Starting phenix.real_space_refine on Sat Dec 28 22:58:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8csx_26974/12_2024/8csx_26974.cif Found real_map, /net/cci-nas-00/data/ceres_data/8csx_26974/12_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/cci-nas-00/data/ceres_data/8csx_26974/12_2024/8csx_26974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8csx_26974/12_2024/8csx_26974.map" model { file = "/net/cci-nas-00/data/ceres_data/8csx_26974/12_2024/8csx_26974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8csx_26974/12_2024/8csx_26974.cif" } 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. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 7.58, per 1000 atoms: 0.83 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.6 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... Secondary structure from input PDB file: 55 helices and 3 sheets defined 79.2% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'K' and resid 11 through 31 Processing helix chain 'K' and resid 43 through 60 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 60 through 66 removed outlier: 3.872A pdb=" N THR K 66 " --> pdb=" O LEU K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 99 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 109 through 128 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) Processing helix chain 'K' and resid 135 through 162 Processing helix chain 'K' and resid 166 through 170 removed outlier: 3.562A pdb=" N LEU K 169 " --> pdb=" O HIS K 166 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG K 170 " --> pdb=" O MET K 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 166 through 170' Processing helix chain 'K' and resid 171 through 187 removed outlier: 3.569A pdb=" N CYS K 186 " --> pdb=" O THR K 182 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU K 187 " --> pdb=" O VAL K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 225 Proline residue: K 221 - end of helix Processing helix chain 'K' and resid 230 through 256 Processing helix chain 'K' and resid 266 through 274 removed outlier: 3.628A pdb=" N SER K 272 " --> pdb=" O THR K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 275 through 282 Processing helix chain 'K' and resid 290 through 312 removed outlier: 3.701A pdb=" N ALA K 294 " --> pdb=" O SER K 290 " (cutoff:3.500A) Processing helix chain 'K' and resid 326 through 350 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 389 Processing helix chain 'K' and resid 390 through 394 Processing helix chain 'K' and resid 397 through 401 removed outlier: 3.714A pdb=" N TYR K 401 " --> pdb=" O VAL K 398 " (cutoff:3.500A) Processing helix chain 'K' and resid 403 through 407 Processing helix chain 'L' and resid 3 through 23 Processing helix chain 'L' and resid 50 through 63 Processing helix chain 'L' and resid 63 through 69 Processing helix chain 'L' and resid 75 through 104 removed outlier: 3.739A pdb=" N GLN L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 133 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 137 through 162 removed outlier: 3.639A pdb=" N VAL L 150 " --> pdb=" O ILE L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 174 through 189 Processing helix chain 'L' and resid 191 through 195 Processing helix chain 'L' and resid 204 through 228 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 233 through 261 removed outlier: 3.714A pdb=" N LEU L 252 " --> pdb=" O ALA L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 266 Processing helix chain 'L' and resid 268 through 275 Processing helix chain 'L' and resid 277 through 283 removed outlier: 3.657A pdb=" N VAL L 281 " --> pdb=" O LEU L 277 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 321 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 329 through 334 Processing helix chain 'L' and resid 334 through 351 Processing helix chain 'L' and resid 357 through 384 Processing helix chain 'L' and resid 398 through 402 removed outlier: 3.619A pdb=" N VAL L 401 " --> pdb=" O ASP L 398 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 23 Processing helix chain 'Q' and resid 47 through 63 Proline residue: Q 52 - end of helix Processing helix chain 'Q' and resid 63 through 69 removed outlier: 3.621A pdb=" N MET Q 69 " --> pdb=" O PHE Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 70 through 72 No H-bonds generated for 'chain 'Q' and resid 70 through 72' Processing helix chain 'Q' and resid 75 through 104 removed outlier: 3.812A pdb=" N GLN Q 92 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 133 removed outlier: 3.507A pdb=" N MET Q 115 " --> pdb=" O GLY Q 111 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA Q 131 " --> pdb=" O ILE Q 127 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL Q 132 " --> pdb=" O SER Q 128 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 162 