Starting phenix.real_space_refine on Fri Mar 15 05:01:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xox_22283/03_2024/6xox_22283_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xox_22283/03_2024/6xox_22283.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xox_22283/03_2024/6xox_22283_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xox_22283/03_2024/6xox_22283_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xox_22283/03_2024/6xox_22283_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xox_22283/03_2024/6xox_22283.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xox_22283/03_2024/6xox_22283.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xox_22283/03_2024/6xox_22283_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xox_22283/03_2024/6xox_22283_updated.pdb" } resolution = 3.1 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= 0.003 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: 5 Type Number sf(0) Gaussians S 64 5.16 5 C 6778 2.51 5 N 1828 2.21 5 O 1957 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 374": "NH1" <-> "NH2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "N PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "R ARG 121": "NH1" <-> "NH2" Residue "R TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 176": "NH1" <-> "NH2" Residue "R ARG 227": "NH1" <-> "NH2" Residue "R PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 310": "NH1" <-> "NH2" Residue "R ARG 326": "NH1" <-> "NH2" Residue "R ARG 348": "NH1" <-> "NH2" Residue "R PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 380": "NH1" <-> "NH2" Residue "R ARG 414": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10629 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1792 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 213} Chain breaks: 5 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2581 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "G" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 453 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "N" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 966 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3054 Unusual residues: {'V6G': 1} Classifications: {'peptide': 380, 'undetermined': 1} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 44} Link IDs: {'PTRANS': 14, 'TRANS': 365, None: 1} Not linked: pdbres="ARG R 421 " pdbres="V6G R 501 " Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 126 Time building chain proxies: 6.07, per 1000 atoms: 0.57 Number of scatterers: 10629 At special positions: 0 Unit cell: (159.12, 113.36, 101.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 F 2 9.00 O 1957 8.00 N 1828 7.00 C 6778 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.02 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " 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: 4.14 Conformation dependent library (CDL) restraints added in 1.9 seconds 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2540 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 15 sheets defined 30.6% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 16 through 37 Processing helix chain 'A' and resid 236 through 240 removed outlier: 4.608A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 350 Processing helix chain 'A' and resid 372 through 389 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 32 through 52 removed outlier: 4.918A pdb=" N GLU R 52 " --> pdb=" O ARG R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 140 No H-bonds generated for 'chain 'R' and resid 137 through 140' Processing helix chain 'R' and resid 142 through 167 Processing helix chain 'R' and resid 175 through 209 Processing helix chain 'R' and resid 215 through 222 WARNING: missing atoms! Processing helix chain 'R' and resid 224 through 255 Processing helix chain 'R' and resid 262 through 291 removed outlier: 3.855A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Proline residue: R 277 - end of helix Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 303 through 336 removed outlier: 3.881A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 360 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 368 Processing helix chain 'R' and resid 379 through 402 removed outlier: 4.762A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 407 through 418 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 361 removed outlier: 7.116A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 79 through 83 Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.757A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.155A 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: 6.863A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 189 through 191 Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.806A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.875A 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: 6.513A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.753A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.550A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 128 through 130 Processing sheet with id= L, first strand: chain 'E' and resid 213 through 219 removed outlier: 5.397A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= N, first strand: chain 'N' and resid 122 through 124 removed outlier: 5.439A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'R' and resid 79 through 83 470 hydrogen bonds defined for protein. 