Starting phenix.real_space_refine on Thu Jul 2 21:32:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v0s_26949/07_2026/7v0s_26949.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v0s_26949/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7v0s_26949/07_2026/7v0s_26949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v0s_26949/07_2026/7v0s_26949.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7v0s_26949/07_2026/7v0s_26949.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v0s_26949/07_2026/7v0s_26949.cif" model { file = "/net/cci-nas-00/data/ceres_data/7v0s_26949/07_2026/7v0s_26949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v0s_26949/07_2026/7v0s_26949.cif" } 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-dev-6108/lib/python3.11/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: 1 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: 2.70, per 1000 atoms: 0.26 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: 0.66 Conformation dependent library (CDL) restraints added in 480.1 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: 0.27 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: 1.77 Time building geometry restraints manager: 0.98 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: 5214 17.70 - 35.39: 548 35.39 - 53.09: 134 53.09 - 70.79: 35 70.79 - 88.49: 15 Dihedral angle restraints: 5946 sinusoidal: 2201 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 5943 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.490 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.290 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:8.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 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 : 16.592 88.487 3552 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/Z covalent geometry : bond 0.00426 / 0.24 (10370) covalent geometry : angle 0.72918 / 0.42 (14103) hydrogen bonds : bond 0.12042 / 7.76 ( 728) hydrogen bonds : angle 5.49008 / 4.04 ( 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 : 0.407 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: 0.5820 time to fit residues: 129.8145 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 : 0.391 ------------------------------------------------------------------------------- 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... ** 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 = 0.3257 r_free = 0.3257 target = 0.121436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.095717 restraints weight = 26078.996| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.72 r_work: 0.2796 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 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 = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.0734 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= 0.130 Angle : 0.530 7.236 14103 Z= 0.278 Chirality : 0.039 0.221 1665 Planarity : 0.004 0.051 1726 Dihedral : 6.058 56.496 1437 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.39 % Favored : 98.53 % Rotamer: Outliers : 2.84 % Allowed : 15.03 % Favored : 82.14 % 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 0.003 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 0.004 0.001 HIS J 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (10370) covalent geometry : angle 0.53011 / 0.28 (14103) hydrogen bonds : bond 0.05177 / 3.36 ( 728) hydrogen bonds : angle 4.68461 / 3.47 ( 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 224 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 0.496 Fit side-chains REVERT: K 200 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.6626 (mm110) REVERT: L 161 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8137 (mm-30) REVERT: L 394 GLN cc_start: 0.8045 (pt0) cc_final: 0.7337 (pm20) REVERT: L 404 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8399 (ttpp) REVERT: Q 264 ARG cc_start: 0.7492 (mtp180) cc_final: 0.7279 (mtm180) REVERT: Q 317 LEU cc_start: 0.8279 (tt) cc_final: 0.8058 (tm) REVERT: Q 323 ARG cc_start: 0.8178 (mpt90) cc_final: 0.7668 (mpt90) REVERT: J 47 ASN cc_start: 0.8024 (p0) cc_final: 0.7816 (p0) REVERT: J 110 LYS cc_start: 0.8126 (mtpt) cc_final: 0.7871 (mtpt) REVERT: J 164 ILE cc_start: 0.8006 (pt) cc_final: 0.7790 (pt) outliers start: 29 outliers final: 8 residues processed: 205 average time/residue: 0.5759 time to fit residues: 127.2210 Evaluate side-chains 200 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 190 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 111 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3194 r_free = 0.3194 target = 0.116823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.092210 restraints weight = 23818.437| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.67 r_work: 0.2733 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.0796 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 : 0.607 7.407 14103 Z= 0.318 Chirality : 0.043 0.222 1665 Planarity : 0.005 0.052 1726 Dihedral : 5.768 58.988 1414 