Starting phenix.real_space_refine on Wed Feb 4 11:16:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v0s_26949/02_2026/7v0s_26949.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v0s_26949/02_2026/7v0s_26949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v0s_26949/02_2026/7v0s_26949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v0s_26949/02_2026/7v0s_26949.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v0s_26949/02_2026/7v0s_26949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v0s_26949/02_2026/7v0s_26949.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.292 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 69 5.16 5 C 6657 2.51 5 N 1642 2.21 5 O 1935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10303 Number of models: 1 Model: "" Number of chains: 10 Chain: "K" Number of atoms: 2954 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: 2949 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: "J" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1191 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'AJP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 24 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: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Chain: "Q" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "J" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ATYR K 34 " occ=0.42 ... (22 atoms not shown) pdb=" OH BTYR K 34 " occ=0.58 residue: pdb=" N APHE K 239 " occ=0.58 ... (20 atoms not shown) pdb=" CZ BPHE K 239 " occ=0.42 residue: pdb=" N ATYR K 242 " occ=0.62 ... (22 atoms not shown) pdb=" OH BTYR K 242 " occ=0.38 Time building chain proxies: 2.40, per 1000 atoms: 0.23 Number of scatterers: 10303 At special positions: 0 Unit cell: (98.355, 94.205, 99.6, 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 69 16.00 O 1935 8.00 N 1642 7.00 C 6657 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: 0.71 Conformation dependent library (CDL) restraints added in 539.9 milliseconds 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2394 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 3 sheets defined 77.5% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'K' and resid 11 through 31 removed outlier: 3.533A pdb=" N LEU K 15 " --> pdb=" O ARG K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 60 removed outlier: 3.844A pdb=" N VAL K 50 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY K 51 " --> pdb=" O SER K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 66 removed outlier: 3.892A pdb=" N THR K 66 " --> pdb=" O LEU K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 98 removed outlier: 3.816A pdb=" N GLN K 89 " --> pdb=" O ALA K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 127 removed outlier: 3.523A pdb=" N VAL K 123 " --> pdb=" O SER K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 130 No H-bonds generated for 'chain 'K' and resid 128 through 130' Processing helix chain 'K' and resid 135 through 161 Processing helix chain 'K' and resid 166 through 170 removed outlier: 3.671A pdb=" N ARG K 170 " --> pdb=" O MET K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 187 Processing helix chain 'K' and resid 202 through 224 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: 3.529A pdb=" N SER K 272 " --> pdb=" O THR K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 275 through 281 Processing helix chain 'K' and resid 290 through 312 removed outlier: 3.651A pdb=" N ALA K 294 " --> pdb=" O SER K 290 " (cutoff:3.500A) Processing helix chain 'K' and resid 326 through 350 removed outlier: 3.589A pdb=" N VAL K 348 " --> pdb=" O ILE K 344 " (cutoff:3.500A) removed outlier: 3.995A 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 removed outlier: 3.525A pdb=" N TRP K 393 " --> pdb=" O LEU K 390 " (cutoff:3.500A) Processing helix chain 'K' and resid 397 through 401 removed outlier: 3.746A 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: 3.733A pdb=" N GLN L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 133 removed outlier: 3.743A pdb=" N ALA L 131 " --> pdb=" O ILE L 127 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL L 132 " --> pdb=" O SER L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 162 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 226 removed outlier: 3.746A pdb=" N ILE L 213 " --> pdb=" O LEU L 209 " (cutoff:3.500A) removed outlier: 3.810A 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 262 removed outlier: 3.712A pdb=" N LEU L 252 " --> pdb=" O ALA L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 