1329 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: 3.25 Time building geometry restraints manager: 4.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3110 1.33 - 1.45: 2339 1.45 - 1.57: 5339 1.57 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 10876 Sorted by residual: bond pdb=" C29 V6G R 501 " pdb=" N08 V6G R 501 " ideal model delta sigma weight residual 1.523 1.353 0.170 2.00e-02 2.50e+03 7.22e+01 bond pdb=" C13 V6G R 501 " pdb=" N03 V6G R 501 " ideal model delta sigma weight residual 1.486 1.318 0.168 2.00e-02 2.50e+03 7.06e+01 bond pdb=" C29 V6G R 501 " pdb=" N07 V6G R 501 " ideal model delta sigma weight residual 1.527 1.366 0.161 2.00e-02 2.50e+03 6.49e+01 bond pdb=" C12 V6G R 501 " pdb=" N02 V6G R 501 " ideal model delta sigma weight residual 1.394 1.256 0.138 2.00e-02 2.50e+03 4.73e+01 bond pdb=" C15 V6G R 501 " pdb=" N04 V6G R 501 " ideal model delta sigma weight residual 1.512 1.384 0.128 2.00e-02 2.50e+03 4.09e+01 ... (remaining 10871 not shown) Histogram of bond angle deviations from ideal: 59.22 - 74.35: 3 74.35 - 89.49: 0 89.49 - 104.62: 150 104.62 - 119.75: 9326 119.75 - 134.89: 5299 Bond angle restraints: 14778 Sorted by residual: angle pdb=" C15 V6G R 501 " pdb=" C08 V6G R 501 " pdb=" N01 V6G R 501 " ideal model delta sigma weight residual 47.03 122.70 -75.67 3.00e+00 1.11e-01 6.36e+02 angle pdb=" C03 V6G R 501 " pdb=" N01 V6G R 501 " pdb=" C09 V6G R 501 " ideal model delta sigma weight residual 73.34 126.04 -52.70 3.00e+00 1.11e-01 3.09e+02 angle pdb=" C08 V6G R 501 " pdb=" N01 V6G R 501 " pdb=" C09 V6G R 501 " ideal model delta sigma weight residual 103.62 128.08 -24.46 3.00e+00 1.11e-01 6.65e+01 angle pdb=" N ILE B 80 " pdb=" CA ILE B 80 " pdb=" C ILE B 80 " ideal model delta sigma weight residual 107.75 116.93 -9.18 1.46e+00 4.69e-01 3.95e+01 angle pdb=" C07 V6G R 501 " pdb=" C08 V6G R 501 " pdb=" C15 V6G R 501 " ideal model delta sigma weight residual 110.15 128.28 -18.13 3.00e+00 1.11e-01 3.65e+01 ... (remaining 14773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 6036 17.76 - 35.53: 275 35.53 - 53.29: 61 53.29 - 71.05: 8 71.05 - 88.82: 8 Dihedral angle restraints: 6388 sinusoidal: 2449 harmonic: 3939 Sorted by residual: dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -174.82 88.82 1 1.00e+01 1.00e-02 9.40e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 51.53 41.47 1 1.00e+01 1.00e-02 2.41e+01 dihedral pdb=" CB CYS R 226 " pdb=" SG CYS R 226 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual -86.00 -127.36 41.36 1 1.00e+01 1.00e-02 2.39e+01 ... (remaining 6385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1292 0.076 - 0.152: 309 0.152 - 0.227: 32 0.227 - 0.303: 6 0.303 - 0.379: 2 Chirality restraints: 1641 Sorted by residual: chirality pdb=" CG LEU R 159 " pdb=" CB LEU R 159 " pdb=" CD1 LEU R 159 " pdb=" CD2 LEU R 159 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CB VAL A 241 " pdb=" CA VAL A 241 " pdb=" CG1 VAL A 241 " pdb=" CG2 VAL A 241 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CB VAL N 110 " pdb=" CA VAL N 110 " pdb=" CG1 VAL N 110 " pdb=" CG2 VAL N 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 1638 not shown) Planarity restraints: 1868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.047 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO G 49 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 242 " -0.024 2.00e-02 2.50e+03 1.88e-02 7.10e+00 pdb=" CG TYR R 242 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR R 242 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR R 242 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR R 242 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR R 242 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR R 242 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR R 242 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 239 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" CG ASN A 239 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN A 239 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 239 " 0.015 2.00e-02 2.50e+03 ... (remaining 1865 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1999 2.76 - 3.29: 10010 3.29 - 3.83: 18545 3.83 - 4.36: 21543 4.36 - 4.90: 36900 Nonbonded interactions: 88997 Sorted by model distance: nonbonded pdb=" N SER R 31 " pdb=" OE2 GLU R 34 " model vdw 2.223 2.520 nonbonded pdb=" OD2 ASP B 254 " pdb=" N ALA B 257 " model vdw 2.239 2.520 nonbonded pdb=" NH1 ARG E 67 " pdb=" OD2 ASP E 90 " model vdw 2.246 2.520 nonbonded pdb=" OG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.250 2.440 nonbonded pdb=" O GLY R 295 " pdb=" OG1 THR R 298 " model vdw 2.273 2.440 ... (remaining 88992 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.540 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.960 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 : 0.012 0.170 10876 Z= 0.799 Angle : 1.405 75.667 14778 Z= 0.659 Chirality : 0.065 0.379 1641 Planarity : 0.007 0.071 1868 Dihedral : 11.485 77.788 3824 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.99 % Allowed : 4.41 % Favored : 94.