removed outlier: 3.688A pdb=" N VAL Q 150 " --> pdb=" O ILE Q 146 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 189 Processing helix chain 'Q' and resid 191 through 195 Processing helix chain 'Q' and resid 204 through 228 Proline residue: Q 223 - end of helix Processing helix chain 'Q' and resid 233 through 262 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 266 Processing helix chain 'Q' and resid 268 through 275 Processing helix chain 'Q' and resid 277 through 283 Processing helix chain 'Q' and resid 292 through 321 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 329 through 334 Processing helix chain 'Q' and resid 335 through 351 Processing helix chain 'Q' and resid 357 through 385 removed outlier: 4.028A pdb=" N LEU Q 385 " --> pdb=" O LEU Q 381 " (cutoff:3.500A) Processing helix chain 'Q' and resid 398 through 402 removed outlier: 3.583A pdb=" N VAL Q 401 " --> pdb=" O ASP Q 398 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 32 through 34 removed outlier: 6.923A pdb=" N HIS K 33 " --> pdb=" O ILE K 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'L' and resid 24 through 25 Processing sheet with id=AA3, first strand: chain 'Q' and resid 24 through 25 658 hydrogen bonds defined for protein. 1933 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: 2.82 Time building geometry restraints manager: 2.85 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: 0.00 - 1.85: 12044 1.85 - 3.70: 417 3.70 - 5.56: 51 5.56 - 7.41: 12 7.41 - 9.26: 4 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: 1044 2.75 - 3.28: 9611 3.28 - 3.82: 17718 3.82 - 4.36: 21251 4.36 - 4.90: 35084 Nonbonded interactions: 84708 Sorted by model distance: nonbonded pdb=" OD2 ASP Q 399 " pdb=" O HOH Q 601 " model vdw 2.208 3.040 nonbonded pdb=" OD1 ASP Q 398 " pdb=" OG SER Q 400 " model vdw 2.226 3.040 nonbonded pdb=" O TYR K 178 " pdb=" OG1 THR K 182 " model vdw 2.236 3.040 nonbonded pdb=" OG1 THR L 408 " pdb=" O HOH L 601 " model vdw 2.242 3.040 nonbonded pdb=" O LYS L 404 " pdb=" O HOH L 602 " model vdw 2.266 3.040 ... (remaining 84703 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.290 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 26.610 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.070 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:14.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.470 ------------------------------------------------------------------------------- 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= 0.370 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 to be fit. rotamer outliers: 36 poor density : 214 time to evaluate : 1.049 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: 1.2490 time to fit residues: 310.1844 Evaluate side-chains 198 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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: 9.9990 chunk 87 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 L 263 HIS Q 55 GLN Q 106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9199 Z= 0.229 Angle : 0.586 7.488 12528 Z= 0.314 Chirality : 0.042 0.138 1491 Planarity : 0.005 0.057 1505 Dihedral : 10.361 179.910 1602 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.49 % Favored : 98.42 % Rotamer: Outliers : 3.86 % Allowed : 10.30 % Favored : 85.84 % 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: 2.17 (0.24), residues: 1143 helix: 2.05 (0.17), residues: 808 sheet: None (None), residues: 0 loop : -0.02 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 16 HIS 0.004 0.001 HIS Q 154 PHE 0.018 0.002 PHE L 54 TYR 0.021 0.002 TYR Q 244 ARG 0.002 0.000 ARG K 71 *********************** 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 to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 1.022 Fit side-chains REVERT: K 11 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6880 (mtt90) REVERT: K 16 TRP cc_start: 0.7645 (OUTLIER) cc_final: 0.5699 (t-100) REVERT: K 100 GLN cc_start: 0.5473 (OUTLIER) cc_final: 0.4875 (tp-100) REVERT: K 201 ARG cc_start: 0.8207 (mmt180) cc_final: 0.7895 (tpp-160) REVERT: K 329 HIS cc_start: 0.6504 (OUTLIER) cc_final: 0.6061 (m-70) REVERT: K 382 LEU cc_start: 0.8335 (mt) cc_final: 0.7862 (tp) REVERT: L 199 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6723 (pm20) REVERT: L 202 GLU cc_start: 0.7977 (tt0) cc_final: 0.7723 (tt0) REVERT: L 305 MET cc_start: 0.8261 (ttm) cc_final: 0.8028 (ttp) REVERT: Q 199 GLU cc_start: 0.7258 (pt0) cc_final: 0.7035 (pp20) REVERT: Q 231 GLU cc_start: 0.7049 (tp30) cc_final: 0.6574 (tp30) REVERT: Q 321 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7820 (mppt) REVERT: Q 323 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7771 (mtt-85) outliers start: 36 outliers final: 13 residues processed: 204 average time/residue: 1.2578 time to fit residues: 274.7889 Evaluate side-chains 211 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 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 290 SER Chi-restraints excluded: chain K residue 329 HIS Chi-restraints excluded: chain K residue 334 LEU Chi-restraints excluded: chain K residue 371 SER 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 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=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: 0.8980 chunk 71 optimal weight: 0.0070 chunk 28 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 overall best weight: 2.