Starting phenix.real_space_refine on Thu Mar 14 15:04:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csx_26974/03_2024/8csx_26974_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csx_26974/03_2024/8csx_26974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csx_26974/03_2024/8csx_26974.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csx_26974/03_2024/8csx_26974.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csx_26974/03_2024/8csx_26974_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csx_26974/03_2024/8csx_26974_updated.pdb" } resolution = 2.4 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= 0.003 sd= 0.322 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5941 2.51 5 N 1424 2.21 5 O 1685 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9116 Number of models: 1 Model: "" Number of chains: 8 Chain: "K" Number of atoms: 2943 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 380, 2919 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 365} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 380, 2919 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 365} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 2962 Chain: "L" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2938 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 2954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2954 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 378} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'AJP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 43 Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "L" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "Q" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ATYR K 34 " occ=0.55 ... (22 atoms not shown) pdb=" OH BTYR K 34 " occ=0.45 residue: pdb=" N ATYR K 242 " occ=0.53 ... (22 atoms not shown) pdb=" OH BTYR K 242 " occ=0.47 Time building chain proxies: 6.82, per 1000 atoms: 0.75 Number of scatterers: 9116 At special positions: 0 Unit cell: (91.3, 89.64, 92.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1685 8.00 N 1424 7.00 C 5941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.90 Conformation dependent library (CDL) restraints added in 2.1 seconds 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 1 sheets defined 71.2% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'K' and resid 12 through 31 Processing helix chain 'K' and resid 44 through 59 removed outlier: 3.889A pdb=" N VAL K 50 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY K 51 " --> pdb=" O SER K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 65 Processing helix chain 'K' and resid 73 through 98 removed outlier: 3.647A pdb=" N GLN K 89 " --> pdb=" O ALA K 85 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU K 93 " --> pdb=" O GLN K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 129 removed outlier: 3.592A pdb=" N VAL K 123 " --> pdb=" O SER K 119 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA K 129 " --> pdb=" O ILE K 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 160 Processing helix chain 'K' and resid 167 through 186 removed outlier: 3.592A pdb=" N ARG K 170 " --> pdb=" O MET K 167 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS K 171 " --> pdb=" O ASN K 168 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE K 172 " --> pdb=" O LEU K 169 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR K 173 " --> pdb=" O ARG K 170 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE K 175 " --> pdb=" O PHE K 172 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE K 179 " --> pdb=" O ALA K 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 224 Proline residue: K 221 - end of helix Processing helix chain 'K' and resid 231 through 255 Processing helix chain 'K' and resid 267 through 281 removed outlier: 3.628A pdb=" N SER K 272 " --> pdb=" O THR K 268 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N LEU K 275 " --> pdb=" O HIS K 271 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA K 276 " --> pdb=" O SER K 272 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N GLY K 277 " --> pdb=" O ALA K 273 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLY K 278 " --> pdb=" O VAL K 274 " (cutoff:3.500A) Processing helix chain 'K' and resid 291 through 311 Processing helix chain 'K' and resid 327 through 349 removed outlier: 3.602A pdb=" N VAL K 348 " --> pdb=" O ILE K 344 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU K 349 " --> pdb=" O VAL K 345 " (cutoff:3.500A) Processing helix chain 'K' and resid 361 through 388 Processing helix chain 'K' and resid 391 through 393 No H-bonds generated for 'chain 'K' and resid 391 through 393' Processing helix chain 'K' and resid 398 through 400 No H-bonds generated for 'chain 'K' and resid 398 through 400' Processing helix chain 'K' and resid 404 through 406 No H-bonds generated for 'chain 'K' and resid 404 through 406' Processing helix chain 'L' and resid 4 through 23 Processing helix chain 'L' and resid 51 through 62 Processing helix chain 