263 through 266 Processing helix chain 'L' and resid 268 through 275 Processing helix chain 'L' and resid 277 through 283 removed outlier: 3.633A pdb=" N VAL L 281 " --> pdb=" O LEU L 277 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 321 removed outlier: 3.580A pdb=" N GLY L 295 " --> pdb=" O ILE L 291 " (cutoff:3.500A) removed outlier: 4.457A 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: 3.698A 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: 3.581A pdb=" N MET Q 69 " --> pdb=" O PHE Q 65 " (cutoff:3.500A) 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 132 removed outlier: 3.799A pdb=" N ALA Q 131 " --> pdb=" O ILE Q 127 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL Q 132 " --> pdb=" O SER Q 128 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 162 removed outlier: 3.610A 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: 3.630A 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 313 Processing helix chain 'Q' and resid 313 through 321 Processing helix chain 'Q' and resid 329 through 334 Processing helix chain 'Q' and resid 334 through 352 Processing helix chain 'Q' and resid 357 through 384 Processing helix chain 'Q' and resid 398 through 402 removed outlier: 3.611A pdb=" N VAL Q 401 " --> pdb=" O ASP Q 398 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 23 Processing helix chain 'J' and resid 24 through 35 Processing helix chain 'J' and resid 47 through 56 Processing helix chain 'J' and resid 57 through 67 Processing helix chain 'J' and resid 80 through 89 Processing helix chain 'J' and resid 90 through 100 Processing helix chain 'J' and resid 113 through 121 Processing helix chain 'J' and resid 123 through 133 Processing helix chain 'J' and resid 146 through 155 Processing helix chain 'J' and resid 156 through 167 Processing sheet with id=AA1, first strand: chain 'K' and resid 32 through 33 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 25 728 hydrogen bonds defined for protein. 2148 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: 1.34 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1589 1.32 - 1.45: 2820 1.45 - 1.57: 5839 1.57 - 1.70: 0 1.70 - 1.82: 122 Bond restraints: 10370 Sorted by residual: bond pdb=" C PRO Q 293 " pdb=" O PRO Q 293 " ideal model delta sigma weight residual 1.237 1.194 0.043 1.26e-02 6.30e+03 1.17e+01 bond pdb=" N THR Q 315 " pdb=" CA THR Q 315 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.04e-02 9.25e+03 1.11e+01 bond pdb=" N LEU Q 322 " pdb=" CA LEU Q 322 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.32e-02 5.74e+03 9.13e+00 bond pdb=" N ILE Q 346 " pdb=" CA ILE Q 346 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.23e+00 bond pdb=" N LEU Q 314 " pdb=" CA LEU Q 314 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.23e-02 6.61e+03 6.79e+00 ... (remaining 10365 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 13748 2.01 - 4.03: 291 4.03 - 6.04: 46 6.04 - 8.05: 14 8.05 - 10.07: 4 Bond angle restraints: 14103 Sorted by residual: angle pdb=" C BTYR K 34 " pdb=" N ASP K 35 " pdb=" CA ASP K 35 " ideal model delta sigma weight residual 121.70 129.19 -7.49 1.80e+00 3.09e-01 1.73e+01 angle pdb=" N SER Q 354 " pdb=" CA SER Q 354 " pdb=" C SER Q 354 " ideal model delta sigma weight residual 109.85 116.17 -6.32 1.58e+00 4.01e-01 1.60e+01 angle pdb=" N GLY Q 284 " pdb=" CA GLY Q 284 " pdb=" C GLY Q 284 " ideal model delta sigma weight residual 112.50 116.74 -4.24 1.16e+00 7.43e-01 1.34e+01 angle pdb=" C THR Q 319 " pdb=" N THR Q 320 " pdb=" CA THR Q 320 " ideal model delta sigma weight residual 122.60 116.31 6.29 1.88e+00 2.83e-01 1.12e+01 angle pdb=" CA GLY Q 345 " pdb=" C GLY Q 345 " pdb=" O GLY Q 345 " ideal model delta sigma weight residual 120.75 117.32 3.43 1.03e+00 9.43e-01 1.11e+01 ... (remaining 14098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 5392 17.70 - 35.39: 569 35.39 - 53.09: 138 53.09 - 70.79: 35 70.79 - 88.49: 15 Dihedral angle restraints: 6149 sinusoidal: 2404 harmonic: 3745 Sorted by residual: dihedral pdb=" CA TRP L 403 " pdb=" C TRP L 403 " pdb=" N LYS L 404 " pdb=" CA LYS L 404 " ideal model delta harmonic sigma weight residual 180.00 162.75 17.25 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA TRP Q 403 " pdb=" C TRP Q 403 " pdb=" N LYS Q 404 " pdb=" CA LYS Q 404 " ideal model delta harmonic sigma weight residual 180.00 163.10 16.90 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA PHE L 23 " pdb=" C PHE L 23 " pdb=" N VAL L 24 " pdb=" CA VAL L 24 " ideal model delta harmonic sigma weight residual -180.00 -163.80 -16.20 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 6146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1416 0.063 - 0.125: 230 0.125 - 0.188: 15 0.188 - 0.251: 3 0.251 - 0.314: 1 Chirality restraints: 1665 Sorted by residual: chirality pdb=" CG LEU K 386 " pdb=" CB LEU K 386 " pdb=" CD1 LEU K 386 " pdb=" CD2 LEU K 386 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.46e+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 2.45 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" C08 AJP Q 501 " pdb=" C07 AJP Q 501 " pdb=" C10 AJP Q 501 " pdb=" O09 AJP Q 501 " both_signs ideal model delta sigma weight residual False 2.56 2.79 -0.22 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1662 not shown) Planarity restraints: 1726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP K 220 " 0.038 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO K 221 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO K 221 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO K 221 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY Q 352 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.51e+00 pdb=" C GLY Q 352 " -0.032 2.00e-02 2.50e+03 pdb=" O GLY Q 352 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA Q 353 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP Q 222 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO Q 223 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO Q 223 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO Q 223 " 0.025 5.00e-02 4.00e+02 ... (remaining 1723 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1125 2.75 - 3.28: 10814 3.28 - 3.82: 20111 3.82 - 4.36: 23717 4.36 - 4.90: 39586 Nonbonded interactions: 95353 Sorted by model distance: nonbonded pdb=" OE2 GLU Q 202 " pdb=" O HOH Q 601 " model vdw 2.208 3.040 nonbonded pdb=" NH2 ARG K 70 " pdb=" O GLY J 155 " model vdw 2.232 3.120 nonbonded pdb=" O SER Q 367 " pdb=" OG1 THR Q 371 " model vdw 2.263 3.040 nonbonded pdb=" OG SER K 284 " pdb=" O HOH K 501 " model vdw 2.268 3.040 nonbonded pdb=" O HOH L 659 " pdb=" O HOH Q 643 " model vdw 2.271 3.040 ... (remaining 95348 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=0.38 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: 1.790 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: 0.390 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.740 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:8.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10370 Z= 0.239 Angle : 0.729 10.067 14103 Z= 0.424 Chirality : 0.045 0.314 1665 Planarity : 0.005 0.057 1726 Dihedral : 16.386 88.487 3755 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.70 % Favored : 98.22 % Rotamer: Outliers : 2.55 % Allowed : 16.35 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.22), residues: 1301 helix: 1.57 (0.16), residues: 936 sheet: None (None), residues: 0 loop : 0.20 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 195 TYR 0.018 0.002 TYR Q 180 PHE 0.017 0.002 PHE L 54 TRP 0.012 0.002 TRP K 16 HIS 0.007 0.001 HIS J 162 Details of bonding type rmsd covalent geometry : bond 0.00426 (10370) covalent geometry : angle 0.72918 (14103) hydrogen bonds : bond 0.12042 ( 728) hydrogen bonds : angle 5.49008 ( 2148) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.432 Fit side-chains REVERT: L 161 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7917 (mm-30) REVERT: L 394 GLN cc_start: 0.7567 (pt0) cc_final: 0.7042 (pm20) REVERT: Q 323 ARG cc_start: 0.7949 (mpt90) cc_final: 0.7718 (mpt-90) REVERT: Q 384 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7963 (tttm) REVERT: J 110 LYS cc_start: 0.8242 (mtpt) cc_final: 0.8001 (mtpt) REVERT: J 128 LYS cc_start: 0.8361 (mtpp) cc_final: 0.7862 (mttp) outliers start: 26 outliers final: 18 residues processed: 207 average time/residue: 0.4866 time to fit residues: 108.2439 Evaluate side-chains 203 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 230 SER Chi-restraints excluded: chain K residue 248 SER Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 311 CYS Chi-restraints excluded: chain K residue 330 SER Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain K residue 372 LEU Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain Q residue 294 PHE Chi-restraints excluded: chain Q residue 314 LEU Chi-restraints excluded: chain Q residue 321 LYS Chi-restraints excluded: chain Q residue 384 LYS Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 73 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Q 55 GLN Q 104 GLN J 103 