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.50 % Allowed : 14.74 % 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: 2.08 (0.22), residues: 1301 helix: 1.90 (0.16), residues: 935 sheet: None (None), residues: 0 loop : 0.13 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 70 TYR 0.021 0.002 TYR Q 180 PHE 0.022 0.002 PHE L 54 TRP 0.009 0.002 TRP K 16 HIS 0.006 0.002 HIS Q 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (10370) covalent geometry : angle 0.60720 / 0.32 (14103) hydrogen bonds : bond 0.06299 / 4.08 ( 728) hydrogen bonds : angle 4.83065 / 3.58 ( 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 220 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 0.349 Fit side-chains REVERT: K 200 GLN cc_start: 0.6991 (OUTLIER) cc_final: 0.6465 (mm-40) REVERT: K 293 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8589 (tp) REVERT: L 161 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8106 (mm-30) REVERT: L 394 GLN cc_start: 0.8059 (pt0) cc_final: 0.7392 (pm20) REVERT: L 404 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8393 (ttpp) REVERT: Q 317 LEU cc_start: 0.8301 (tt) cc_final: 0.8038 (tm) REVERT: Q 323 ARG cc_start: 0.8193 (mpt90) cc_final: 0.7955 (mpt-90) REVERT: J 47 ASN cc_start: 0.8266 (p0) cc_final: 0.8004 (p0) REVERT: J 110 LYS cc_start: 0.8221 (mtpt) cc_final: 0.7938 (mtpt) outliers start: 36 outliers final: 20 residues processed: 200 average time/residue: 0.6118 time to fit residues: 131.4001 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 : 0.386 ------------------------------------------------------------------------------- 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 293 LEU Chi-restraints excluded: chain K residue 374 ILE 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 73 THR Chi-restraints excluded: chain J residue 120 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 95 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 27 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3236 r_free = 0.3236 target = 0.119935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.094451 restraints weight = 24531.138| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.65 r_work: 0.2779 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10370 Z= 0.135 Angle : 0.530 7.209 14103 Z= 0.277 Chirality : 0.039 0.187 1665 Planarity : 0.004 0.051 1726 Dihedral : 5.509 59.983 1414 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.65 % Allowed : 15.50 % Favored : 81.85 % 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: 2.35 (0.22), residues: 1301 helix: 2.12 (0.16), residues: 935 sheet: None (None), residues: 0 loop : 0.14 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 195 TYR 0.015 0.002 TYR Q 244 PHE 0.016 0.001 PHE L 54 TRP 0.012 0.001 TRP K 16 HIS 0.008 0.001 HIS Q 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (10370) covalent geometry : angle 0.52966 / 0.28 (14103) hydrogen bonds : bond 0.05202 / 3.37 ( 728) hydrogen bonds : angle 4.62469 / 3.43 ( 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 221 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.430 Fit side-chains REVERT: K 200 GLN cc_start: 0.6965 (OUTLIER) cc_final: 0.6586 (mm110) REVERT: L 161 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8106 (mm-30) REVERT: L 394 GLN cc_start: 0.8062 (pt0) cc_final: 0.7366 (pm20) REVERT: L 404 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8409 (ttpp) REVERT: Q 317 LEU cc_start: 0.8265 (tt) cc_final: 0.8045 (tm) REVERT: Q 323 ARG cc_start: 0.8172 (mpt90) cc_final: 0.7743 (mpt90) REVERT: J 47 ASN cc_start: 0.8153 (p0) cc_final: 0.7925 (p0) REVERT: J 91 ASP cc_start: 0.7023 (OUTLIER) cc_final: 0.6684 (m-30) REVERT: J 128 LYS cc_start: 0.8419 (mtpp) cc_final: 0.7685 (mttp) REVERT: J 145 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.7619 (m-80) outliers start: 27 outliers final: 15 residues processed: 204 average time/residue: 0.5682 time to fit residues: 125.0251 Evaluate side-chains 209 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 374 ILE Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 349 VAL 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 384 LYS Chi-restraints excluded: chain J residue 58 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 62 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 7 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.118024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.092432 restraints weight = 31634.887| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 1.98 r_work: 0.2728 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.0875 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= 0.158 Angle : 0.563 7.584 14103 Z= 0.295 Chirality : 0.041 0.227 1665 Planarity : 0.004 0.050 1726 Dihedral : 5.400 58.820 1412 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.50 % Allowed : 15.12 % 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: 2.25 (0.22), residues: 1301 helix: 2.05 (0.16), residues: 936 sheet: None (None), residues: 0 loop : 0.12 (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 0.020 0.002 PHE L 54 TRP 0.010 0.001 TRP K 16 HIS 0.007 0.001 HIS Q 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (10370) covalent geometry : angle 0.56320 / 0.29 (14103) hydrogen bonds : bond 0.05721 / 3.71 ( 728) hydrogen bonds : angle 4.69807 / 3.48 ( 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 228 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 0.439 Fit side-chains REVERT: K 200 GLN cc_start: 0.6996 (OUTLIER) cc_final: 0.6491 (mm-40) REVERT: L 394 GLN cc_start: 0.8104 (pt0) cc_final: 0.7384 (pm20) REVERT: L 404 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8446 (ttpp) REVERT: Q 85 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8735 (tp) REVERT: Q 317 LEU cc_start: 0.8294 (tt) cc_final: 0.8055 (tm) REVERT: Q 323 ARG cc_start: 0.8216 (mpt90) cc_final: 0.7775 (mpt90) REVERT: J 18 ARG cc_start: 0.6263 (OUTLIER) cc_final: 0.5917 (mmm160) REVERT: J 47 ASN cc_start: 0.8240 (p0) cc_final: 0.7991 (p0) REVERT: J 91 ASP cc_start: 0.7074 (OUTLIER) cc_final: 0.6748 (m-30) REVERT: J 145 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.7640 (m-80) outliers start: 37 outliers final: 20 residues processed: 209 average time/residue: 0.5985 time to fit residues: 134.5274 Evaluate side-chains 213 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 349 VAL 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 120 GLN 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: 6.9990 chunk 24 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Q 83 ASN Q 104 GLN Q 263 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.119428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.093798 restraints weight = 25077.652| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 1.66 r_work: 0.2768 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10370 Z= 0.141 Angle : 0.543 7.845 14103 Z= 0.283 Chirality : 0.040 0.233 1665 Planarity : 0.004 0.049 1726 Dihedral : 5.317 58.258 1412 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.93 % Allowed : 16.07 % Favored : 81.00 % 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: 2.33 (0.22), residues: 1301 helix: 2.12 (0.16), residues: 935 sheet: None (None), residues: 0 loop : 0.12 (0.32), residues: 366 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 0.018 0.002 PHE L 54 TRP 0.011 0.001 TRP K 16 HIS 0.006 0.001 HIS Q 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (10370) covalent geometry : angle 0.54260 / 0.28 (14103) hydrogen bonds : bond 0.05363 / 3.48 ( 728) hydrogen bonds : angle 4.63493 / 3.44 ( 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 223 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 0.403 Fit side-chains REVERT: K 200 GLN cc_start: 0.6966 (OUTLIER) cc_final: 0.6438 (mm-40) REVERT: K 235 LYS cc_start: 0.8256 (ttmt) cc_final: 0.8010 (tttt) REVERT: L 394 GLN cc_start: 0.8068 (pt0) cc_final: 0.7361 (pm20) REVERT: L 404 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8422 (ttpp) REVERT: Q 85 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8724 (tp) REVERT: Q 264 ARG cc_start: 0.7483 (mmm160) cc_final: 0.7052 (mtp85) REVERT: Q 317 LEU cc_start: 0.8279 (tt) cc_final: 0.8054 (tm) REVERT: Q 323 ARG cc_start: 0.8190 (mpt90) cc_final: 0.7761 (mpt90) REVERT: J 18 ARG cc_start: 0.6252 (OUTLIER) cc_final: 0.5908 (mmm160) REVERT: J 47 ASN cc_start: 0.8198 (p0) cc_final: 0.7935 (p0) REVERT: J 91 ASP cc_start: 0.7024 (OUTLIER) cc_final: 0.6694 (m-30) REVERT: J 128 LYS cc_start: 0.8400 (mtpp) cc_final: 0.7638 (mttp) REVERT: J 145 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.7614 (m-80) outliers start: 31 outliers final: 18 residues processed: 208 average time/residue: 0.5989 time to fit residues: 134.0191 Evaluate side-chains 214 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 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 349 VAL 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 73 THR Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 120 GLN 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: 6.9990 chunk 99 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3204 r_free = 0.3204 target = 0.117565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.092033 restraints weight = 25648.890| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 1.67 r_work: 0.2735 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2608 r_free = 0.2608 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2608 r_free = 0.2608 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.0938 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= 0.174 Angle : 0.589 7.773 14103 Z= 0.307 Chirality : 0.042 0.262 1665 Planarity : 0.004 0.051 1726 Dihedral : 5.414 57.738 1412 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.21 % Allowed : 15.97 % 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: 2.16 (0.22), residues: 1301 helix: 1.98 (0.16), residues: 936 sheet: None (None), residues: 0 loop : 0.08 