Starting phenix.real_space_refine on Fri Feb 16 21:03:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhb_42268/02_2024/8uhb_42268_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhb_42268/02_2024/8uhb_42268.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhb_42268/02_2024/8uhb_42268_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhb_42268/02_2024/8uhb_42268_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhb_42268/02_2024/8uhb_42268_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhb_42268/02_2024/8uhb_42268.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhb_42268/02_2024/8uhb_42268.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhb_42268/02_2024/8uhb_42268_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhb_42268/02_2024/8uhb_42268_trim_updated.pdb" } resolution = 3.35 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= 0.038 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 65 5.16 5 C 5346 2.51 5 N 1453 2.21 5 O 1553 1.98 5 H 8144 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "C PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 240": "OD1" <-> "OD2" Residue "C GLU 392": "OE1" <-> "OE2" Residue "G ASP 26": "OD1" <-> "OD2" Residue "N TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N ASP 106": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16561 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 4754 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 11, 'TRANS': 304} Chain breaks: 1 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 5106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5106 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 3890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3890 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 2 Chain: "G" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 884 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 1911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1911 Classifications: {'peptide': 128} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'WV8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.40, per 1000 atoms: 0.45 Number of scatterers: 16561 At special positions: 0 Unit cell: (85.52, 100.486, 136.832, 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 65 16.00 O 1553 8.00 N 1453 7.00 C 5346 6.00 H 8144 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 178 " distance=2.03 Simple disulfide: pdb=" SG CYS A 13 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 182 " 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=2.03 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: 12.80 Conformation dependent library (CDL) restraints added in 1.7 seconds 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2026 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 11 sheets defined 35.0% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 20 through 50 removed outlier: 3.835A pdb=" N ILE A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 75 removed outlier: 3.629A pdb=" N LEU A 61 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 62 " --> pdb=" O ASN A 59 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N HIS A 63 " --> pdb=" O TRP A 60 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET A 65 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA A 66 " --> pdb=" O HIS A 63 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 67 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 68 " --> pdb=" O MET A 65 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU A 75 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 removed outlier: 3.764A pdb=" N ARG A 83 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 100 removed outlier: 3.882A pdb=" N ILE A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 125 Processing helix chain 'A' and resid 131 through 134 No H-bonds generated for 'chain 'A' and resid 131 through 134' Processing helix chain 'A' and resid 137 through 156 Proline residue: A 151 - end of helix Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 188 through 198 Processing helix chain 'A' and resid 200 through 227 removed outlier: 4.152A pdb=" N ARG A 212 " --> pdb=" O CYS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 272 removed outlier: 3.807A pdb=" N PHE A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Proline residue: A 266 - end of helix Processing helix chain 'A' and resid 274 through 277 No H-bonds generated for 'chain 'A' and resid 274 through 277' Processing helix chain 'A' and resid 283 through 304 removed outlier: 3.592A pdb=" N SER A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) Proline residue: A 301 - end of helix Processing helix chain 'A' and resid 309 through 318 Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.761A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'C' and resid 11 through 37 Processing helix chain 'C' and resid 56 through 59 No H-bonds generated for 'chain 'C' and resid 56 through 59' Processing helix chain 'C' and resid 270 through 278 removed outlier: 3.526A pdb=" N ASP C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 302 Processing helix chain 'C' and resid 335 through 351 removed outlier: 3.830A pdb=" N ARG C 342 " --> pdb=" O LYS C 338 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU C 344 " --> pdb=" O PHE C 340 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N PHE C 345 " --> pdb=" O ILE C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 390 removed outlier: 3.662A