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.121339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.095535 restraints weight = 26032.714| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.72 r_work: 0.2797 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.0738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10370 Z= 0.131 Angle : 0.529 7.244 14103 Z= 0.278 Chirality : 0.039 0.223 1665 Planarity : 0.004 0.051 1726 Dihedral : 6.514 56.599 1640 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.39 % Favored : 98.53 % Rotamer: Outliers : 2.74 % Allowed : 15.22 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.22), residues: 1301 helix: 2.05 (0.16), residues: 933 sheet: None (None), residues: 0 loop : 0.25 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 70 TYR 0.016 0.002 TYR Q 180 PHE 0.016 0.001 PHE L 54 TRP 0.012 0.001 TRP K 16 HIS 0.005 0.001 HIS J 162 Details of bonding type rmsd covalent geometry : bond 0.00261 (10370) covalent geometry : angle 0.52871 (14103) hydrogen bonds : bond 0.05200 ( 728) hydrogen bonds : angle 4.68974 ( 2148) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 0.397 Fit side-chains REVERT: K 200 GLN cc_start: 0.6988 (OUTLIER) cc_final: 0.6620 (mm110) REVERT: L 161 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8132 (mm-30) REVERT: L 394 GLN cc_start: 0.8050 (pt0) cc_final: 0.7341 (pm20) REVERT: L 404 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8423 (ttpp) REVERT: Q 264 ARG cc_start: 0.7484 (mtp180) cc_final: 0.7271 (mtm180) REVERT: Q 317 LEU cc_start: 0.8286 (tt) cc_final: 0.8061 (tm) REVERT: Q 323 ARG cc_start: 0.8173 (mpt90) cc_final: 0.7660 (mpt90) REVERT: J 47 ASN cc_start: 0.8033 (p0) cc_final: 0.7822 (p0) REVERT: J 110 LYS cc_start: 0.8129 (mtpt) cc_final: 0.7876 (mtpt) REVERT: J 164 ILE cc_start: 0.8003 (pt) cc_final: 0.7788 (pt) outliers start: 28 outliers final: 9 residues processed: 204 average time/residue: 0.5329 time to fit residues: 116.8993 Evaluate side-chains 201 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 190 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 200 GLN Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 404 LYS Chi-restraints excluded: chain Q residue 314 LEU Chi-restraints excluded: chain J residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 41 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 233 GLN ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Q 83 ASN Q 104 GLN J 103 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.115503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.089784 restraints weight = 23484.767| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 1.60 r_work: 0.2710 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2585 r_free = 0.2585 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2585 r_free = 0.2585 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10370 Z= 0.236 Angle : 0.650 7.613 14103 Z= 0.342 Chirality : 0.046 0.243 1665 Planarity : 0.005 0.052 1726 Dihedral : 6.675 59.832 1617 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.69 % Allowed : 14.08 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.22), residues: 1301 helix: 1.79 (0.16), residues: 934 sheet: None (None), residues: 0 loop : 0.10 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 70 TYR 0.022 0.003 TYR Q 180 PHE 0.024 0.003 PHE L 54 TRP 0.009 0.002 TRP Q 219 HIS 0.007 0.002 HIS Q 263 Details of bonding type rmsd covalent geometry : bond 0.00538 (10370) covalent geometry : angle 0.65049 (14103) hydrogen bonds : bond 0.06766 ( 728) hydrogen bonds : angle 4.92172 ( 2148) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 0.374 Fit side-chains REVERT: K 200 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.6527 (mm-40) REVERT: L 161 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8149 (mm-30) REVERT: L 394 GLN cc_start: 0.8033 (pt0) cc_final: 0.7421 (pm20) REVERT: L 404 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8401 (ttpp) REVERT: Q 317 LEU cc_start: 0.8312 (tt) cc_final: 0.8040 (tm) REVERT: Q 323 ARG cc_start: 0.8211 (mpt90) cc_final: 0.7971 (mpt-90) REVERT: J 47 ASN cc_start: 0.8345 (p0) cc_final: 0.8072 (p0) REVERT: J 91 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6717 (m-30) REVERT: J 110 LYS cc_start: 0.8271 (mtpt) cc_final: 0.7987 (mtpt) outliers start: 38 outliers final: 18 residues processed: 199 average time/residue: 0.5329 time to fit residues: 113.5740 Evaluate side-chains 201 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 200 GLN Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 