'L' and resid 64 through 68 Processing helix chain 'L' and resid 76 through 103 removed outlier: 3.739A pdb=" N GLN L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 132 removed outlier: 3.711A pdb=" N ALA L 131 " --> pdb=" O ILE L 127 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL L 132 " --> pdb=" O SER L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 161 removed outlier: 3.639A pdb=" N VAL L 150 " --> pdb=" O ILE L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 175 through 188 Processing helix chain 'L' and resid 192 through 194 No H-bonds generated for 'chain 'L' and resid 192 through 194' Processing helix chain 'L' and resid 205 through 227 removed outlier: 3.743A pdb=" N ILE L 213 " --> pdb=" O LEU L 209 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY L 214 " --> pdb=" O PHE L 210 " (cutoff:3.500A) Proline residue: L 223 - end of helix Processing helix chain 'L' and resid 234 through 260 removed outlier: 3.714A pdb=" N LEU L 252 " --> pdb=" O ALA L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 263 through 265 No H-bonds generated for 'chain 'L' and resid 263 through 265' Processing helix chain 'L' and resid 269 through 282 removed outlier: 4.290A pdb=" N THR L 276 " --> pdb=" O ILE L 272 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU L 277 " --> pdb=" O GLN L 273 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA L 278 " --> pdb=" O ASN L 274 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY L 279 " --> pdb=" O ALA L 275 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N GLY L 280 " --> pdb=" O THR L 276 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL L 281 " --> pdb=" O LEU L 277 " (cutoff:3.500A) Processing helix chain 'L' and resid 292 through 320 removed outlier: 4.546A pdb=" N THR L 315 " --> pdb=" O TYR L 311 " (cutoff:3.500A) Proline residue: L 316 - end of helix Processing helix chain 'L' and resid 330 through 333 No H-bonds generated for 'chain 'L' and resid 330 through 333' Processing helix chain 'L' and resid 335 through 350 Processing helix chain 'L' and resid 358 through 383 Processing helix chain 'L' and resid 399 through 401 No H-bonds generated for 'chain 'L' and resid 399 through 401' Processing helix chain 'Q' and resid 4 through 23 Processing helix chain 'Q' and resid 47 through 62 Proline residue: Q 52 - end of helix Processing helix chain 'Q' and resid 64 through 71 removed outlier: 3.621A pdb=" N MET Q 69 " --> pdb=" O PHE Q 65 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR Q 70 " --> pdb=" O GLY Q 66 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N PHE Q 71 " --> pdb=" O PHE Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 103 removed outlier: 3.812A pdb=" N GLN Q 92 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 112 through 131 removed outlier: 3.717A pdb=" N ALA Q 131 " --> pdb=" O ILE Q 127 " (cutoff:3.500A) Processing helix chain 'Q' and resid 138 through 161 removed outlier: 3.688A pdb=" N VAL Q 150 " --> pdb=" O ILE Q 146 " (cutoff:3.500A) Processing helix chain 'Q' and resid 175 through 188 Processing helix chain 'Q' and resid 192 through 194 No H-bonds generated for 'chain 'Q' and resid 192 through 194' Processing helix chain 'Q' and resid 205 through 227 Proline residue: Q 223 - end of helix Processing helix chain 'Q' and resid 234 through 261 removed outlier: 3.716A pdb=" N LEU Q 252 " --> pdb=" O ALA Q 248 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 265 No H-bonds generated for 'chain 'Q' and resid 263 through 265' Processing helix chain 'Q' and resid 269 through 282 removed outlier: 4.438A pdb=" N THR Q 276 " --> pdb=" O ILE Q 272 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU Q 277 " --> pdb=" O GLN Q 273 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA Q 278 " --> pdb=" O ASN Q 274 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY Q 279 " --> pdb=" O ALA Q 275 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLY Q 280 " --> pdb=" O THR Q 276 " (cutoff:3.500A) Processing helix chain 'Q' and resid 293 through 320 removed outlier: 4.513A pdb=" N THR Q 315 " --> pdb=" O TYR Q 311 " (cutoff:3.500A) Proline residue: Q 316 - end of helix Processing helix chain 'Q' and resid 330 through 333 No H-bonds generated for 'chain 'Q' and resid 330 through 333' Processing helix chain 'Q' and resid 336 through 350 Processing helix chain 'Q' and resid 358 through 384 Processing helix chain 'Q' and resid 399 through 401 No H-bonds generated for 'chain 'Q' and resid 399 through 401' Processing sheet with id= A, first strand: chain 'K' and resid 32 through 34 removed outlier: 6.119A pdb=" N VAL K 106 " --> pdb=" O HIS K 33 " (cutoff:3.500A) No H-bonds generated for sheet with id= A 572 hydrogen bonds defined for protein. 