Starting phenix.real_space_refine on Mon Jul 28 13:52:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v0s_26949/07_2025/7v0s_26949.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v0s_26949/07_2025/7v0s_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_2025/7v0s_26949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v0s_26949/07_2025/7v0s_26949.map" model { file = "/net/cci-nas-00/data/ceres_data/7v0s_26949/07_2025/7v0s_26949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v0s_26949/07_2025/7v0s_26949.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10303 Number of models: 1 Model: "" Number of chains: 10 Chain: "K" Number of atoms: 2954 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 380, 2919 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 365} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 380, 2919 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 365} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 2949 Chain: "L" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2938 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 2954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2954 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 378} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1191 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "L" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'AJP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 24 Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "L" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Chain: "Q" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "J" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ATYR K 34 " occ=0.42 ... (22 atoms not shown) pdb=" OH BTYR K 34 " occ=0.58 residue: pdb=" N APHE K 239 " occ=0.58 ... (20 atoms not shown) pdb=" CZ BPHE K 239 " occ=0.42 residue: pdb=" N ATYR K 242 " occ=0.62 ... (22 atoms not shown) pdb=" OH BTYR K 242 " occ=0.38 Time building chain proxies: 8.78, per 1000 atoms: 0.85 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: 2.68 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 0.90 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: 3.29 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1589 1.32 - 1.45: 2820 1.45 - 1.57: 5839 1.57 - 1.70: 0 1.70 - 1.82: 122 Bond restraints: 10370 Sorted by residual: bond pdb=" C PRO Q 293 " pdb=" O PRO Q 293 " ideal model delta sigma weight residual 1.237 1.194 0.043 1.26e-02 6.30e+03 1.17e+01 bond pdb=" N THR Q 315 " pdb=" CA THR Q 315 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.04e-02 9.25e+03 1.11e+01 bond pdb=" N LEU Q 322 " pdb=" CA LEU Q 322 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.32e-02 5.74e+03 9.13e+00 bond pdb=" N ILE Q 346 " pdb=" CA ILE Q 346 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.23e+00 bond pdb=" N LEU Q 314 " pdb=" CA LEU Q 314 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.23e-02 6.61e+03 6.79e+00 ... (remaining 10365 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 13748 2.01 - 4.03: 291 4.03 - 6.04: 46 6.04 - 8.05: 14 8.05 - 10.07: 4 Bond angle restraints: 14103 Sorted by residual: angle pdb=" C BTYR K 34 " pdb=" N ASP K 35 " pdb=" CA ASP K 35 " ideal model delta sigma weight residual 121.70 129.19 -7.49 1.80e+00 3.09e-01 1.73e+01 angle pdb=" N SER Q 354 " pdb=" CA SER Q 354 " pdb=" C SER Q 354 " ideal model delta sigma weight residual 109.85 116.17 -6.32 1.58e+00 4.01e-01 1.60e+01 angle pdb=" N GLY Q 284 " pdb=" CA GLY Q 284 " pdb=" C GLY Q 284 " ideal model delta sigma weight residual 112.50 116.74 -4.24 1.16e+00 7.43e-01 1.34e+01 angle pdb=" C THR Q 319 " pdb=" N THR Q 320 " pdb=" CA THR Q 320 " ideal model delta sigma weight residual 122.60 116.31 6.29 1.88e+00 2.83e-01 1.12e+01 angle pdb=" CA GLY Q 345 " pdb=" C GLY Q 345 " pdb=" O GLY Q 345 " ideal model delta sigma weight residual 120.75 117.32 3.43 1.03e+00 9.43e-01 1.11e+01 ... (remaining 14098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 5392 17.70 - 35.39: 569 35.39 - 53.09: 138 53.09 - 70.79: 35 70.79 - 88.49: 15 Dihedral angle restraints: 6149 sinusoidal: 2404 harmonic: 3745 Sorted by residual: dihedral pdb=" CA TRP L 403 " pdb=" C TRP L 403 " pdb=" N LYS L 404 " pdb=" CA LYS L 404 " ideal model delta harmonic sigma weight residual 180.00 162.75 17.25 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA TRP Q 403 " pdb=" C TRP Q 403 " pdb=" N LYS Q 404 " pdb=" CA LYS Q 404 " ideal model delta harmonic sigma weight residual 180.00 163.10 16.90 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA PHE L 23 " pdb=" C PHE L 23 " pdb=" N VAL L 24 " pdb=" CA VAL L 24 " ideal model delta harmonic sigma weight residual -180.00 -163.80 -16.20 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 6146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1416 0.063 - 0.125: 230 0.125 - 0.188: 15 0.188 - 0.251: 3 0.251 - 0.314: 1 Chirality restraints: 1665 Sorted by residual: chirality pdb=" CG LEU K 386 " pdb=" CB LEU K 386 " pdb=" CD1 LEU K 386 " pdb=" CD2 LEU K 386 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C11 AJP Q 501 " pdb=" C10 AJP Q 501 " pdb=" C12 AJP Q 501 " pdb=" C16 AJP Q 501 " both_signs ideal model delta sigma weight residual False 2.20 2.45 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" C08 AJP Q 501 " pdb=" C07 AJP Q 501 " pdb=" C10 AJP Q 501 " pdb=" O09 AJP Q 501 " both_signs ideal model delta sigma weight residual False 2.56 2.79 -0.22 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1662 not shown) Planarity restraints: 1726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP K 220 " 0.038 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO K 221 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO K 221 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO K 221 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY Q 352 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.51e+00 pdb=" C GLY Q 352 " -0.032 2.00e-02 2.50e+03 pdb=" O GLY Q 352 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA Q 353 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP Q 222 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO Q 223 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO Q 223 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO Q 223 " 0.025 5.00e-02 4.00e+02 ... (remaining 1723 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1125 2.75 - 3.28: 10814 3.28 - 3.82: 20111 3.82 - 4.36: 23717 4.36 - 4.90: 39586 Nonbonded interactions: 95353 Sorted by model distance: nonbonded pdb=" OE2 GLU Q 202 " pdb=" O HOH Q 601 " model vdw 2.208 3.040 nonbonded pdb=" NH2 ARG K 70 " pdb=" O GLY J 155 " model vdw 2.232 3.120 nonbonded pdb=" O SER Q 367 " pdb=" OG1 THR Q 371 " model vdw 2.263 3.040 nonbonded pdb=" OG SER K 284 " pdb=" O HOH K 501 " model vdw 2.268 3.040 nonbonded pdb=" O HOH L 659 " pdb=" O HOH Q 643 " model vdw 2.271 3.040 ... (remaining 95348 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'L' and resid 1 through 409) selection = (chain 'Q' and (resid 1 through 26 or resid 48 through 409)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 46.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.220 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10370 Z= 0.239 Angle : 0.729 10.067 14103 Z= 0.424 Chirality : 0.045 0.314 1665 Planarity : 0.005 0.057 1726 Dihedral : 16.386 88.487 3755 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.09 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (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 TRP 0.012 0.002 TRP K 16 HIS 0.007 0.001 HIS J 162 PHE 0.017 0.002 PHE L 54 TYR 0.018 0.002 TYR Q 180 ARG 0.004 0.000 ARG Q 195 Details of bonding type rmsd hydrogen bonds : bond 0.12042 ( 728) hydrogen bonds : angle 5.49008 ( 2148) covalent geometry : bond 0.00426 (10370) covalent geometry : angle 0.72918 (14103) *********************** 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 : 0.970 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: 1.3927 time to fit residues: 309.7013 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 : 1.198 ------------------------------------------------------------------------------- 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 109 optimal weight: 0.4980 chunk 98 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 52 GLN ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Q 55 GLN 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 = 0.3207 r_free = 0.3207 target = 0.117746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.091280 restraints weight = 28920.111| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 1.81 r_work: 0.2728 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.0673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10370 Z= 0.169 Angle : 0.581 7.498 14103 Z= 0.307 Chirality : 0.041 0.247 1665 Planarity : 0.005 0.051 1726 Dihedral : 6.865 58.307 1640 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.62 % Favored : 98.30 % Rotamer: Outliers : 3.02 % Allowed : 15.03 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.22), residues: 1301 helix: 1.88 (0.16), residues: 934 sheet: None (None), residues: 