404 LYS Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain Q residue 314 LEU Chi-restraints excluded: chain Q residue 384 LYS Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 60 MET Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 91 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 95 optimal weight: 7.9990 chunk 17 optimal weight: 0.0970 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Q 83 ASN Q 104 GLN Q 155 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.123846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.099571 restraints weight = 26599.525| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.79 r_work: 0.2809 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10370 Z= 0.120 Angle : 0.506 7.298 14103 Z= 0.265 Chirality : 0.038 0.173 1665 Planarity : 0.004 0.050 1726 Dihedral : 5.940 59.901 1617 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.24 % Favored : 98.69 % Rotamer: Outliers : 2.65 % Allowed : 15.60 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.23), residues: 1301 helix: 2.17 (0.16), residues: 936 sheet: None (None), residues: 0 loop : 0.17 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 2 TYR 0.015 0.001 TYR Q 244 PHE 0.014 0.001 PHE L 62 TRP 0.013 0.001 TRP K 16 HIS 0.008 0.001 HIS Q 263 Details of bonding type rmsd covalent geometry : bond 0.00233 (10370) covalent geometry : angle 0.50606 (14103) hydrogen bonds : bond 0.04762 ( 728) hydrogen bonds : angle 4.56417 ( 2148) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 0.339 Fit side-chains REVERT: L 394 GLN cc_start: 0.8046 (pt0) cc_final: 0.7422 (pm20) REVERT: L 404 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8419 (ttpp) REVERT: Q 231 GLU cc_start: 0.7596 (tp30) cc_final: 0.7055 (tt0) REVERT: Q 317 LEU cc_start: 0.8264 (tt) cc_final: 0.8062 (tm) REVERT: Q 323 ARG cc_start: 0.8176 (mpt90) cc_final: 0.7757 (mpt90) REVERT: J 47 ASN cc_start: 0.8070 (p0) cc_final: 0.7825 (p0) REVERT: J 128 LYS cc_start: 0.8383 (mtpp) cc_final: 0.7683 (mttp) REVERT: J 145 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.7558 (m-80) REVERT: J 164 ILE cc_start: 0.7966 (pt) cc_final: 0.7739 (pt) outliers start: 27 outliers final: 12 residues processed: 206 average time/residue: 0.4600 time to fit residues: 102.0822 Evaluate side-chains 205 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 404 LYS Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain Q residue 384 LYS Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 145 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 62 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Q 83 ASN Q 104 GLN J 103 ASN J 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.116757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.090817 restraints weight = 31430.467| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.00 r_work: 0.2695 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10370 Z= 0.192 Angle : 0.600 7.306 14103 Z= 0.315 Chirality : 0.043 0.243 1665 Planarity : 0.004 0.050 1726 Dihedral : 6.210 58.487 1615 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.40 % Allowed : 15.50 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.23), residues: 1301 helix: 1.96 (0.16), residues: 936 sheet: None (None), residues: 0 loop : 0.10 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 70 TYR 0.020 0.002 TYR Q 180 PHE 0.022 0.002 PHE L 54 TRP 0.008 0.002 TRP K 16 HIS 0.007 0.001 HIS Q 263 Details of bonding type rmsd covalent geometry : bond 0.00427 (10370) covalent geometry : angle 0.59964 (14103) hydrogen bonds : bond 0.06186 ( 728) hydrogen bonds : angle 4.78316 ( 2148) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 0.404 Fit side-chains REVERT: K 200 GLN cc_start: 0.7070 (OUTLIER) cc_final: 0.6563 (mm-40) REVERT: K 293 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8633 (tp) REVERT: L 394 GLN cc_start: 0.8144 (pt0) cc_final: 0.7495 (pm20) REVERT: L 404 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8487 (ttpp) REVERT: Q 317 LEU cc_start: 0.8322 (tt) cc_final: 0.8065 (tm) REVERT: Q 323 ARG cc_start: 0.8251 (mpt90) cc_final: 0.8039 (mpt-90) REVERT: J 47 ASN cc_start: 0.8329 (p0) cc_final: 0.8053 (p0) REVERT: J 91 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6893 (m-30) REVERT: J 145 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.7706 (m-80) outliers start: 36 outliers final: 17 residues processed: 203 average time/residue: 0.5015 time to fit residues: 109.3859 Evaluate side-chains 204 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 