1684 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1413 1.32 - 1.44: 2492 1.44 - 1.57: 5177 1.57 - 1.69: 0 1.69 - 1.81: 117 Bond restraints: 9199 Sorted by residual: bond pdb=" C PRO Q 293 " pdb=" O PRO Q 293 " ideal model delta sigma weight residual 1.237 1.197 0.040 1.26e-02 6.30e+03 1.01e+01 bond pdb=" N VAL Q 373 " pdb=" CA VAL Q 373 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.02e+00 bond pdb=" N TYR Q 180 " pdb=" CA TYR Q 180 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.21e-02 6.83e+03 7.97e+00 bond pdb=" N LEU Q 383 " pdb=" CA LEU Q 383 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.28e-02 6.10e+03 7.70e+00 bond pdb=" N ILE Q 188 " pdb=" CA ILE Q 188 " ideal model delta sigma weight residual 1.461 1.492 -0.032 1.19e-02 7.06e+03 7.13e+00 ... (remaining 9194 not shown) Histogram of bond angle deviations from ideal: 97.65 - 104.98: 176 104.98 - 112.31: 4795 112.31 - 119.64: 3069 119.64 - 126.97: 4376 126.97 - 134.30: 112 Bond angle restraints: 12528 Sorted by residual: angle pdb=" N LEU Q 189 " pdb=" CA LEU Q 189 " pdb=" C LEU Q 189 " ideal model delta sigma weight residual 113.02 107.62 5.40 1.20e+00 6.94e-01 2.03e+01 angle pdb=" N ALA Q 353 " pdb=" CA ALA Q 353 " pdb=" C ALA Q 353 " ideal model delta sigma weight residual 111.28 106.39 4.89 1.09e+00 8.42e-01 2.01e+01 angle pdb=" C ARG Q 323 " pdb=" N ILE Q 324 " pdb=" CA ILE Q 324 " ideal model delta sigma weight residual 123.12 117.34 5.78 1.30e+00 5.92e-01 1.98e+01 angle pdb=" CA TYR Q 180 " pdb=" C TYR Q 180 " pdb=" O TYR Q 180 " ideal model delta sigma weight residual 120.55 116.12 4.43 1.06e+00 8.90e-01 1.75e+01 angle pdb=" C TYR Q 180 " pdb=" CA TYR Q 180 " pdb=" CB TYR Q 180 " ideal model delta sigma weight residual 110.79 117.41 -6.62 1.66e+00 3.63e-01 1.59e+01 ... (remaining 12523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.86: 5362 30.86 - 61.72: 152 61.72 - 92.58: 20 92.58 - 123.44: 8 123.44 - 154.30: 2 Dihedral angle restraints: 5544 sinusoidal: 2250 harmonic: 3294 Sorted by residual: dihedral pdb=" C TYR Q 180 " pdb=" N TYR Q 180 " pdb=" CA TYR Q 180 " pdb=" CB TYR Q 180 " ideal model delta harmonic sigma weight residual -122.60 -134.06 11.46 0 2.50e+00 1.60e-01 2.10e+01 dihedral pdb=" C29 AJP Q 502 " pdb=" C30 AJP Q 502 " pdb=" C32 AJP Q 502 " pdb=" O33 AJP Q 502 " ideal model delta sinusoidal sigma weight residual 299.04 144.74 154.30 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" O31 AJP Q 502 " pdb=" C30 AJP Q 502 " pdb=" C32 AJP Q 502 " pdb=" O33 AJP Q 502 " ideal model delta sinusoidal sigma weight residual 177.28 23.48 153.80 1 3.00e+01 1.11e-03 2.02e+01 ... (remaining 5541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1263 0.067 - 0.134: 197 0.134 - 0.202: 22 0.202 - 0.269: 7 0.269 - 0.336: 2 Chirality restraints: 1491 Sorted by residual: chirality pdb=" CA TYR Q 180 " pdb=" N TYR Q 180 " pdb=" C TYR Q 180 " pdb=" CB TYR Q 180 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" C11 AJP Q 501 " pdb=" C10 AJP Q 501 " pdb=" C12 AJP Q 501 " pdb=" C16 AJP Q 501 " both_signs ideal model delta sigma weight residual False 2.20 2.49 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C08 AJP Q 502 " pdb=" C07 AJP Q 502 " pdb=" C10 AJP Q 502 " pdb=" O09 AJP Q 502 " both_signs ideal model delta sigma weight residual False 2.56 2.82 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1488 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS Q 384 " 0.013 2.00e-02 2.50e+03 2.73e-02 7.46e+00 pdb=" C LYS Q 384 " -0.047 2.00e-02 2.50e+03 pdb=" O LYS Q 384 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU Q 385 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE Q 324 " -0.012 2.00e-02 2.50e+03 2.45e-02 5.98e+00 pdb=" C ILE Q 324 " 0.042 2.00e-02 2.50e+03 pdb=" O ILE Q 324 " -0.016 2.00e-02 2.50e+03 pdb=" N HIS Q 325 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY Q 345 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.88e+00 pdb=" C GLY Q 345 " 0.038 2.00e-02 2.50e+03 pdb=" O GLY Q 345 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE Q 346 " -0.013 2.00e-02 2.50e+03 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1047 2.75 - 3.28: 9687 3.28 - 3.82: 17802 3.82 - 4.36: 21412 4.36 - 4.90: 35104 Nonbonded interactions: 85052 Sorted by model distance: nonbonded pdb=" OD2 ASP Q 399 " pdb=" O HOH Q 601 " model vdw 2.208 2.440 nonbonded pdb=" OD1 ASP Q 398 " pdb=" OG SER Q 400 " model vdw 2.226 2.440 nonbonded pdb=" O TYR K 178 " pdb=" OG1 THR K 182 " model vdw 2.236 2.440 nonbonded pdb=" OG1 THR L 408 " pdb=" O HOH L 601 " model vdw 2.242 2.440 nonbonded pdb=" O LYS L 404 " pdb=" O HOH L 602 " model vdw 2.266 2.440 ... (remaining 85047 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'L' and resid 1 through 409) selection = (chain 'Q' and (resid 1 through 26 or resid 48 through 409)) } 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=0.45 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: 0.750 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: 4.320 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 30.250 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 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:11.