pdb=" N ASP C 381 " --> pdb=" O ASN C 377 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 383 " --> pdb=" O CYS C 379 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 47 removed outlier: 4.933A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) 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 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.560A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.864A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.984A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.307A 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 150 removed outlier: 6.906A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.979A 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 removed outlier: 3.581A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.586A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.191A 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: 4.792A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.547A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 208 through 214 Processing sheet with id= I, first strand: chain 'C' and resid 246 through 249 removed outlier: 3.937A pdb=" N LEU C 291 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'N' and resid 122 through 124 removed outlier: 5.777A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 351 hydrogen bonds defined for protein. 981 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: 5.53 Time building geometry restraints manager: 13.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8118 1.03 - 1.23: 141 1.23 - 1.43: 3560 1.43 - 1.62: 4828 1.62 - 1.82: 94 Bond restraints: 16741 Sorted by residual: bond pdb=" C8 WV8 A 401 " pdb=" N10 WV8 A 401 " ideal model delta sigma weight residual 1.439 1.291 0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" C8 WV8 A 401 " pdb=" N9 WV8 A 401 " ideal model delta sigma weight residual 1.451 1.326 0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C6 WV8 A 401 " pdb=" O7 WV8 A 401 " ideal model delta sigma weight residual 1.546 1.451 0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C5 WV8 A 401 " pdb=" N10 WV8 A 401 " ideal model delta sigma weight residual 1.384 1.478 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" C4 WV8 A 401 " pdb=" C5 WV8 A 401 " ideal model delta sigma weight residual 1.553 1.515 0.038 2.00e-02 2.50e+03 3.63e+00 ... (remaining 16736 not shown) Histogram of bond angle deviations from ideal: 100.37 - 107.13: 358 107.13 - 113.89: 19466 113.89 - 120.65: 5811 120.65 - 127.41: 4350 127.41 - 134.17: 88 Bond angle restraints: 30073 Sorted by residual: angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.20 109.67 3.53 9.60e-01 1.09e+00 1.35e+01 angle pdb=" N ILE C 372 " pdb=" CA ILE C 372 " pdb=" C ILE C 372 " ideal model delta sigma weight residual 112.35 107.30 5.05 1.41e+00 5.03e-01 1.28e+01 angle pdb=" C16 WV8 A 401 " pdb=" C11 WV8 A 401 " pdb=" C3 WV8 A 401 " ideal model delta sigma weight residual 109.81 120.49 -10.68 3.00e+00 1.11e-01 1.27e+01 angle pdb=" N ILE C 235 " pdb=" CA ILE C 235 " pdb=" C ILE C 235 " ideal model delta sigma weight residual 113.07 108.53 4.54 1.37e+00 5.33e-01 1.10e+01 angle pdb=" N ASP C 310 " pdb=" CA ASP C 310 " pdb=" C ASP C 310 " ideal model delta sigma weight residual 114.04 110.13 3.91 1.24e+00 6.50e-01 9.93e+00 ... (remaining 30068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 7173 17.66 - 35.32: 602 35.32 - 52.98: 132 52.98 - 70.64: 21 70.64 - 88.30: 10 Dihedral angle restraints: 7938 sinusoidal: 4190 harmonic: 3748 Sorted by residual: dihedral pdb=" CB CYS A 5 " pdb=" SG CYS A 5 " pdb=" SG CYS A 178 " pdb=" CB CYS A 178 " ideal model delta sinusoidal sigma weight residual 93.00 175.02 -82.02 1 1.00e+01 1.00e-02 8.27e+01 dihedral pdb=" CB CYS A 96 " pdb=" SG CYS A 96 " pdb=" SG CYS A 182 " pdb=" CB CYS A 182 " ideal model delta sinusoidal sigma weight residual -86.00 -154.02 68.02 1 1.00e+01 1.00e-02 6.01e+01 dihedral pdb=" CA ILE C 341 " pdb=" C ILE C 341 " pdb=" N ARG C 342 " pdb=" CA ARG C 342 " ideal model delta harmonic sigma weight residual 180.00 155.50 24.50 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 7935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1119 0.056 - 0.112: 162 0.112 - 0.168: 22 0.168 - 0.224: 0 0.224 - 0.281: 1 Chirality restraints: 1304 Sorted by residual: chirality pdb=" C3 WV8 A 401 " pdb=" C11 WV8 A 401 " pdb=" C2 WV8 A 401 " pdb=" C4 WV8 A 401 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA ILE C 341 " pdb=" N ILE C 341 " pdb=" C ILE C 341 " pdb=" CB ILE C 341 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CB VAL A 46 " pdb=" CA VAL A 46 " pdb=" CG1 VAL A 46 " pdb=" CG2 VAL A 46 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 1301 not shown) Planarity restraints: 2509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5 WV8 A 401 " 0.048 2.00e-02 2.50e+03 3.77e-02 1.78e+01 pdb=" C8 WV8 A 401 " -0.013 2.00e-02 2.50e+03 pdb=" N10 WV8 A 401 " -0.051 2.00e-02 2.50e+03 pdb=" N9 WV8 A 401 " 0.039 2.00e-02 2.50e+03 pdb=" O7 WV8 A 401 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 234 " 0.020 2.00e-02 2.50e+03 1.16e-02 4.04e+00 pdb=" CG PHE B 234 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE B 234 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 234 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 234 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 234 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 234 " 