200 GLN Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 404 LYS Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain Q residue 314 LEU Chi-restraints excluded: chain Q residue 384 LYS Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 145 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 83 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 262 GLN L 58 HIS Q 83 ASN Q 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.117696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.092308 restraints weight = 25016.646| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 1.66 r_work: 0.2741 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10370 Z= 0.168 Angle : 0.578 7.847 14103 Z= 0.303 Chirality : 0.042 0.252 1665 Planarity : 0.004 0.049 1726 Dihedral : 6.113 58.092 1615 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.93 % Allowed : 15.97 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.22), residues: 1301 helix: 1.97 (0.16), residues: 936 sheet: None (None), residues: 0 loop : 0.09 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 70 TYR 0.018 0.002 TYR Q 180 PHE 0.019 0.002 PHE L 54 TRP 0.010 0.001 TRP K 220 HIS 0.006 0.001 HIS Q 263 Details of bonding type rmsd covalent geometry : bond 0.00365 (10370) covalent geometry : angle 0.57801 (14103) hydrogen bonds : bond 0.05861 ( 728) hydrogen bonds : angle 4.73932 ( 2148) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.294 Fit side-chains REVERT: K 200 GLN cc_start: 0.6998 (OUTLIER) cc_final: 0.6483 (mm-40) REVERT: K 235 LYS cc_start: 0.8256 (ttmt) cc_final: 0.7998 (tttt) REVERT: L 394 GLN cc_start: 0.8050 (pt0) cc_final: 0.7392 (pm20) REVERT: L 404 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8402 (ttpp) REVERT: Q 85 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8728 (tp) REVERT: Q 317 LEU cc_start: 0.8267 (tt) cc_final: 0.8016 (tm) REVERT: Q 321 LYS cc_start: 0.8313 (mmtm) cc_final: 0.8089 (mmtm) REVERT: Q 323 ARG cc_start: 0.8192 (mpt90) cc_final: 0.7748 (mpt90) REVERT: J 47 ASN cc_start: 0.8250 (p0) cc_final: 0.7983 (p0) REVERT: J 91 ASP cc_start: 0.7038 (OUTLIER) cc_final: 0.6713 (m-30) REVERT: J 145 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.7630 (m-80) outliers start: 31 outliers final: 18 residues processed: 202 average time/residue: 0.4980 time to fit residues: 108.0541 Evaluate side-chains 206 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 200 GLN Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 262 GLN Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 404 LYS Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain Q residue 314 LEU Chi-restraints excluded: chain Q residue 384 LYS Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 145 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 81 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Q 83 ASN Q 104 GLN J 103 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.117661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.092155 restraints weight = 25649.229| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 1.67 r_work: 0.2737 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10370 Z= 0.169 Angle : 0.583 7.885 14103 Z= 0.305 Chirality : 0.042 0.268 1665 Planarity : 0.004 0.049 1726 Dihedral : 6.102 57.825 1615 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.84 % Allowed : 15.78 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.22), residues: 1301 helix: 1.96 (0.16), residues: 936 sheet: None (None), residues: 0 loop : 0.10 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 70 TYR 0.018 0.002 TYR Q 180 PHE 0.020 0.002 PHE L 54 TRP 0.012 0.001 TRP K 220 HIS 0.006 0.001 HIS Q 263 Details of bonding type rmsd covalent geometry : bond 0.00368 (10370) covalent geometry : angle 0.58324 (14103) hydrogen bonds : bond 0.05877 ( 728) hydrogen bonds : angle 4.74457 ( 2148) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 0.483 Fit side-chains REVERT: K 200 GLN cc_start: 0.7008 (OUTLIER) cc_final: 0.6493 (mm-40) REVERT: K 235 LYS cc_start: 0.8267 (ttmt) cc_final: 0.8000 (tttt) REVERT: L 394 GLN cc_start: 0.8062 (pt0) cc_final: 0.7403 (pm20) REVERT: L 404 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8408 (ttpp) REVERT: Q 85 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8732 (tp) REVERT: Q 317 LEU cc_start: 0.8277 (tt) cc_final: 0.8025 (tm) REVERT: Q 323 ARG cc_start: 0.8193 (mpt90) cc_final: 0.7973 (mpt-90) REVERT: J 18 ARG cc_start: 0.6280 (OUTLIER) cc_final: 0.5949 (mmm160) REVERT: J 47 ASN cc_start: 0.8266 (p0) cc_final: 0.7990 (p0) REVERT: J 91 ASP cc_start: 0.7058 (OUTLIER) cc_final: 0.6732 (m-30) REVERT: J 128 LYS cc_start: 0.8429 (mtpp) cc_final: 0.7632 (mttp) REVERT: J 145 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.7636 (m-80) outliers start: 30 outliers final: 18 residues processed: 202 average time/residue: 0.6324 time to fit residues: 136.8059 Evaluate side-chains 207 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 42 LYS Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 200 GLN Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 404 LYS Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain Q residue 314 LEU Chi-restraints excluded: chain Q residue 384 LYS Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 145 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 43 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Q 83 ASN Q 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.116110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.091399 restraints weight = 24831.083| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.69 r_work: 0.2721 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10370 Z= 0.205 Angle : 0.628 7.944 14103 Z= 0.328 Chirality : 0.044 0.301 1665 Planarity : 0.005 0.050 1726 Dihedral : 6.291 57.712 1615 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.02 % Allowed : 15.50 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.22), residues: 1301 helix: 1.84 (0.16), residues: 936 sheet: None (None), residues: 0 loop : 0.02 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 70 TYR 0.020 0.002 TYR Q 180 PHE 0.022 0.002 PHE L 54 TRP 0.012 0.002 TRP K 220 HIS 0.006 0.001 HIS Q 263 Details of bonding type rmsd covalent geometry : bond 0.00460 (10370) covalent geometry : angle 0.62780 (14103) hydrogen bonds : bond 0.06365 ( 728) hydrogen bonds : angle 4.84315 ( 2148) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 0.431 Fit side-chains REVERT: K 200 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.6485 (mm-40) REVERT: L 394 GLN cc_start: 0.8068 (pt0) cc_final: 0.7401 (pm20) REVERT: L 404 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8394 (ttpp) REVERT: Q 85 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8727 (tp) REVERT: Q 317 LEU cc_start: 0.8288 (tt) cc_final: 0.8013 (tm) REVERT: Q 321 LYS cc_start: 0.8319 (mmtm) cc_final: 0.8089 (mmtm) REVERT: Q 323 ARG cc_start: 0.8188 (mpt90) cc_final: 0.7964 (mpt-90) REVERT: J 47 ASN cc_start: 0.8332 (p0) cc_final: 0.8042 (p0) REVERT: J 91 ASP cc_start: 0.7055 (OUTLIER) cc_final: 0.6720 (m-30) REVERT: J 145 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.7703 (m-80) outliers start: 32 outliers final: 18 residues processed: 198 average time/residue: 0.5579 time to fit residues: 118.4200 Evaluate side-chains 204 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 42 LYS Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 200 GLN Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 404 LYS Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain Q residue 314 LEU Chi-restraints excluded: chain Q residue 384 LYS Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 145 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 54 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 56 optimal weight: 0.0770 chunk 40 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Q 83 ASN Q 104 GLN J 103 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.122979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.097656 restraints weight = 24459.632| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.64 r_work: 0.2828 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10370 Z= 0.121 Angle : 0.525 8.638 14103 Z= 0.271 Chirality : 0.039 0.255 1665 Planarity : 0.004 0.049 1726 Dihedral : 5.670 58.149 1615 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.98 % Allowed : 17.20 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.23), residues: 1301 helix: 2.22 (0.16), residues: 936 sheet: None (None), residues: 0 loop : 0.17 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 2 TYR 0.014 0.001 TYR Q 244 PHE 0.017 0.001 PHE L 62 TRP 0.015 0.001 TRP K 16 HIS 0.005 0.001 HIS Q 263 Details of bonding type rmsd covalent geometry : bond 0.00242 (10370) covalent geometry : angle 0.52479 (14103) hydrogen bonds : bond 0.04705 ( 728) hydrogen bonds : angle 4.53144 ( 2148) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 0.396 Fit side-chains REVERT: L 394 GLN cc_start: 0.8027 (pt0) cc_final: 0.7391 (pm20) REVERT: Q 231 GLU cc_start: 0.7487 (tp30) cc_final: 0.6995 (tt0) REVERT: Q 264 