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9199 Z= 0.200 Angle : 0.554 7.003 12528 Z= 0.297 Chirality : 0.040 0.143 1491 Planarity : 0.004 0.041 1505 Dihedral : 9.296 154.498 1589 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.11 % Allowed : 12.02 % Favored : 84.87 % 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: 2.34 (0.24), residues: 1143 helix: 2.21 (0.17), residues: 808 sheet: None (None), residues: 0 loop : -0.05 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 16 HIS 0.004 0.001 HIS Q 154 PHE 0.016 0.002 PHE L 54 TYR 0.020 0.002 TYR Q 244 ARG 0.003 0.000 ARG Q 195 *********************** 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 222 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 1.039 Fit side-chains REVERT: K 11 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6890 (mtt90) REVERT: K 16 TRP cc_start: 0.7541 (OUTLIER) cc_final: 0.5475 (t-100) REVERT: K 100 GLN cc_start: 0.5448 (OUTLIER) cc_final: 0.4895 (tp-100) REVERT: K 329 HIS cc_start: 0.6455 (OUTLIER) cc_final: 0.6000 (m-70) REVERT: K 379 THR cc_start: 0.8377 (m) cc_final: 0.8125 (t) REVERT: K 382 LEU cc_start: 0.8337 (mt) cc_final: 0.7767 (tp) REVERT: L 199 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6713 (pm20) REVERT: L 202 GLU cc_start: 0.7983 (tt0) cc_final: 0.7731 (tt0) REVERT: L 305 MET cc_start: 0.8248 (ttm) cc_final: 0.8012 (ttp) REVERT: Q 199 GLU cc_start: 0.7237 (pt0) cc_final: 0.7025 (pp20) REVERT: Q 231 GLU cc_start: 0.7031 (tp30) cc_final: 0.6556 (tp30) REVERT: Q 323 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7793 (mtt-85) REVERT: Q 390 GLN cc_start: 0.8371 (pm20) cc_final: 0.7986 (mp10) outliers start: 29 outliers final: 14 residues processed: 205 average time/residue: 1.2965 time to fit residues: 283.2002 Evaluate side-chains 207 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 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 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 100 ILE Chi-restraints excluded: chain L residue 110 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 323 ARG Chi-restraints excluded: chain Q residue 357 SER Chi-restraints excluded: chain Q residue 377 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 29 optimal weight: 0.0980 chunk 92 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9199 Z= 0.150 Angle : 0.502 6.200 12528 Z= 0.268 Chirality : 0.038 0.124 1491 Planarity : 0.004 0.042 1505 Dihedral : 7.898 114.546 1585 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.43 % Allowed : 12.55 % Favored : 84.01 % 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: 2.66 (0.24), residues: 1143 helix: 2.45 (0.17), residues: 816 sheet: None (None), residues: 0 loop : -0.02 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 16 HIS 0.003 0.001 HIS L 58 PHE 0.015 0.001 PHE L 294 TYR 0.018 0.002 TYR Q 244 ARG 0.004 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 231 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 0.953 Fit side-chains REVERT: K 11 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6929 (mtt90) REVERT: K 100 GLN cc_start: 0.5356 (OUTLIER) cc_final: 0.4894 (tp-100) REVERT: K 329 HIS cc_start: 0.6391 (OUTLIER) cc_final: 0.5851 (m-70) REVERT: K 364 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6712 (mm) REVERT: K 379 THR cc_start: 0.8370 (m) cc_final: 0.8139 (p) REVERT: K 382 LEU cc_start: 0.8333 (mt) cc_final: 0.7769 (tp) REVERT: K 403 ASP cc_start: 0.8212 (t70) cc_final: 0.8000 (t0) REVERT: L 48 PHE cc_start: 0.6799 (t80) cc_final: 0.6473 (t80) REVERT: L 199 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6687 (pm20) REVERT: L 202 GLU cc_start: 0.7987 (tt0) cc_final: 0.7747 (tt0) REVERT: L 305 MET cc_start: 0.8123 (ttm) cc_final: 0.7901 (ttp) REVERT: L 369 ILE cc_start: 0.8224 (mt) cc_final: 0.7933 (mm) REVERT: Q 199 GLU cc_start: 0.7248 (pt0) cc_final: 0.7033 (pp20) REVERT: Q 231 GLU cc_start: 0.6959 (tp30) cc_final: 0.6555 (tp30) REVERT: Q 323 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7774 (mtt-85) REVERT: Q 390 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7998 (mp10) outliers start: 32 outliers final: 17 residues processed: 213 average time/residue: 1.3156 time to fit residues: 298.3836 Evaluate side-chains 215 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 