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -3.29 (0.19), residues: 1328 helix: -2.03 (0.19), residues: 422 sheet: -2.23 (0.24), residues: 345 loop : -2.07 (0.23), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP E 111 HIS 0.019 0.003 HIS A 357 PHE 0.038 0.004 PHE E 227 TYR 0.045 0.004 TYR R 242 ARG 0.020 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 262 time to evaluate : 1.168 Fit side-chains REVERT: A 239 ASN cc_start: 0.8692 (p0) cc_final: 0.8472 (p0) REVERT: A 270 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9351 (mm) REVERT: A 289 LEU cc_start: 0.9201 (tp) cc_final: 0.8950 (tp) REVERT: A 295 ASP cc_start: 0.7729 (p0) cc_final: 0.7085 (m-30) REVERT: A 296 LEU cc_start: 0.8347 (mp) cc_final: 0.7990 (mt) REVERT: A 378 ASP cc_start: 0.7952 (m-30) cc_final: 0.7582 (m-30) REVERT: B 32 GLN cc_start: 0.8224 (mt0) cc_final: 0.8017 (mt0) REVERT: B 262 MET cc_start: 0.7726 (tpp) cc_final: 0.7377 (ttt) REVERT: E 222 GLU cc_start: 0.7534 (pt0) cc_final: 0.7290 (pt0) REVERT: G 36 ASP cc_start: 0.7983 (m-30) cc_final: 0.7747 (m-30) REVERT: N 87 LYS cc_start: 0.8997 (mttt) cc_final: 0.8619 (mtpt) REVERT: N 125 THR cc_start: 0.9106 (m) cc_final: 0.8819 (t) REVERT: R 192 LEU cc_start: 0.9026 (tp) cc_final: 0.8802 (tt) outliers start: 11 outliers final: 4 residues processed: 271 average time/residue: 0.2522 time to fit residues: 92.5125 Evaluate side-chains 165 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 160 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain R residue 349 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 104 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 213 GLN A 220 HIS B 6 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 295 ASN E 174 GLN N 31 ASN N 35 ASN N 120 GLN R 240 ASN R 304 ASN R 320 ASN R 363 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10876 Z= 0.186 Angle : 0.930 50.668 14778 Z= 0.395 Chirality : 0.043 0.174 1641 Planarity : 0.004 0.063 1868 Dihedral : 6.306 74.015 1505 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.97 % Allowed : 9.00 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.87 (0.22), residues: 1328 helix: -0.20 (0.24), residues: 427 sheet: -1.96 (0.25), residues: 352 loop : -1.41 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 243 HIS 0.005 0.001 HIS R 171 PHE 0.023 0.002 PHE R 280 TYR 0.022 0.002 TYR R 148 ARG 0.007 0.000 ARG R 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 209 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 ASN cc_start: 0.8410 (p0) cc_final: 0.8113 (p0) REVERT: A 344 GLU cc_start: 0.8305 (tm-30) cc_final: 0.8026 (tm-30) REVERT: A 386 MET cc_start: 0.8334 (tmm) cc_final: 0.7999 (tmm) REVERT: B 273 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.8039 (pt) REVERT: E 39 GLN cc_start: 0.7821 (tt0) cc_final: 0.7522 (tt0) REVERT: E 171 GLN cc_start: 0.8053 (mp10) cc_final: 0.7650 (mp10) REVERT: G 11 GLN cc_start: 0.8070 (tm-30) cc_final: 0.7834 (tm-30) outliers start: 33 outliers final: 11 residues processed: 231 average time/residue: 0.2143 time to fit residues: 71.0920 Evaluate side-chains 185 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 173 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 320 ASN Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 366 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 32 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN R 320 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10876 Z= 0.355 Angle : 0.953 50.769 14778 Z= 0.407 Chirality : 0.044 0.155 1641 Planarity : 0.004 0.060 1868 Dihedral : 5.869 73.334 1499 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.69 % Allowed : 11.07 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.27 (0.23), residues: 1328 helix: 0.53 (0.25), residues: 423 sheet: -1.75 (0.25), residues: 351 loop : -1.16 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 243 HIS 0.007 0.001 HIS A 357 PHE 0.018 0.002 PHE A 345 TYR 0.023 0.002 TYR R 148 ARG 0.003 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 178 time to evaluate : 1.220 Fit side-chains revert: symmetry clash REVERT: A 56 ILE cc_start: 0.7148 (mp) cc_final: 0.6715 (mp) REVERT: A 372 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.8895 (mt) REVERT: E 171 GLN cc_start: 0.8191 (mp10) cc_final: 0.7826 (mp10) REVERT: G 11 GLN cc_start: 0.8050 (tm-30) cc_final: 0.7805 (tm-30) REVERT: N 