 894 helix: 2.10 (0.26), residues: 390 sheet: -0.13 (0.41), residues: 164 loop : -0.86 (0.33), residues: 340 *********************** 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 131 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 0.787 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 126 average time/residue: 0.1660 time to fit residues: 29.4343 Evaluate side-chains 111 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 0.874 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0751 time to fit residues: 2.0786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 58 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.3980 chunk 76 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 28 optimal weight: 0.0010 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7006 Z= 0.154 Angle : 0.483 7.548 9530 Z= 0.244 Chirality : 0.039 0.131 1126 Planarity : 0.003 0.047 1199 Dihedral : 4.516 77.306 963 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.57 % Allowed : 16.67 % Favored : 81.77 % 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: 2.12 (0.27), residues: 393 sheet: -0.10 (0.41), residues: 164 loop : -0.90 (0.33), residues: 337 *********************** 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 118 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 0.723 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 113 average time/residue: 0.1444 time to fit residues: 23.8265 Evaluate side-chains 109 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.785 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0688 time to fit residues: 2.2086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 7006 Z= 0.380 Angle : 0.597 8.391 9530 Z= 0.306 Chirality : 0.043 0.144 1126 Planarity : 0.004 0.047 1199 Dihedral : 5.126 84.032 963 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.56 % Allowed : 16.10 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.28), residues: 894 helix: 1.83 (0.26), residues: 390 sheet: -0.64 (0.39), residues: 171 loop : -1.10 (0.33), residues: 333 *********************** 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 134 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 0.834 Fit side-chains outliers start: 18 outliers final: 13 residues processed: 129 average time/residue: 0.1379 time to fit residues: 26.0843 Evaluate side-chains 118 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 0.784 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0692 time to fit residues: 2.6818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 71 optimal weight: 6.9990 chunk 47 optimal weight: 0.4980 chunk 84 optimal weight: 9.9990 chunk 53 optimal weight: 0.0980 chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7006 Z= 0.171 Angle : 0.528 10.353 9530 Z= 0.261 Chirality : 0.040 0.131 1126 Planarity : 0.003 0.046 1199 Dihedral : 4.697 75.737 963 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.71 % Allowed : 17.95 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.28), residues: 894 helix: 1.87 (0.27), residues: 392 sheet: -0.50 (0.40), residues: 165 loop : -0.96 (0.33), residues: 337 *********************** 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 124 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 119 time to evaluate : 0.786 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 123 average time/residue: 0.1527 time to fit residues: 27.0835 Evaluate side-chains 117 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 0.811 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0794 time to fit residues: 1.8535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 53 optimal weight: 0.0050 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 0.1980 chunk 66 optimal weight: 0.7980 chunk 77 optimal weight: 0.0570 chunk 81 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 overall best weight: 0.3112 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7006 Z= 0.143 Angle : 0.511 8.767 9530 Z= 0.251 Chirality : 0.040 0.142 1126 Planarity : 0.003 0.045 1199 Dihedral : 4.525 74.813 963 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.43 % Allowed : 19.37 % Favored : 80.20 % 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: 0.67 (0.29), residues: 894 helix: 1.95 (0.27), residues: 394 sheet: -0.40 (0.40), residues: 162 loop : -0.90 (0.33), residues: 338 *********************** 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 116 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 113 time to evaluate : 0.816 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 114 average time/residue: 0.1452 time to fit residues: 24.2108 Evaluate side-chains 105 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 0.771 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0836 time to fit residues: 1.2635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 62 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 0.0870 chunk 78 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- 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 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7006 Z= 0.221 Angle : 0.553 8.851 9530 Z= 0.272 Chirality : 0.041 0.166 1126 Planarity : 0.003 0.045 1199 Dihedral : 4.688 77.696 963 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.28 % Allowed : 20.09 % Favored : 79.63 % 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: 0.62 (0.28), residues: 894 helix: 1.95 (0.26), residues: 394 sheet: -0.41 (0.42), residues: 149 loop : -1.00 (0.32), residues: 351 *********************** 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 113 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 0.776 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 113 average time/residue: 0.1509 time to fit residues: 24.9055 Evaluate side-chains 113 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 0.840 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0696 time to fit residues: 1.3752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.3404 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= 0.217 Angle : 0.549 8.992 9530 Z= 0.271 Chirality : 0.041 0.158 1126 Planarity : 0.003 0.046 1199 Dihedral : 4.700 77.389 963 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.28 % Allowed : 19.80 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.28), residues: 894 helix: 1.93 (0.26), residues: 394 sheet: -0.51 (0.41), residues: 150 loop : -0.98 (0.32), residues: 350 ********************** 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 115 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 113 time to evaluate : 0.904 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 113 average time/residue: 0.1423 time to fit residues: 23.5657 Evaluate side-chains 110 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 0.702 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0670 time to fit residues: 1.2272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 0.0970 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ** 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 = 0.4055 r_free = 0.4055 target = 0.169581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.130755 restraints weight = 7254.021| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.90 r_work: 0.3456 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3449 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= 0.215 Angle : 0.555 8.925 9530 Z= 0.273 Chirality : 0.041 0.153 1126 Planarity : 0.003 0.046 1199 Dihedral : 4.708 77.251 963 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.14 % Allowed : 19.94 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.28), residues: 894 helix: 1.92 (0.26), residues: 392 sheet: -0.73 (0.41), residues: 154 loop : -0.90 (0.32), residues: 348 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1770.29 seconds wall clock time: 32 minutes 54.95 seconds (1974.95 seconds total)