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 110 ILE Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 269 MET 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 156 GLU Chi-restraints excluded: chain Q residue 253 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9199 Z= 0.308 Angle : 0.639 7.661 12528 Z= 0.339 Chirality : 0.045 0.156 1491 Planarity : 0.005 0.041 1505 Dihedral : 8.354 104.480 1583 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.43 % Allowed : 13.63 % 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: 2.23 (0.24), residues: 1143 helix: 2.14 (0.17), residues: 807 sheet: None (None), residues: 0 loop : -0.11 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP Q 219 HIS 0.006 0.002 HIS Q 154 PHE 0.023 0.003 PHE L 54 TYR 0.021 0.003 TYR Q 180 ARG 0.005 0.001 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 222 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 1.159 Fit side-chains REVERT: K 11 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7031 (mtt90) REVERT: K 100 GLN cc_start: 0.5491 (OUTLIER) cc_final: 0.5126 (tp-100) REVERT: K 329 HIS cc_start: 0.6490 (OUTLIER) cc_final: 0.6008 (m-70) REVERT: K 364 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6635 (mm) REVERT: K 382 LEU cc_start: 0.8359 (mt) cc_final: 0.7915 (tp) REVERT: L 48 PHE cc_start: 0.6967 (t80) cc_final: 0.6766 (t80) REVERT: L 202 GLU cc_start: 0.7987 (tt0) cc_final: 0.7717 (tt0) REVERT: L 305 MET cc_start: 0.8301 (ttm) cc_final: 0.8062 (ttp) REVERT: Q 25 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7749 (mm-30) REVERT: Q 199 GLU cc_start: 0.7257 (pt0) cc_final: 0.7044 (pp20) REVERT: Q 231 GLU cc_start: 0.7054 (tp30) cc_final: 0.6566 (tp30) REVERT: Q 323 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7795 (mtt-85) REVERT: Q 390 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7996 (mp10) outliers start: 32 outliers final: 14 residues processed: 203 average time/residue: 1.3282 time to fit residues: 287.2539 Evaluate side-chains 208 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 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 110 ILE Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 25 GLU 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 390 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 9 optimal weight: 0.4980 chunk 36 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 GLN L 58 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1413 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= 0.178 Angle : 0.537 7.101 12528 Z= 0.287 Chirality : 0.039 0.128 1491 Planarity : 0.004 0.041 1505 Dihedral : 6.881 56.873 1580 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.33 % Allowed : 13.84 % Favored : 82.83 % 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: 2.51 (0.24), residues: 1143 helix: 2.33 (0.17), residues: 815 sheet: None (None), residues: 0 loop : -0.03 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 16 HIS 0.003 0.001 HIS Q 58 PHE 0.014 0.002 PHE L 294 TYR 0.019 0.002 TYR Q 244 ARG 0.003 0.000 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 223 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 1.050 Fit side-chains REVERT: K 11 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6940 (mtt90) REVERT: K 100 GLN cc_start: 0.5462 (OUTLIER) cc_final: 0.5180 (tp-100) REVERT: K 329 HIS cc_start: 0.6436 (OUTLIER) cc_final: 0.5854 (m-70) REVERT: K 364 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6689 (mm) REVERT: K 379 THR cc_start: 0.8366 (m) cc_final: 0.8117 (t) REVERT: K 382 LEU cc_start: 0.8331 (mt) cc_final: 0.7780 (tp) REVERT: L 48 PHE cc_start: 0.6850 (t80) cc_final: 0.6601 (t80) REVERT: L 199 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6918 (pm20) REVERT: L 202 GLU cc_start: 0.7979 (tt0) cc_final: 0.7725 (tt0) REVERT: L 305 MET cc_start: 0.8190 (ttm) cc_final: 0.7955 (ttp) REVERT: Q 101 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7404 (mp) REVERT: Q 199 GLU cc_start: 0.7244 (pt0) cc_final: 0.7024 (pp20) REVERT: Q 231 GLU cc_start: 0.7025 (tp30) cc_final: 0.6544 (tp30) REVERT: Q 323 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7787 (mtt-85) REVERT: Q 390 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8012 (mp10) outliers start: 31 outliers final: 15 residues processed: 206 average time/residue: 1.2822 time to fit residues: 281.7649 Evaluate side-chains 212 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 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 110 ILE Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 269 MET 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 253 THR 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: 10.0000 chunk 63 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 110 optimal weight: 0.5980 chunk 69 