82 GLN cc_start: 0.8004 (tp40) cc_final: 0.7477 (tp40) outliers start: 41 outliers final: 21 residues processed: 207 average time/residue: 0.2154 time to fit residues: 64.0043 Evaluate side-chains 178 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 156 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 366 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 0.0980 chunk 90 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 121 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10876 Z= 0.176 Angle : 0.903 50.407 14778 Z= 0.374 Chirality : 0.042 0.150 1641 Planarity : 0.004 0.058 1868 Dihedral : 5.484 73.661 1499 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.88 % Allowed : 14.22 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.74 (0.23), residues: 1328 helix: 1.09 (0.25), residues: 423 sheet: -1.57 (0.25), residues: 354 loop : -0.86 (0.28), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.001 PHE A 345 TYR 0.017 0.001 TYR R 148 ARG 0.005 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 197 time to evaluate : 1.281 Fit side-chains revert: symmetry clash REVERT: A 56 ILE cc_start: 0.7051 (mp) cc_final: 0.6697 (mp) REVERT: A 239 ASN cc_start: 0.8586 (p0) cc_final: 0.8343 (p0) REVERT: A 372 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8915 (mt) REVERT: B 101 MET cc_start: 0.8683 (mtp) cc_final: 0.8346 (mtp) REVERT: B 314 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.8001 (ptt180) REVERT: E 126 ILE cc_start: 0.8275 (mm) cc_final: 0.7856 (mm) REVERT: E 128 MET cc_start: 0.8198 (mmm) cc_final: 0.7805 (mmm) REVERT: E 171 GLN cc_start: 0.8209 (mp10) cc_final: 0.7875 (mp10) REVERT: G 11 GLN cc_start: 0.8043 (tm-30) cc_final: 0.7777 (tm-30) REVERT: R 367 PHE cc_start: 0.6678 (p90) cc_final: 0.6442 (p90) REVERT: R 411 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8476 (tt) outliers start: 32 outliers final: 19 residues processed: 221 average time/residue: 0.2099 time to fit residues: 66.7989 Evaluate side-chains 188 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 166 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 109 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 271 ASN B 9 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN N 31 ASN N 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10876 Z= 0.203 Angle : 0.915 50.398 14778 Z= 0.379 Chirality : 0.042 0.145 1641 Planarity : 0.003 0.059 1868 Dihedral : 5.359 73.330 1499 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.42 % Allowed : 14.67 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.44 (0.24), residues: 1328 helix: 1.39 (0.26), residues: 424 sheet: -1.47 (0.26), residues: 342 loop : -0.71 (0.28), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.017 0.001 TYR R 148 ARG 0.003 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 175 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 ILE cc_start: 0.7157 (mp) cc_final: 0.6857 (mp) REVERT: A 372 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8947 (mt) REVERT: B 10 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7675 (mp0) REVERT: B 59 TYR cc_start: 0.7822 (t80) cc_final: 0.7592 (t80) REVERT: B 101 MET cc_start: 0.8672 (mtp) cc_final: 0.8344 (mtp) REVERT: B 273 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7718 (pt) REVERT: B 314 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7987 (ptt180) REVERT: E 128 MET cc_start: 0.8369 (mmm) cc_final: 0.7815 (mmm) REVERT: G 32 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8484 (tmtt) REVERT: N 82 GLN cc_start: 0.7694 (tp40) cc_final: 0.7292 (tp40) REVERT: R 202 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8093 (tppt) REVERT: R 272 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8776 (mp) REVERT: R 411 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8461 (tt) REVERT: R 413 PHE cc_start: 0.7923 (OUTLIER) cc_final: 0.7481 (m-80) outliers start: 38 outliers final: 24 residues processed: 204 average time/residue: 0.2200 time to fit residues: 64.1487 Evaluate side-chains 197 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 165 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 272 ILE Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 403 CYS Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 413 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 75 optimal weight: 0.0670 chunk 31 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 6 GLN B 9 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10876 Z= 0.194 Angle : 0.911 50.353 14778 Z= 0.377 Chirality : 0.042 0.141 1641 Planarity : 0.003 0.060 1868 Dihedral : 5.248 73.248 1499 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.78 % Allowed : 14.49 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.23 (0.24), residues: 1328 helix: 1.56 (0.26), residues: 424 sheet: -1.32 (0.26), residues: 342 loop : -0.60 (0.28), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.030 0.001 PHE R 367 TYR 0.015 0.001 TYR R 148 ARG 0.005 