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 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 : 0.006 0.049 9199 Z= 0.364 Angle : 0.787 9.260 12528 Z= 0.483 Chirality : 0.053 0.336 1491 Planarity : 0.006 0.055 1505 Dihedral : 15.459 154.298 3440 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.67 % Favored : 98.24 % Rotamer: Outliers : 3.86 % Allowed : 5.58 % Favored : 90.56 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.24), residues: 1143 helix: 1.68 (0.17), residues: 815 sheet: None (None), residues: 0 loop : -0.01 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 16 HIS 0.006 0.002 HIS Q 154 PHE 0.021 0.003 PHE L 54 TYR 0.027 0.003 TYR Q 180 ARG 0.004 0.001 ARG L 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 214 time to evaluate : 1.089 Fit side-chains REVERT: K 11 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6807 (mtm-85) REVERT: K 16 TRP cc_start: 0.7806 (OUTLIER) cc_final: 0.5828 (t-100) REVERT: K 100 GLN cc_start: 0.5257 (OUTLIER) cc_final: 0.4697 (tp-100) REVERT: K 201 ARG cc_start: 0.8316 (mmt180) cc_final: 0.7921 (tpp-160) REVERT: K 329 HIS cc_start: 0.6475 (OUTLIER) cc_final: 0.6212 (m-70) REVERT: K 364 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6714 (mm) REVERT: K 382 LEU cc_start: 0.8329 (mt) cc_final: 0.7832 (tp) REVERT: K 390 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7760 (mp) REVERT: L 2 ARG cc_start: 0.7458 (ptt90) cc_final: 0.7235 (ptt180) REVERT: L 199 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6711 (pm20) REVERT: L 202 GLU cc_start: 0.7898 (tt0) cc_final: 0.7632 (tt0) REVERT: L 305 MET cc_start: 0.8291 (ttm) cc_final: 0.8054 (ttp) REVERT: Q 196 LYS cc_start: 0.7637 (mmmm) cc_final: 0.7370 (mmtt) REVERT: Q 231 GLU cc_start: 0.7068 (tp30) cc_final: 0.6561 (tp30) outliers start: 36 outliers final: 9 residues processed: 233 average time/residue: 1.2096 time to fit residues: 300.6161 Evaluate side-chains 198 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 182 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain K residue 329 HIS Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 302 ILE Chi-restraints excluded: chain Q residue 321 LYS Chi-restraints excluded: chain Q residue 384 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 41 GLN K 49 GLN K 260 HIS L 58 HIS Q 55 GLN Q 106 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9199 Z= 0.160 Angle : 0.505 6.547 12528 Z= 0.269 Chirality : 0.038 0.127 1491 Planarity : 0.005 0.063 1505 Dihedral : 9.763 167.555 1602 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 3.43 % Allowed : 10.30 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.24), residues: 1143 helix: 2.03 (0.17), residues: 820 sheet: None (None), residues: 0 loop : 0.08 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 16 HIS 0.003 0.001 HIS Q 58 PHE 0.012 0.001 PHE Q 257 TYR 0.020 0.002 TYR Q 244 ARG 0.001 0.000 ARG K 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 191 time to evaluate : 1.071 Fit side-chains REVERT: K 11 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7107 (mtm110) REVERT: K 100 GLN cc_start: 0.5330 (OUTLIER) cc_final: 0.4694 (tp-100) REVERT: K 329 HIS cc_start: 0.6414 (OUTLIER) cc_final: 0.6082 (m-70) REVERT: K 379 THR cc_start: 0.8397 (m) cc_final: 0.8129 (t) REVERT: K 382 LEU cc_start: 0.8330 (mt) cc_final: 0.7771 (tp) REVERT: L 199 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6710 (pm20) REVERT: L 202 GLU cc_start: 0.7964 (tt0) cc_final: 0.7724 (tt0) REVERT: L 305 MET cc_start: 0.8200 (ttm) cc_final: 0.7969 (ttp) REVERT: Q 101 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7539 (mp) REVERT: Q 199 GLU cc_start: 0.7212 (pt0) cc_final: 0.7001 (pp20) REVERT: Q 231 GLU cc_start: 0.7057 (tp30) cc_final: 0.6565 (tp30) REVERT: Q 323 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7694 (mtt-85) outliers start: 32 outliers final: 9 residues processed: 208 average time/residue: 1.1951 time to fit residues: 265.5798 Evaluate side-chains 207 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 192 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 329 HIS Chi-restraints excluded: chain K residue 334 LEU Chi-restraints excluded: chain K residue 391 LYS Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 357 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 5.9990 chunk 32 optimal weight: 30.0000 chunk 86 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 103 optimal weight: 0.5980 chunk 35 optimal weight: 0.0270 chunk 83 optimal weight: 0.9980 overall best weight: 2.