ARG cc_start: 0.7472 (mmm160) cc_final: 0.7068 (mtp85) REVERT: Q 317 LEU cc_start: 0.8261 (tt) cc_final: 0.8053 (tm) REVERT: Q 321 LYS cc_start: 0.8264 (mmtm) cc_final: 0.8057 (mmtm) REVERT: Q 323 ARG cc_start: 0.8138 (mpt90) cc_final: 0.7749 (mpt90) REVERT: J 18 ARG cc_start: 0.6251 (OUTLIER) cc_final: 0.5930 (mmm160) REVERT: J 47 ASN cc_start: 0.8060 (p0) cc_final: 0.7658 (p0) REVERT: J 91 ASP cc_start: 0.6980 (OUTLIER) cc_final: 0.6633 (m-30) REVERT: J 128 LYS cc_start: 0.8392 (mtpp) cc_final: 0.7628 (mttp) REVERT: J 145 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.7561 (m-80) outliers start: 21 outliers final: 12 residues processed: 208 average time/residue: 0.5008 time to fit residues: 112.0517 Evaluate side-chains 207 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain Q residue 314 LEU Chi-restraints excluded: chain Q residue 384 LYS Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 145 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 124 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 52 GLN ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Q 83 ASN Q 104 GLN Q 109 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.118833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.093361 restraints weight = 24901.889| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.65 r_work: 0.2756 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10370 Z= 0.159 Angle : 0.587 8.891 14103 Z= 0.303 Chirality : 0.041 0.304 1665 Planarity : 0.004 0.050 1726 Dihedral : 5.724 52.682 1613 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.70 % Allowed : 17.67 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.23), residues: 1301 helix: 2.08 (0.16), residues: 936 sheet: None (None), residues: 0 loop : 0.14 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 70 TYR 0.018 0.002 TYR Q 180 PHE 0.019 0.002 PHE L 54 TRP 0.013 0.001 TRP K 220 HIS 0.005 0.001 HIS Q 263 Details of bonding type rmsd covalent geometry : bond 0.00343 (10370) covalent geometry : angle 0.58690 (14103) hydrogen bonds : bond 0.05664 ( 728) hydrogen bonds : angle 4.67498 ( 2148) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.320 Fit side-chains REVERT: L 394 GLN cc_start: 0.8066 (pt0) cc_final: 0.7411 (pm20) REVERT: Q 264 ARG cc_start: 0.7473 (mmm160) cc_final: 0.7063 (mtp85) REVERT: Q 317 LEU cc_start: 0.8268 (tt) cc_final: 0.8024 (tm) REVERT: Q 321 LYS cc_start: 0.8280 (mmtm) cc_final: 0.8022 (mmtm) REVERT: Q 323 ARG cc_start: 0.8175 (mpt90) cc_final: 0.7768 (mpt90) REVERT: J 47 ASN cc_start: 0.8241 (p0) cc_final: 0.7968 (p0) REVERT: J 91 ASP cc_start: 0.7012 (OUTLIER) cc_final: 0.6684 (m-30) REVERT: J 128 LYS cc_start: 0.8432 (mtpp) cc_final: 0.7648 (mttp) REVERT: J 145 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.7628 (m-80) outliers start: 18 outliers final: 12 residues processed: 201 average time/residue: 0.5701 time to fit residues: 122.6811 Evaluate side-chains 203 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 189 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain Q residue 314 LEU Chi-restraints excluded: chain Q residue 384 LYS Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 145 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 110 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 124 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 52 GLN ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Q 83 ASN Q 104 GLN Q 109 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.118738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.093154 restraints weight = 26193.546| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 1.69 r_work: 0.2753 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10370 Z= 0.159 Angle : 0.589 8.933 14103 Z= 0.305 Chirality : 0.041 0.302 1665 Planarity : 0.004 0.049 1726 Dihedral : 5.750 52.251 1613 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.61 % Allowed : 17.96 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.23), residues: 1301 helix: 2.02 (0.16), residues: 936 sheet: None (None), residues: 0 loop : 0.13 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 70 TYR 0.017 0.002 TYR Q 180 PHE 0.023 0.002 PHE Q 54 TRP 0.014 0.001 TRP K 220 HIS 0.006 0.001 HIS Q 263 Details of bonding type rmsd covalent geometry : bond 0.00344 (10370) covalent geometry : angle 0.58858 (14103) hydrogen bonds : bond 0.05663 ( 728) hydrogen bonds : angle 4.69338 ( 2148) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4645.41 seconds wall clock time: 79 minutes 47.23 seconds (4787.23 seconds total)