0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE B 234 " -0.005 2.00e-02 2.50e+03 pdb=" HD2 PHE B 234 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE B 234 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE B 234 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE B 234 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 281 " 0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO A 282 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " 0.026 5.00e-02 4.00e+02 ... (remaining 2506 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 270 2.06 - 2.69: 26359 2.69 - 3.33: 47828 3.33 - 3.96: 61965 3.96 - 4.60: 97963 Nonbonded interactions: 234385 Sorted by model distance: nonbonded pdb=" HE2 HIS C 362 " pdb=" OD2 ASP C 378 " model vdw 1.420 1.850 nonbonded pdb=" OD1 ASP C 331 " pdb=" H VAL C 334 " model vdw 1.525 1.850 nonbonded pdb=" OD1 ASP B 228 " pdb=" HH TYR N 117 " model vdw 1.564 1.850 nonbonded pdb=" O SER A 187 " pdb=" H GLY A 191 " model vdw 1.585 1.850 nonbonded pdb=" O ARG B 68 " pdb=" HG SER B 84 " model vdw 1.606 1.850 ... (remaining 234380 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: 0.010 Construct map_model_manager: 0.240 Extract box with map and model: 4.280 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 52.940 Find NCS groups from input model: 0.280 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 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 : 0.004 0.148 8597 Z= 0.287 Angle : 0.647 10.676 11643 Z= 0.373 Chirality : 0.042 0.281 1304 Planarity : 0.003 0.048 1482 Dihedral : 14.160 88.305 3076 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.26), residues: 1059 helix: 0.13 (0.28), residues: 385 sheet: -1.84 (0.33), residues: 218 loop : -1.30 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.035 0.001 PHE B 234 TYR 0.013 0.001 TYR C 311 ARG 0.009 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.5939 time to fit residues: 136.5769 Evaluate side-chains 116 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 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 41 ASN B 16 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8597 Z= 0.204 Angle : 0.549 5.594 11643 Z= 0.298 Chirality : 0.040 0.139 1304 Planarity : 0.004 0.035 1482 Dihedral : 5.738 88.594 1173 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.67 % Allowed : 8.47 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.19 (0.26), residues: 1059 helix: 0.25 (0.27), residues: 394 sheet: -1.66 (0.33), residues: 220 loop : -1.14 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.019 0.001 PHE B 234 TYR 0.012 0.001 TYR C 358 ARG 0.005 0.000 ARG C 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.7706 (tpt) cc_final: 0.7502 (tpt) outliers start: 6 outliers final: 6 residues processed: 127 average time/residue: 0.5246 time to fit residues: 87.8196 Evaluate side-chains 119 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 113 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 379 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 84 optimal weight: 0.0370 chunk 93 optimal weight: 0.0470 chunk 32 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.9158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8597 Z= 0.164 Angle : 0.513 6.171 11643 Z= 0.273 Chirality : 0.039 0.142 1304 Planarity : 0.003 0.028 1482 Dihedral : 5.399 84.530 1173 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.00 % Allowed : 8.92 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.79 (0.27), residues: 1059 helix: 0.62 (0.27), residues: 395 sheet: -1.42 (0.34), residues: 223 loop : -0.96 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS C 220 PHE 0.015 0.001 PHE C 212 TYR 0.010 0.001 TYR C 358 ARG 0.002 0.000 ARG C 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 123 average time/residue: 0.5330 time to fit residues: 87.0178 Evaluate side-chains 122 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8597 Z= 0.171 Angle : 0.497 6.228 11643 Z= 0.267 Chirality : 0.039 0.142 1304 Planarity : 0.003 0.029 1482 Dihedral : 5.224 83.620 1173 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.11 % Allowed : 9.70 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.43 (0.27), residues: 1059 helix: 1.06 (0.28), residues: 385 sheet: -1.28 (0.33), residues: 224 loop : -0.85 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS C 220 PHE 0.015 0.001 PHE C 212 TYR 0.010 0.001 TYR A 200 ARG 0.003 0.000 ARG C 283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 119 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 124 average time/residue: 0.5281 time to fit residues: 86.8925 Evaluate side-chains 120 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 51 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8597 Z= 0.241 Angle : 0.517 6.581 11643 Z= 0.279 Chirality : 0.039 0.135 1304 Planarity : 0.003 0.033 1482 Dihedral : 5.264 86.126 1173 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.34 % Allowed : 10.03 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.38 (0.27), residues: 1059 helix: 1.15 (0.28), residues: 385 sheet: -1.21 (0.34), residues: 214 loop : -0.91 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS C 220 PHE 0.024 0.001 PHE C 222 TYR 0.010 0.001 TYR C 311 ARG 0.002 0.000 ARG C 283 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.7854 (tpt) cc_final: 0.7530 (tpt) outliers start: 12 outliers final: 10 residues processed: 114 average time/residue: 0.5445 time to fit residues: 81.7199 Evaluate