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 70 TYR 0.019 0.002 TYR Q 180 PHE 0.020 0.002 PHE L 54 TRP 0.010 0.001 TRP K 220 HIS 0.004 0.001 HIS L 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (10370) covalent geometry : angle 0.58872 / 0.31 (14103) hydrogen bonds : bond 0.05941 / 3.85 ( 728) hydrogen bonds : angle 4.74496 / 3.52 ( 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 226 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 0.422 Fit side-chains REVERT: K 200 GLN cc_start: 0.6996 (OUTLIER) cc_final: 0.6463 (mm-40) REVERT: L 394 GLN cc_start: 0.8074 (pt0) cc_final: 0.7409 (pm20) REVERT: L 404 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8414 (ttpp) REVERT: Q 85 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8722 (tp) REVERT: Q 264 ARG cc_start: 0.7482 (mmm160) cc_final: 0.7065 (mtp85) REVERT: Q 317 LEU cc_start: 0.8286 (tt) cc_final: 0.8022 (tm) REVERT: Q 321 LYS cc_start: 0.8322 (mmtm) cc_final: 0.8119 (mmtm) REVERT: Q 323 ARG cc_start: 0.8185 (mpt90) cc_final: 0.7758 (mpt90) REVERT: J 18 ARG cc_start: 0.6288 (OUTLIER) cc_final: 0.5951 (mmm160) REVERT: J 47 ASN cc_start: 0.8292 (p0) cc_final: 0.8013 (p0) REVERT: J 91 ASP cc_start: 0.7059 (OUTLIER) cc_final: 0.6726 (m-30) REVERT: J 145 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.7683 (m-80) outliers start: 34 outliers final: 20 residues processed: 210 average time/residue: 0.6023 time to fit residues: 135.9646 Evaluate side-chains 212 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 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 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 120 GLN 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: 0.9990 chunk 78 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3226 r_free = 0.3226 target = 0.119250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.093520 restraints weight = 25416.890| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.68 r_work: 0.2765 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10370 Z= 0.142 Angle : 0.556 8.243 14103 Z= 0.288 Chirality : 0.040 0.257 1665 Planarity : 0.004 0.049 1726 Dihedral : 5.294 57.596 1412 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.84 % Allowed : 16.64 % Favored : 80.53 % 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: 2.09 (0.16), residues: 935 sheet: None (None), residues: 0 loop : 0.11 (0.31), residues: 366 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 0.017 0.002 PHE L 54 TRP 0.012 0.001 TRP K 220 HIS 0.004 0.001 HIS J 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (10370) covalent geometry : angle 0.55590 / 0.29 (14103) hydrogen bonds : bond 0.05384 / 3.49 ( 728) hydrogen bonds : angle 4.64712 / 3.44 ( 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 217 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 0.425 Fit side-chains REVERT: K 200 GLN cc_start: 0.6989 (OUTLIER) cc_final: 0.6467 (mm-40) REVERT: L 394 GLN cc_start: 0.8071 (pt0) cc_final: 0.7356 (pm20) REVERT: L 404 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8420 (ttpp) REVERT: Q 85 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8734 (tp) REVERT: Q 264 ARG cc_start: 0.7482 (mmm160) cc_final: 0.7084 (mtp85) REVERT: Q 317 LEU cc_start: 0.8276 (tt) cc_final: 0.8048 (tm) REVERT: Q 321 LYS cc_start: 0.8322 (mmtm) cc_final: 0.8068 (mmtm) REVERT: Q 323 ARG cc_start: 0.8190 (mpt90) cc_final: 0.7764 (mpt90) REVERT: J 18 ARG cc_start: 0.6255 (OUTLIER) cc_final: 0.5916 (mmm160) REVERT: J 47 ASN cc_start: 0.8200 (p0) cc_final: 0.7936 (p0) REVERT: J 91 ASP cc_start: 0.7006 (OUTLIER) cc_final: 0.6664 (m-30) REVERT: J 128 LYS cc_start: 0.8411 (mtpp) cc_final: 0.7632 (mttp) REVERT: J 145 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.7619 (m-80) outliers start: 30 outliers final: 20 residues processed: 202 average time/residue: 0.6118 time to fit residues: 132.8960 Evaluate side-chains 211 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 119 ASP 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 120 GLN 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: 9.9990 chunk 31 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.116802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.091379 restraints weight = 24322.600| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.63 r_work: 0.2730 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.0979 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= 0.191 Angle : 0.622 8.654 14103 Z= 0.322 Chirality : 0.043 0.308 1665 Planarity : 0.004 0.050 1726 Dihedral : 5.433 57.432 1412 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.84 % Allowed : 16.54 % 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: 2.07 (0.22), residues: 1301 helix: 1.91 (0.16), residues: 936 sheet: None (None), residues: 0 loop : 0.06 (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 L 180 PHE 0.021 0.002 PHE L 54 TRP 0.013 0.002 TRP K 220 HIS 0.004 0.001 HIS L 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (10370) covalent geometry : angle 