0 loop : 0.21 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 16 HIS 0.006 0.001 HIS Q 263 PHE 0.020 0.002 PHE L 54 TYR 0.020 0.002 TYR Q 180 ARG 0.003 0.000 ARG K 70 Details of bonding type rmsd hydrogen bonds : bond 0.05982 ( 728) hydrogen bonds : angle 4.82255 ( 2148) covalent geometry : bond 0.00363 (10370) covalent geometry : angle 0.58129 (14103) *********************** 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 220 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 1.200 Fit side-chains REVERT: K 189 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7517 (mmmm) REVERT: K 200 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6551 (mm-40) REVERT: L 161 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8165 (mm-30) REVERT: L 394 GLN cc_start: 0.8097 (pt0) cc_final: 0.7373 (pm20) REVERT: L 404 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8422 (ttpp) REVERT: Q 264 ARG cc_start: 0.7518 (mtp180) cc_final: 0.7308 (mtm180) REVERT: Q 317 LEU cc_start: 0.8334 (tt) cc_final: 0.8086 (tm) REVERT: Q 323 ARG cc_start: 0.8207 (mpt90) cc_final: 0.7726 (mpt90) REVERT: J 47 ASN cc_start: 0.8186 (p0) cc_final: 0.7957 (p0) REVERT: J 110 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7922 (mtpt) outliers start: 31 outliers final: 15 residues processed: 200 average time/residue: 1.2209 time to fit residues: 262.7229 Evaluate side-chains 203 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 189 LYS 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 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 119 ASP 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 J residue 58 VAL Chi-restraints excluded: chain J residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 55 optimal weight: 0.2980 chunk 124 optimal weight: 20.0000 chunk 120 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 233 GLN ** K 405 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.123697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.098773 restraints weight = 21993.129| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.56 r_work: 0.2851 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2733 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10370 Z= 0.116 Angle : 0.498 7.116 14103 Z= 0.260 Chirality : 0.038 0.192 1665 Planarity : 0.004 0.051 1726 Dihedral : 5.927 59.736 1620 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.24 % Favored : 98.69 % Rotamer: Outliers : 2.27 % Allowed : 15.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.22), residues: 1301 helix: 2.22 (0.16), residues: 935 sheet: None (None), residues: 0 loop : 0.25 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 16 HIS 0.005 0.001 HIS J 162 PHE 0.013 0.001 PHE L 62 TYR 0.016 0.001 TYR Q 244 ARG 0.002 0.000 ARG Q 2 Details of bonding type rmsd hydrogen bonds : bond 0.04665 ( 728) hydrogen bonds : angle 4.54157 ( 2148) covalent geometry : bond 0.00225 (10370) covalent geometry : angle 0.49828 (14103) *********************** 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 226 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 1.039 Fit side-chains REVERT: L 394 GLN cc_start: 0.7997 (pt0) cc_final: 0.7376 (pm20) REVERT: Q 231 GLU cc_start: 0.7509 (tp30) cc_final: 0.6956 (tt0) REVERT: Q 264 ARG cc_start: 0.7481 (mtp180) cc_final: 0.7276 (mmm160) REVERT: Q 323 ARG cc_start: 0.8154 (mpt90) cc_final: 0.7731 (mpt90) REVERT: J 47 ASN cc_start: 0.7993 (p0) cc_final: 0.7726 (p0) REVERT: J 128 LYS cc_start: 0.8321 (mtpp) cc_final: 0.7599 (mttp) REVERT: J 164 ILE cc_start: 0.7960 (pt) cc_final: 0.7733 (pt) outliers start: 23 outliers final: 10 residues processed: 210 average time/residue: 1.1588 time to fit residues: 262.7027 Evaluate side-chains 203 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 193 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 249 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain Q residue 314 LEU Chi-restraints excluded: chain J residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 76 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 112 optimal weight: 0.0470 chunk 4 optimal weight: 0.4980 chunk 16 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 25 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 overall best weight: 2.6882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Q 83 ASN Q 104 GLN Q 155 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.118091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.091784 restraints weight = 32276.119| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.12 r_work: 0.2701 