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 171 time to evaluate : 1.311 Fit side-chains REVERT: A 56 ILE cc_start: 0.7149 (mp) cc_final: 0.6931 (mp) REVERT: A 372 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8955 (mt) REVERT: A 378 ASP cc_start: 0.7994 (m-30) cc_final: 0.7748 (m-30) REVERT: B 10 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7664 (mp0) REVERT: B 101 MET cc_start: 0.8652 (mtp) cc_final: 0.8341 (mtp) REVERT: B 273 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7687 (pt) REVERT: B 314 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7989 (ptt180) REVERT: E 128 MET cc_start: 0.8437 (mmm) cc_final: 0.7826 (mmm) REVERT: E 171 GLN cc_start: 0.8106 (mp10) cc_final: 0.7769 (mp10) REVERT: G 32 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8552 (tmtt) REVERT: N 82 GLN cc_start: 0.7745 (tp40) cc_final: 0.7364 (tp40) REVERT: R 202 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8061 (tppt) REVERT: R 407 ASN cc_start: 0.8407 (t0) cc_final: 0.8072 (t0) REVERT: R 411 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8524 (tt) REVERT: R 413 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7663 (m-80) outliers start: 42 outliers final: 24 residues processed: 204 average time/residue: 0.2076 time to fit residues: 60.7348 Evaluate side-chains 196 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 165 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 403 CYS Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 413 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 72 optimal weight: 0.3980 chunk 108 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 78 optimal weight: 0.4980 chunk 59 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10876 Z= 0.199 Angle : 0.912 50.448 14778 Z= 0.378 Chirality : 0.042 0.151 1641 Planarity : 0.004 0.062 1868 Dihedral : 5.178 72.875 1499 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.78 % Allowed : 15.03 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.09 (0.24), residues: 1328 helix: 1.65 (0.26), residues: 424 sheet: -1.20 (0.27), residues: 341 loop : -0.53 (0.28), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.028 0.001 PHE R 367 TYR 0.014 0.001 TYR N 60 ARG 0.003 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 173 time to evaluate : 1.328 Fit side-chains REVERT: A 56 ILE cc_start: 0.7172 (mp) cc_final: 0.6954 (mp) REVERT: A 378 ASP cc_start: 0.7964 (m-30) cc_final: 0.7723 (m-30) REVERT: B 10 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7672 (mp0) REVERT: B 101 MET cc_start: 0.8655 (mtp) cc_final: 0.8351 (mtp) REVERT: B 273 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7714 (pt) REVERT: B 314 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7990 (ptt180) REVERT: G 32 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8533 (tmtt) REVERT: R 202 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8052 (tppt) REVERT: R 407 ASN cc_start: 0.8455 (t0) cc_final: 0.8125 (t0) REVERT: R 411 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8526 (tt) REVERT: R 413 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7852 (m-80) outliers start: 42 outliers final: 26 residues processed: 202 average time/residue: 0.2161 time to fit residues: 62.2843 Evaluate side-chains 193 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 161 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 403 CYS Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 413 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 38 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN E 174 GLN G 24 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 0.041 10876 Z= 0.207 Angle : 0.919 50.299 14778 Z= 0.382 Chirality : 0.042 0.156 1641 Planarity : 0.004 0.064 1868 Dihedral : 5.180 73.218 1499 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.78 % Allowed : 16.02 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.03 (0.24), residues: 1328 helix: 1.81 (0.26), residues: 418 sheet: -1.18 (0.26), residues: 347 loop : -0.43 (0.29), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.028 0.001 PHE R 367 TYR 0.018 0.001 TYR R 88 ARG 0.005 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 170 time to evaluate : 1.348 Fit side-chains REVERT: A 378 ASP cc_start: 0.7965 (m-30) cc_final: 0.7722 (m-30) REVERT: B 10 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7635 (mp0) REVERT: B 101 MET cc_start: 0.8648 (mtp) cc_final: 0.8357 (mtp) REVERT: B 273 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7719 (pt) REVERT: B 314 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7947 (ptt180) REVERT: E 180 MET cc_start: 0.8100 (ptm) cc_final: 0.7871 (ptm) REVERT: E 234 GLU cc_start: 0.6828 (mm-30) cc_final: 0.6541 (mp0) REVERT: G 32 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8577 (tmtt) REVERT: N 82 GLN cc_start: 0.7743 (tp40) cc_final: 0.7321 (tp40) REVERT: R 202 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8045 (tppt) REVERT: R 407 ASN cc_start: 0.8475 (t0) cc_final: 