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9199 Z= 0.334 Angle : 0.660 8.666 12528 Z= 0.349 Chirality : 0.046 0.162 1491 Planarity : 0.005 0.041 1505 Dihedral : 7.516 59.765 1580 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.86 % Allowed : 14.06 % Favored : 82.08 % 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: 2.11 (0.24), residues: 1143 helix: 2.05 (0.17), residues: 805 sheet: None (None), residues: 0 loop : -0.17 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 220 HIS 0.007 0.002 HIS Q 154 PHE 0.024 0.003 PHE L 54 TYR 0.022 0.003 TYR Q 180 ARG 0.005 0.001 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 225 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 1.014 Fit side-chains REVERT: K 11 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7015 (mtt90) REVERT: K 329 HIS cc_start: 0.6496 (OUTLIER) cc_final: 0.6040 (m-70) REVERT: K 364 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6671 (mm) REVERT: K 382 LEU cc_start: 0.8362 (mt) cc_final: 0.7926 (tp) REVERT: L 2 ARG cc_start: 0.7499 (ptt180) cc_final: 0.7279 (ptt180) REVERT: L 199 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6881 (pm20) REVERT: L 202 GLU cc_start: 0.7985 (tt0) cc_final: 0.7713 (tt0) REVERT: L 305 MET cc_start: 0.8304 (ttm) cc_final: 0.8066 (ttp) REVERT: Q 199 GLU cc_start: 0.7257 (pt0) cc_final: 0.7034 (pp20) REVERT: Q 231 GLU cc_start: 0.7069 (tp30) cc_final: 0.6577 (tp30) REVERT: Q 323 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7825 (mtt-85) REVERT: Q 356 THR cc_start: 0.7067 (p) cc_final: 0.6866 (t) REVERT: Q 390 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7992 (mp10) outliers start: 36 outliers final: 17 residues processed: 206 average time/residue: 1.2753 time to fit residues: 280.0184 Evaluate side-chains 211 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG 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 386 LEU Chi-restraints excluded: chain K residue 391 LYS Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 110 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 283 VAL Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 357 SER 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: 0.9980 chunk 21 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 GLN L 58 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1223 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= 0.275 Angle : 0.619 8.045 12528 Z= 0.329 Chirality : 0.043 0.143 1491 Planarity : 0.005 0.042 1505 Dihedral : 7.180 59.575 1577 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.79 % Allowed : 15.34 % Favored : 81.87 % 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: 2.12 (0.24), residues: 1143 helix: 2.05 (0.17), residues: 808 sheet: None (None), residues: 0 loop : -0.14 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 220 HIS 0.005 0.001 HIS Q 154 PHE 0.020 0.002 PHE L 54 TYR 0.020 0.003 TYR Q 244 ARG 0.004 0.000 ARG L 195 *********************** 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 213 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.978 Fit side-chains REVERT: K 11 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.6987 (mtt90) REVERT: K 329 HIS cc_start: 0.6493 (OUTLIER) cc_final: 0.6034 (m-70) REVERT: K 364 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6677 (mm) REVERT: K 382 LEU cc_start: 0.8355 (mt) cc_final: 0.7916 (tp) REVERT: K 390 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7630 (mp) REVERT: L 199 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6879 (pm20) REVERT: L 202 GLU cc_start: 0.7985 (tt0) cc_final: 0.7718 (tt0) REVERT: L 305 MET cc_start: 0.8272 (ttm) cc_final: 0.8034 (ttp) REVERT: Q 231 GLU cc_start: 0.7066 (tp30) cc_final: 0.6573 (tp30) REVERT: Q 323 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7813 (mtt-85) REVERT: Q 390 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8000 (mp10) outliers start: 26 outliers final: 16 residues processed: 198 average time/residue: 1.2937 time to fit residues: 273.1931 Evaluate side-chains 209 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG 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 386 LEU Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 391 LYS Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 110 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 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: 6.9990 chunk 106 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9199 Z= 0.179 Angle : 0.544 9.220 12528 Z= 0.288 Chirality : 0.039 0.125 1491 Planarity : 0.004 0.041 1505 Dihedral : 6.583 56.563 1577 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.00 % Allowed : 15.13 % Favored : 81.87 % 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: 2.48 (0.24), residues: 1143 helix: 2.31 (0.17), residues: 815 sheet: None (None), residues: 0 loop : -0.04 