0.62181 / 0.32 (14103) hydrogen bonds : bond 0.06163 / 3.99 ( 728) hydrogen bonds : angle 4.79181 / 3.55 ( 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 214 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.405 Fit side-chains REVERT: K 200 GLN cc_start: 0.6972 (OUTLIER) cc_final: 0.6449 (mm-40) REVERT: L 394 GLN cc_start: 0.8072 (pt0) cc_final: 0.7410 (pm20) REVERT: L 404 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8413 (ttpp) REVERT: Q 317 LEU cc_start: 0.8293 (tt) cc_final: 0.8030 (tm) REVERT: Q 321 LYS cc_start: 0.8328 (mmtm) cc_final: 0.8110 (mmtm) REVERT: Q 323 ARG cc_start: 0.8193 (mpt90) cc_final: 0.7972 (mpt-90) REVERT: J 47 ASN cc_start: 0.8321 (p0) cc_final: 0.8046 (p0) REVERT: J 91 ASP cc_start: 0.7017 (OUTLIER) cc_final: 0.6665 (m-30) REVERT: J 128 LYS cc_start: 0.8451 (mtpp) cc_final: 0.7661 (mttp) REVERT: J 145 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.7699 (m-80) outliers start: 30 outliers final: 19 residues processed: 199 average time/residue: 0.5808 time to fit residues: 124.3045 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 : 0.410 ------------------------------------------------------------------------------- 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 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 120 GLN 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: 20.0000 chunk 64 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 75 optimal weight: 0.0870 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 J 103 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.118317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.092962 restraints weight = 24821.420| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 1.65 r_work: 0.2750 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.0959 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= 0.160 Angle : 0.590 9.038 14103 Z= 0.305 Chirality : 0.041 0.312 1665 Planarity : 0.004 0.049 1726 Dihedral : 5.334 57.442 1412 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.46 % Allowed : 16.73 % 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: 2.17 (0.22), residues: 1301 helix: 1.98 (0.16), residues: 936 sheet: None (None), residues: 0 loop : 0.08 (0.31), 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 0.021 0.002 PHE Q 54 TRP 0.015 0.001 TRP K 220 HIS 0.004 0.001 HIS J 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (10370) covalent geometry : angle 0.59018 / 0.30 (14103) hydrogen bonds : bond 0.05705 / 3.70 ( 728) hydrogen bonds : angle 4.71921 / 3.50 ( 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 215 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.400 Fit side-chains REVERT: K 200 GLN cc_start: 0.6970 (OUTLIER) cc_final: 0.6458 (mm-40) REVERT: L 394 GLN cc_start: 0.8058 (pt0) cc_final: 0.7331 (pm20) REVERT: L 404 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8416 (ttpp) REVERT: Q 264 ARG cc_start: 0.7464 (mmm160) cc_final: 0.7039 (mtp85) REVERT: Q 317 LEU cc_start: 0.8271 (tt) cc_final: 0.8021 (tm) REVERT: Q 321 LYS cc_start: 0.8316 (mmtm) cc_final: 0.8058 (mmtm) REVERT: Q 323 ARG cc_start: 0.8173 (mpt90) cc_final: 0.7734 (mpt90) REVERT: J 47 ASN cc_start: 0.8250 (p0) cc_final: 0.7978 (p0) REVERT: J 91 ASP cc_start: 0.7005 (OUTLIER) cc_final: 0.6652 (m-30) REVERT: J 128 LYS cc_start: 0.8412 (mtpp) cc_final: 0.7627 (mttp) REVERT: J 145 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.7622 (m-80) outliers start: 26 outliers final: 19 residues processed: 201 average time/residue: 0.5584 time to fit residues: 120.5600 Evaluate side-chains 209 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 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 120 GLN 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: 9.9990 chunk 49 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 124 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.116937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.091309 restraints weight = 26134.936| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.69 r_work: 0.2728 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.0984 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= 0.188 Angle : 0.622 8.985 14103 Z= 0.322 Chirality : 0.043 0.319 1665 Planarity : 0.004 0.051 1726 Dihedral : 5.402 57.377 1412 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.55 % Allowed : 16.82 % 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: 2.04 (0.22), residues: 1301 helix: 1.88 (0.16), residues: 936 sheet: None (None), residues: 0 loop : 0.06 (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 L 180 PHE 0.021 0.002 PHE L 54 TRP 0.015 0.002 TRP K 220 HIS 0.005 0.001 HIS L 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (10370) covalent geometry : angle 0.62183 / 0.32 (14103) hydrogen bonds : bond 0.06103 / 3.96 ( 728) hydrogen bonds : angle 4.79577 / 3.55 ( 2148) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5158.85 seconds wall clock time: 88 minutes 49.21 seconds (5329.21 seconds total)