0.8150 (t0) REVERT: R 411 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8515 (tt) REVERT: R 413 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.8037 (m-80) outliers start: 42 outliers final: 28 residues processed: 203 average time/residue: 0.2140 time to fit residues: 62.2429 Evaluate side-chains 195 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 161 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 403 CYS Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 413 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 78 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10876 Z= 0.233 Angle : 0.925 50.322 14778 Z= 0.386 Chirality : 0.042 0.198 1641 Planarity : 0.004 0.064 1868 Dihedral : 5.190 73.186 1499 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.24 % Allowed : 16.47 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.05 (0.24), residues: 1328 helix: 1.83 (0.26), residues: 418 sheet: -1.15 (0.26), residues: 352 loop : -0.44 (0.29), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.031 0.002 PHE R 367 TYR 0.015 0.001 TYR N 60 ARG 0.006 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 169 time to evaluate : 1.277 Fit side-chains REVERT: A 378 ASP cc_start: 0.8001 (m-30) cc_final: 0.7755 (m-30) REVERT: B 10 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7679 (mp0) REVERT: B 101 MET cc_start: 0.8658 (mtp) cc_final: 0.8356 (mtp) REVERT: B 273 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7766 (pt) REVERT: B 314 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.8013 (ptt180) REVERT: G 20 LYS cc_start: 0.8647 (mttt) cc_final: 0.8227 (mtmm) REVERT: G 32 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8562 (tmtt) REVERT: R 202 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8040 (tppt) REVERT: R 407 ASN cc_start: 0.8463 (t0) cc_final: 0.8180 (t0) REVERT: R 411 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8533 (tt) outliers start: 36 outliers final: 28 residues processed: 195 average time/residue: 0.2234 time to fit residues: 62.6179 Evaluate side-chains 194 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 161 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 403 CYS Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 112 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10876 Z= 0.203 Angle : 0.921 50.268 14778 Z= 0.383 Chirality : 0.042 0.156 1641 Planarity : 0.004 0.063 1868 Dihedral : 5.162 73.316 1499 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.33 % Allowed : 16.65 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.10 (0.24), residues: 1328 helix: 1.84 (0.26), residues: 418 sheet: -1.07 (0.26), residues: 352 loop : -0.41 (0.29), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.031 0.001 PHE R 367 TYR 0.018 0.001 TYR R 88 ARG 0.008 0.000 ARG E 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 168 time to evaluate : 1.285 Fit side-chains revert: symmetry clash REVERT: A 378 ASP cc_start: 0.7961 (m-30) cc_final: 0.7721 (m-30) REVERT: B 10 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7673 (mp0) REVERT: B 101 MET cc_start: 0.8633 (mtp) cc_final: 0.8351 (mtp) REVERT: B 273 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7780 (pt) REVERT: B 314 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7904 (ptt180) REVERT: G 20 LYS cc_start: 0.8639 (mttt) cc_final: 0.8232 (mtmm) REVERT: R 202 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8022 (tppt) REVERT: R 300 ASN cc_start: 0.5999 (p0) cc_final: 0.5750 (p0) REVERT: R 407 ASN cc_start: 0.8453 (t0) cc_final: 0.8177 (t0) REVERT: R 411 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8534 (tt) outliers start: 37 outliers final: 26 residues processed: 196 average time/residue: 0.2080 time to fit residues: 58.6740 Evaluate side-chains 190 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 160 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 403 CYS Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 108 optimal weight: 0.0570 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 overall best weight: 2.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.102202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.079045 restraints weight = 25269.385| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.73 r_work: 0.3152 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10876 Z= 0.301 Angle : 0.946 50.409 14778 Z= 0.399 Chirality : 0.043 0.170 1641 Planarity : 0.004 0.065 1868 Dihedral : 5.280 73.075 1499 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.06 % Allowed : 17.01 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.05 (0.24), residues: 1328 helix: 1.78 (0.26), residues: 418 sheet: -1.05 (0.26), residues: 353 loop : -0.46 (0.29), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.031 0.002 PHE R 367 TYR 0.016 0.002 TYR A 318 ARG 0.007 0.000 ARG E 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2503.64 seconds wall clock time: 45 minutes 53.09 seconds (2753.09 seconds total)