side-chains 115 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 105 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8597 Z= 0.320 Angle : 0.546 6.491 11643 Z= 0.297 Chirality : 0.040 0.137 1304 Planarity : 0.003 0.035 1482 Dihedral : 5.353 89.380 1173 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.56 % Allowed : 9.92 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.37 (0.27), residues: 1059 helix: 1.14 (0.27), residues: 385 sheet: -1.26 (0.33), residues: 216 loop : -0.85 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS C 220 PHE 0.025 0.001 PHE C 222 TYR 0.009 0.001 TYR C 311 ARG 0.003 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 13 residues processed: 112 average time/residue: 0.5524 time to fit residues: 81.5554 Evaluate side-chains 115 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8597 Z= 0.204 Angle : 0.516 6.358 11643 Z= 0.275 Chirality : 0.039 0.138 1304 Planarity : 0.003 0.034 1482 Dihedral : 5.274 89.167 1173 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.45 % Allowed : 11.15 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.16 (0.27), residues: 1059 helix: 1.32 (0.27), residues: 391 sheet: -1.02 (0.34), residues: 212 loop : -0.84 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS C 220 PHE 0.021 0.001 PHE C 222 TYR 0.007 0.001 TYR C 318 ARG 0.003 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.7843 (tpt) cc_final: 0.7569 (tpt) outliers start: 13 outliers final: 12 residues processed: 116 average time/residue: 0.5669 time to fit residues: 87.0097 Evaluate side-chains 116 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 68 optimal weight: 0.0870 chunk 49 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 91 optimal weight: 0.0970 chunk 96 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 93 optimal weight: 8.9990 overall best weight: 0.6156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 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 : 0.002 0.029 8597 Z= 0.151 Angle : 0.504 6.065 11643 Z= 0.266 Chirality : 0.039 0.144 1304 Planarity : 0.003 0.036 1482 Dihedral : 5.132 88.192 1173 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.89 % Allowed : 11.82 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.07 (0.27), residues: 1059 helix: 1.51 (0.28), residues: 390 sheet: -0.87 (0.34), residues: 212 loop : -0.72 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS C 220 PHE 0.017 0.001 PHE C 222 TYR 0.007 0.001 TYR C 318 ARG 0.003 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.7860 (tpt) cc_final: 0.7560 (tpt) outliers start: 8 outliers final: 7 residues processed: 112 average time/residue: 0.5342 time to fit residues: 79.1493 Evaluate side-chains 115 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 0.4980 chunk 56 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 93 optimal weight: 0.3980 chunk 61 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8597 Z= 0.152 Angle : 0.507 7.634 11643 Z= 0.266 Chirality : 0.039 0.146 1304 Planarity : 0.003 0.063 1482 Dihedral : 5.077 87.681 1173 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.67 % Allowed : 12.26 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.18 (0.27), residues: 1059 helix: 1.59 (0.28), residues: 395 sheet: -0.81 (0.34), residues: 214 loop : -0.67 (0.32), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS C 220 PHE 0.016 0.001 PHE C 222 TYR 0.007 0.001 TYR C 358 ARG 0.009 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.7849 (tpt) cc_final: 0.7459 (tpt) outliers start: 6 outliers final: 6 residues processed: 119 average time/residue: 0.5287 time to fit residues: 84.2182 Evaluate side-chains 116 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8597 Z= 0.192 Angle : 0.519 7.707 11643 Z= 0.274 Chirality : 0.039 0.140 1304 Planarity : 0.003 0.055 1482 Dihedral : 5.071 88.035 1173 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.67 % Allowed : 13.04 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.17 (0.27), residues: 1059 helix: 1.60 (0.27), residues: 395 sheet: -0.82 (0.34), residues: 216 loop : -0.69 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS C 220 PHE 0.017 0.001 PHE C 222 TYR 0.016 0.001 TYR C 391 ARG 0.008 0.000 ARG A 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.7876 (tpt) cc_final: 0.7474 (tpt) outliers start: 6 outliers final: 6 residues processed: 115 average time/residue: 0.5154 time to fit residues: 78.9634 Evaluate side-chains 117 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 ASN ** 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 = 0.3477 r_free = 0.3477 target = 0.072048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.057524 restraints weight = 87675.221| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 4.11 r_work: 0.2995 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8597 Z= 0.197 Angle : 0.518 7.681 11643 Z= 0.274 Chirality : 0.039 0.141 1304 Planarity : 0.003 0.055 1482 Dihedral : 5.079 88.534 1173 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.00 % Allowed : 13.04 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.17 (0.27), residues: 1059 helix: 1.55 (0.27), residues: 402 sheet: -0.78 (0.34), residues: 216 loop : -0.70 (0.32), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS C 220 PHE 0.017 0.001 PHE C 222 TYR 0.018 0.001 TYR C 391 ARG 0.008 0.000 ARG A 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3937.21 seconds wall clock time: 70 minutes 36.58 seconds (4236.58 seconds total)