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 49 GLN L 58 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9199 Z= 0.207 Angle : 0.541 7.128 12528 Z= 0.289 Chirality : 0.040 0.135 1491 Planarity : 0.005 0.044 1505 Dihedral : 9.553 177.767 1582 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.65 % Allowed : 11.70 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.24), residues: 1143 helix: 1.99 (0.17), residues: 816 sheet: None (None), residues: 0 loop : 0.17 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 16 HIS 0.004 0.001 HIS Q 154 PHE 0.018 0.002 PHE L 54 TYR 0.020 0.002 TYR Q 244 ARG 0.003 0.000 ARG K 154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 191 time to evaluate : 0.948 Fit side-chains REVERT: K 11 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7118 (mtm110) REVERT: K 100 GLN cc_start: 0.5286 (OUTLIER) cc_final: 0.4613 (tp-100) REVERT: K 172 PHE cc_start: 0.7557 (OUTLIER) cc_final: 0.7318 (p90) REVERT: K 329 HIS cc_start: 0.6449 (OUTLIER) cc_final: 0.6130 (m-70) REVERT: K 364 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6698 (mm) REVERT: K 379 THR cc_start: 0.8401 (m) cc_final: 0.8129 (t) REVERT: K 382 LEU cc_start: 0.8356 (mt) cc_final: 0.7789 (tp) REVERT: L 199 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6705 (pm20) REVERT: L 202 GLU cc_start: 0.7977 (tt0) cc_final: 0.7718 (tt0) REVERT: L 305 MET cc_start: 0.8246 (ttm) cc_final: 0.8015 (ttp) REVERT: Q 199 GLU cc_start: 0.7198 (pt0) cc_final: 0.6992 (pp20) REVERT: Q 231 GLU cc_start: 0.7078 (tp30) cc_final: 0.6581 (tp30) REVERT: Q 321 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8069 (mptt) REVERT: Q 323 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7772 (mtt-85) outliers start: 34 outliers final: 11 residues processed: 203 average time/residue: 1.2773 time to fit residues: 275.6585 Evaluate side-chains 202 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 183 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain K residue 172 PHE Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 329 HIS Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain K residue 391 LYS Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 160 SER Chi-restraints excluded: chain Q residue 321 LYS Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 357 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 49 GLN L 58 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9199 Z= 0.217 Angle : 0.548 7.160 12528 Z= 0.292 Chirality : 0.040 0.133 1491 Planarity : 0.005 0.044 1505 Dihedral : 8.926 154.431 1578 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.86 % Allowed : 12.23 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.24), residues: 1143 helix: 1.94 (0.17), residues: 816 sheet: None (None), residues: 0 loop : 0.16 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 16 HIS 0.004 0.001 HIS Q 154 PHE 0.018 0.002 PHE L 54 TYR 0.020 0.002 TYR Q 244 ARG 0.003 0.000 ARG K 154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 185 time to evaluate : 1.014 Fit side-chains REVERT: K 11 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7112 (mtm110) REVERT: K 100 GLN cc_start: 0.5236 (OUTLIER) cc_final: 0.4581 (tp-100) REVERT: K 172 PHE cc_start: 0.7561 (OUTLIER) cc_final: 0.7307 (p90) REVERT: K 329 HIS cc_start: 0.6451 (OUTLIER) cc_final: 0.6141 (m-70) REVERT: K 364 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6695 (mm) REVERT: K 382 LEU cc_start: 0.8360 (mt) cc_final: 0.7903 (tp) REVERT: L 199 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6694 (pm20) REVERT: L 202 GLU cc_start: 0.7968 (tt0) cc_final: 0.7696 (tt0) REVERT: L 305 MET cc_start: 0.8249 (ttm) cc_final: 0.8018 (ttp) REVERT: Q 141 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8889 (mmp) REVERT: Q 199 GLU cc_start: 0.7216 (pt0) cc_final: 0.7004 (pp20) REVERT: Q 231 GLU cc_start: 0.7087 (tp30) cc_final: 0.6600 (tp30) REVERT: Q 321 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8003 (mptt) REVERT: Q 323 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7773 (mtt-85) outliers start: 36 outliers final: 15 residues processed: 200 average time/residue: 1.2520 time to fit residues: 266.9285 Evaluate side-chains 211 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 187 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain K residue 172 PHE Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 329 HIS Chi-restraints excluded: chain K residue 334 LEU Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain K residue 391 LYS Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 141 MET Chi-restraints excluded: chain Q residue 321 LYS Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 357 SER Chi-restraints excluded: chain Q residue 377 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 49 GLN L 58 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9199 Z= 0.151 Angle : 0.486 6.450 12528 Z= 0.258 Chirality : 0.037 0.123 1491 Planarity : 0.004 0.042 1505 Dihedral : 7.661 114.436 1578 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.22 % Allowed : 13.30 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.24), residues: 1143 helix: 2.16 (0.18), residues: 815 sheet: None (None), residues: 0 loop : 0.15 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 16 HIS 0.003 0.001 HIS L 58 PHE 0.012 0.001 PHE Q 257 TYR 0.018 0.002 TYR Q 244 ARG 0.002 0.000 ARG K 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 195 time to evaluate : 1.017 Fit side-chains REVERT: K 11 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7112 (mtm110) REVERT: K 100 GLN cc_start: 0.5145 (OUTLIER) cc_final: 0.4452 (tp-100) REVERT: K 172 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.7304 (p90) REVERT: K 329 HIS cc_start: 0.6416 (OUTLIER) cc_final: 0.6071 (m-70) REVERT: K 364 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6734 (mm) REVERT: K 379 THR cc_start: 0.8367 (m) cc_final: 0.8105 (t) REVERT: K 382 LEU cc_start: 0.8341 (mt) cc_final: 0.7773 (tp) REVERT: L 48 PHE cc_start: 0.6863 (t80) cc_final: 0.6196 (t80) REVERT: L 202 GLU cc_start: 0.7969 (tt0) cc_final: 0.7712 (tt0) REVERT: L 305 MET cc_start: 0.8140 (ttm) cc_final: 0.7917 (ttp) REVERT: Q 101 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7512 (mp) REVERT: Q 199 GLU cc_start: 0.7193 (pt0) cc_final: 0.6992 (pp20) REVERT: Q 231 GLU cc_start: 0.7070 (tp30) cc_final: 0.6579 (tp30) REVERT: Q 323 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7749 (mtt-85) REVERT: Q 390 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8031 (mp10) outliers start: 30 outliers final: 9 residues processed: 205 average time/residue: 1.2029 time to fit residues: 263.3373 Evaluate side-chains 206 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 189 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain K residue 172 PHE Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 329 HIS Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain K residue 391 LYS Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 357 SER Chi-restraints excluded: chain Q residue 377 LEU Chi-restraints excluded: chain Q residue 390 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 27 optimal weight: 0.3980 chunk 111 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 49 GLN ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 389 ASN L 58 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9199 Z= 0.278 Angle : 0.598 8.181 12528 Z= 0.317 Chirality : 0.043 0.140 1491 Planarity : 0.005 0.044 1505 Dihedral : 7.644 81.265 1575 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.65 % Allowed : 13.41 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.24), residues: 1143 helix: 1.87 (0.17), residues: 816 sheet: None (None), residues: 0 loop : 0.16 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 220 HIS 0.006 0.001 HIS Q 154 PHE 0.022 0.002 PHE L 54 TYR 0.020 0.003 TYR Q 180 ARG 0.005 0.001 ARG K 154 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 187 time to evaluate : 1.042 Fit side-chains REVERT: K 11 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.7121 (mtm110) REVERT: K 100 GLN cc_start: 0.5205 (OUTLIER) cc_final: 0.4526 (tp-100) REVERT: K 172 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.7366 (p90) REVERT: K 329 HIS cc_start: 0.6483 (OUTLIER) cc_final: 0.6201 (m-70) REVERT: K 333 SER cc_start: 0.7175 (p) cc_final: 0.6939 (m) REVERT: K 364 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6696 (mm) REVERT: K 382 LEU cc_start: 0.8379 (mt) cc_final: 0.7927 (tp) REVERT: L 199 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6747 (pm20) REVERT: L 202 GLU cc_start: 0.7963 (tt0) cc_final: 0.7643 (mt-10) REVERT: L 305 MET cc_start: 0.8297 (ttm) cc_final: 0.8060 (ttp) REVERT: Q 141 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8883 (mmp) REVERT: Q 199 GLU cc_start: 0.7230 (pt0) cc_final: 0.7008 (pp20) REVERT: Q 231 GLU cc_start: 0.7095 (tp30) cc_final: 0.6596 (tp30) REVERT: Q 323 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7776 (mtt-85) REVERT: Q 390 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8005 (mp10) outliers start: 34 outliers final: 16 residues processed: 200 average time/residue: 1.2175 time to fit residues: 260.0759 Evaluate side-chains 211 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 186 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain K residue 172 PHE Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain K residue 329 HIS Chi-restraints excluded: chain K residue 334 LEU Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain K residue 391 LYS Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 314 LEU Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 141 MET Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 357 SER Chi-restraints excluded: chain Q residue 377 LEU Chi-restraints excluded: chain Q residue 390 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 49 GLN K 52 GLN ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9199 Z= 0.179 Angle : 0.520 8.322 12528 Z= 0.276 Chirality : 0.038 0.127 1491 Planarity : 0.004 0.043 1505 Dihedral : 6.629 59.384 1575 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.11 % Allowed : 14.27 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.24), residues: 1143 helix: 2.03 (0.18), residues: 815 sheet: None (None), residues: 0 loop : 0.14 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 16 HIS 0.004 0.001 HIS L 58 PHE 0.014 0.002 PHE L 54 TYR 0.019 0.002 TYR Q 244 ARG 0.004 0.000 ARG K 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 184 time to evaluate : 0.819 Fit side-chains REVERT: K 11 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.7090 (mtm110) REVERT: K 100 GLN cc_start: 0.5182 (OUTLIER) cc_final: 0.4453 (tp-100) REVERT: K 172 PHE cc_start: 0.7555 (OUTLIER) cc_final: 0.7306 (p90) REVERT: K 329 HIS cc_start: 0.6450 (OUTLIER) cc_final: 0.6095 (m-70) REVERT: K 364 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6731 (mm) REVERT: K 379 THR cc_start: 0.8386 (m) cc_final: 0.8120 (t) REVERT: K 382 LEU cc_start: 0.8355 (mt) cc_final: 0.7896 (tp) REVERT: L 199 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6885 (pm20) REVERT: L 202 GLU cc_start: 0.7967 (tt0) cc_final: 0.7705 (tt0) REVERT: L 305 MET cc_start: 0.8203 (ttm) cc_final: 0.7968 (ttp) REVERT: Q 101 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7439 (mp) REVERT: Q 199 GLU cc_start: 0.7198 (pt0) cc_final: 0.6996 (pp20) REVERT: Q 231 GLU cc_start: 0.7089 (tp30) cc_final: 0.6588 (tp30) REVERT: Q 323 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7768 (mtt-85) REVERT: Q 390 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8045 (mp10) outliers start: 29 outliers final: 13 residues processed: 196 average time/residue: 1.2404 time to fit residues: 258.9313 Evaluate side-chains 207 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 185 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain K residue 172 PHE Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 329 HIS Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain K residue 391 LYS Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 314 LEU Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 357 SER Chi-restraints excluded: chain Q residue 377 LEU Chi-restraints excluded: chain Q residue 390 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 75 optimal weight: 0.0270 chunk 54 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 49 GLN ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9199 Z= 0.204 Angle : 0.545 8.732 12528 Z= 0.288 Chirality : 0.040 0.130 1491 Planarity : 0.004 0.043 1505 Dihedral : 6.665 59.588 1575 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.33 % Allowed : 14.16 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.24), residues: 1143 helix: 1.96 (0.17), residues: 816 sheet: None (None), residues: 0 loop : 0.15 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 220 HIS 0.004 0.001 HIS Q 154 PHE 0.016 0.002 PHE L 54 TYR 0.019 0.002 TYR Q 244 ARG 0.004 0.000 ARG K 154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 184 time to evaluate : 0.883 Fit side-chains REVERT: K 11 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.7083 (mtm110) REVERT: K 16 TRP cc_start: 0.7570 (OUTLIER) cc_final: 0.5575 (t-100) REVERT: K 100 GLN cc_start: 0.5194 (OUTLIER) cc_final: 0.4433 (tp-100) REVERT: K 172 PHE cc_start: 0.7570 (OUTLIER) cc_final: 0.7323 (p90) REVERT: K 329 HIS cc_start: 0.6456 (OUTLIER) cc_final: 0.6106 (m-70) REVERT: K 364 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6711 (mm) REVERT: K 382 LEU cc_start: 0.8366 (mt) cc_final: 0.7804 (tp) REVERT: L 199 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6882 (pm20) REVERT: L 202 GLU cc_start: 0.7963 (tt0) cc_final: 0.7701 (tt0) REVERT: L 305 MET cc_start: 0.8241 (ttm) cc_final: 0.8010 (ttp) REVERT: Q 231 GLU cc_start: 0.7078 (tp30) cc_final: 0.6586 (tp30) REVERT: Q 323 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7756 (mtt-85) REVERT: Q 390 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8011 (mp10) outliers start: 31 outliers final: 16 residues processed: 197 average time/residue: 1.2393 time to fit residues: 260.2690 Evaluate side-chains 208 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 183 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 68 ASN Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain K residue 172 PHE Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain K residue 329 HIS Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain K residue 391 LYS Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 314 LEU Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 357 SER Chi-restraints excluded: chain Q residue 377 LEU Chi-restraints excluded: chain Q residue 390 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 102 optimal weight: 20.0000 chunk 67 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 49 GLN ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9199 Z= 0.232 Angle : 0.570 9.109 12528 Z= 0.301 Chirality : 0.041 0.133 1491 Planarity : 0.005 0.043 1505 Dihedral : 6.872 59.696 1575 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.22 % Allowed : 14.27 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.24), residues: 1143 helix: 1.88 (0.18), residues: 815 sheet: None (None), residues: 0 loop : 0.12 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 220 HIS 0.005 0.001 HIS Q 154 PHE 0.018 0.002 PHE L 54 TYR 0.020 0.002 TYR Q 244 ARG 0.002 0.000 ARG K 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 183 time to evaluate : 0.971 Fit side-chains REVERT: K 11 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.7056 (mtm110) REVERT: K 16 TRP cc_start: 0.7606 (OUTLIER) cc_final: 0.5605 (t-100) REVERT: K 100 GLN cc_start: 0.5177 (OUTLIER) cc_final: 