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 16 HIS 0.005 0.001 HIS L 58 PHE 0.015 0.002 PHE L 294 TYR 0.019 0.002 TYR Q 244 ARG 0.004 0.000 ARG L 195 *********************** 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 218 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 1.036 Fit side-chains REVERT: K 11 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6922 (mtt90) REVERT: K 329 HIS cc_start: 0.6417 (OUTLIER) cc_final: 0.5874 (m-70) REVERT: K 364 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6714 (mm) REVERT: K 379 THR cc_start: 0.8362 (m) cc_final: 0.8114 (t) REVERT: K 382 LEU cc_start: 0.8336 (mt) cc_final: 0.7786 (tp) REVERT: L 199 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6915 (pm20) REVERT: L 202 GLU cc_start: 0.7974 (tt0) cc_final: 0.7725 (tt0) REVERT: L 305 MET cc_start: 0.8185 (ttm) cc_final: 0.7951 (ttp) REVERT: Q 101 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7461 (mp) REVERT: Q 231 GLU cc_start: 0.7023 (tp30) cc_final: 0.6611 (tp30) REVERT: Q 323 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7788 (mtt-85) REVERT: Q 390 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8014 (mp10) outliers start: 28 outliers final: 14 residues processed: 202 average time/residue: 1.3004 time to fit residues: 280.4236 Evaluate side-chains 210 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 68 ASN 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 110 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 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: 10.0000 chunk 75 optimal weight: 3.9990 chunk 114 optimal weight: 0.3980 chunk 105 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 72 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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: 0.8593 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9199 Z= 0.190 Angle : 0.554 9.314 12528 Z= 0.294 Chirality : 0.039 0.127 1491 Planarity : 0.004 0.040 1505 Dihedral : 6.549 56.830 1577 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.58 % Allowed : 15.24 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.24), residues: 1143 helix: 2.31 (0.17), residues: 815 sheet: None (None), residues: 0 loop : -0.04 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 220 HIS 0.004 0.001 HIS L 58 PHE 0.015 0.002 PHE Q 54 TYR 0.019 0.002 TYR Q 244 ARG 0.004 0.000 ARG L 195 ********************** 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 to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.910 Fit side-chains REVERT: K 11 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6945 (mtt90) REVERT: K 304 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8255 (mt) REVERT: K 329 HIS cc_start: 0.6419 (OUTLIER) cc_final: 0.5900 (m-70) REVERT: K 364 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6700 (mm) REVERT: K 379 THR cc_start: 0.8379 (m) cc_final: 0.8127 (t) REVERT: K 382 LEU cc_start: 0.8342 (mt) cc_final: 0.7790 (tp) REVERT: L 199 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6917 (pm20) REVERT: L 202 GLU cc_start: 0.7974 (tt0) cc_final: 0.7723 (tt0) REVERT: L 305 MET cc_start: 0.8195 (ttm) cc_final: 0.7958 (ttp) REVERT: L 387 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8243 (mt) REVERT: Q 231 GLU cc_start: 0.7005 (tp30) cc_final: 0.6586 (tp30) REVERT: Q 323 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7780 (mtt-85) REVERT: Q 390 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8007 (mp10) outliers start: 24 outliers final: 13 residues processed: 197 average time/residue: 1.3016 time to fit residues: 273.2396 Evaluate side-chains 208 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 68 ASN 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 304 ILE 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 110 ILE Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 387 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 390 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.114297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.094026 restraints weight = 19264.978| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.54 r_work: 0.2781 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9199 Z= 0.307 Angle : 0.645 9.511 12528 Z= 0.342 Chirality : 0.044 0.144 1491 Planarity : 0.005 0.042 1505 Dihedral : 7.022 58.196 1573 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.22 % Allowed : 14.91 % Favored : 81.87 % 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: 2.07 (0.17), residues: 808 sheet: None (None), residues: 0 loop : -0.12 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K 220 HIS 0.007 0.002 HIS Q 154 PHE 0.023 0.002 PHE L 54 TYR 0.021 0.003 TYR Q 180 ARG 0.005 0.001 ARG L 195 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4388.34 seconds wall clock time: 79 minutes 18.41 seconds (4758.41 seconds total)