0.4908 (mm-40) REVERT: K 172 PHE cc_start: 0.7568 (OUTLIER) cc_final: 0.7328 (p90) REVERT: K 329 HIS cc_start: 0.6465 (OUTLIER) cc_final: 0.6125 (m-70) REVERT: K 364 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6694 (mm) REVERT: K 382 LEU cc_start: 0.8367 (mt) cc_final: 0.7791 (tp) REVERT: L 199 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6879 (pm20) REVERT: L 202 GLU cc_start: 0.7956 (tt0) cc_final: 0.7688 (tt0) REVERT: L 305 MET cc_start: 0.8260 (ttm) cc_final: 0.8027 (ttp) REVERT: Q 231 GLU cc_start: 0.7089 (tp30) cc_final: 0.6598 (tp30) REVERT: Q 323 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7768 (mtt-85) REVERT: Q 356 THR cc_start: 0.7107 (p) cc_final: 0.6784 (t) REVERT: Q 390 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8011 (mp10) outliers start: 30 outliers final: 16 residues processed: 196 average time/residue: 1.2295 time to fit residues: 257.0234 Evaluate side-chains 208 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 183 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 68 ASN Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain K residue 172 PHE Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain K residue 329 HIS Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain K residue 391 LYS Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 314 LEU Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 357 SER Chi-restraints excluded: chain Q residue 377 LEU Chi-restraints excluded: chain Q residue 390 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 49 GLN ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9199 Z= 0.258 Angle : 0.589 9.333 12528 Z= 0.311 Chirality : 0.042 0.147 1491 Planarity : 0.005 0.043 1505 Dihedral : 7.018 59.796 1575 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.90 % Allowed : 14.59 % Favored : 82.51 % 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: 1.95 (0.24), residues: 1143 helix: 1.80 (0.17), residues: 815 sheet: None (None), residues: 0 loop : 0.10 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 220 HIS 0.005 0.001 HIS Q 154 PHE 0.020 0.002 PHE L 54 TYR 0.020 0.002 TYR Q 244 ARG 0.005 0.000 ARG K 154 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 184 time to evaluate : 1.081 Fit side-chains REVERT: K 11 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.7060 (mtm110) REVERT: K 16 TRP cc_start: 0.7638 (OUTLIER) cc_final: 0.5629 (t-100) REVERT: K 100 GLN cc_start: 0.5136 (OUTLIER) cc_final: 0.4413 (tp-100) REVERT: K 172 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.7337 (p90) REVERT: K 329 HIS cc_start: 0.6489 (OUTLIER) cc_final: 0.6196 (m-70) REVERT: K 333 SER cc_start: 0.7203 (p) cc_final: 0.6934 (m) REVERT: K 364 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6699 (mm) REVERT: K 382 LEU cc_start: 0.8367 (mt) cc_final: 0.7917 (tp) REVERT: L 199 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6735 (pm20) REVERT: L 202 GLU cc_start: 0.7959 (tt0) cc_final: 0.7682 (tt0) REVERT: L 305 MET cc_start: 0.8271 (ttm) cc_final: 0.8038 (ttp) REVERT: Q 231 GLU cc_start: 0.7093 (tp30) cc_final: 0.6602 (tp30) REVERT: Q 323 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7776 (mtt-85) REVERT: Q 356 THR cc_start: 0.7133 (p) cc_final: 0.6820 (t) outliers start: 27 outliers final: 16 residues processed: 196 average time/residue: 1.2511 time to fit residues: 261.7592 Evaluate side-chains 207 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 183 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 68 ASN Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain K residue 172 PHE Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain K residue 329 HIS Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain K residue 391 LYS Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 314 LEU Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 357 SER Chi-restraints excluded: chain Q residue 377 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 93 optimal weight: 0.1980 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 49 GLN ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 GLN L 58 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.117063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.097412 restraints weight = 19406.321| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.48 r_work: 0.2837 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9199 Z= 0.188 Angle : 0.530 9.244 12528 Z= 0.281 Chirality : 0.039 0.127 1491 Planarity : 0.004 0.042 1505 Dihedral : 6.656 59.631 1575 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.11 % Allowed : 14.16 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.24), residues: 1143 helix: 1.97 (0.18), residues: 816 sheet: None (None), residues: 0 loop : 0.12 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 220 HIS 0.004 0.001 HIS L 58 PHE 0.014 0.002 PHE Q 54 TYR 0.019 0.002 TYR Q 244 ARG 0.004 0.000 ARG K 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4431.07 seconds wall clock time: 78 minutes 24.41 seconds (4704.41 seconds total)