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.0857 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 : 0.568 7.273 14103 Z= 0.296 Chirality : 0.041 0.224 1665 Planarity : 0.004 0.051 1726 Dihedral : 6.165 59.968 1617 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.12 % Allowed : 15.41 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.22), residues: 1301 helix: 2.09 (0.16), residues: 936 sheet: None (None), residues: 0 loop : 0.17 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 16 HIS 0.005 0.001 HIS J 162 PHE 0.020 0.002 PHE L 54 TYR 0.019 0.002 TYR Q 180 ARG 0.003 0.000 ARG K 70 Details of bonding type rmsd hydrogen bonds : bond 0.05759 ( 728) hydrogen bonds : angle 4.69518 ( 2148) covalent geometry : bond 0.00342 (10370) covalent geometry : angle 0.56809 (14103) *********************** 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 226 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 1.136 Fit side-chains REVERT: K 200 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.6570 (mm-40) REVERT: L 394 GLN cc_start: 0.8148 (pt0) cc_final: 0.7439 (pm20) REVERT: L 404 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8509 (ttpp) REVERT: Q 264 ARG cc_start: 0.7600 (mtp180) cc_final: 0.7372 (mmm160) REVERT: Q 323 ARG cc_start: 0.8239 (mpt90) cc_final: 0.7795 (mpt90) REVERT: J 47 ASN cc_start: 0.8257 (p0) cc_final: 0.8008 (p0) REVERT: J 145 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.7637 (m-80) outliers start: 32 outliers final: 16 residues processed: 209 average time/residue: 1.2449 time to fit residues: 280.4840 Evaluate side-chains 206 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 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 J residue 58 VAL Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 120 GLN 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 111 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3185 r_free = 0.3185 target = 0.116164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.092397 restraints weight = 19934.647| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 1.51 r_work: 0.2731 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10370 Z= 0.204 Angle : 0.622 7.442 14103 Z= 0.325 Chirality : 0.044 0.258 1665 Planarity : 0.005 0.051 1726 Dihedral : 6.304 58.509 1615 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.31 % Allowed : 15.78 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.22), residues: 1301 helix: 1.89 (0.16), residues: 936 sheet: None (None), residues: 0 loop : 0.07 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP Q 219 HIS 0.005 0.001 HIS Q 263 PHE 0.023 0.002 PHE L 54 TYR 0.020 0.002 TYR Q 180 ARG 0.003 0.000 ARG K 70 Details of bonding type rmsd hydrogen bonds : bond 0.06352 ( 728) hydrogen bonds : angle 4.82959 ( 2148) covalent geometry : bond 0.00457 (10370) covalent geometry : angle 0.62169 (14103) *********************** 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 221 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 1.121 Fit side-chains REVERT: K 200 GLN cc_start: 0.6993 (OUTLIER) cc_final: 0.6456 (mm-40) REVERT: L 394 GLN cc_start: 0.8049 (pt0) cc_final: 0.7390 (pm20) REVERT: L 404 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8389 (ttpp) REVERT: Q 264 ARG cc_start: 0.7498 (mtp180) cc_final: 0.7277 (mmm160) REVERT: Q 323 ARG cc_start: 0.8189 (mpt90) cc_final: 0.7965 (mpt-90) REVERT: J 47 ASN cc_start: 0.8327 (p0) cc_final: 0.8054 (p0) REVERT: J 91 ASP cc_start: 0.7023 (OUTLIER) cc_final: 0.6690 (m-30) REVERT: J 145 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.7695 (m-80) outliers start: 35 outliers final: 18 residues processed: 202 average time/residue: 1.3225 time to fit residues: 286.8610 Evaluate side-chains 204 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 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 8 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 58 optimal weight: 0.4980 chunk 105 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 32 optimal weight: 30.0000 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 224 ASN 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 = 0.3208 r_free = 0.3208 target = 0.117840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.093268 restraints weight = 24770.490| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 1.68 r_work: 0.2747 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.0908 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= 0.164 Angle : 0.578 7.882 14103 Z= 0.302 Chirality : 0.041 0.257 1665 Planarity : 0.004 0.051 1726 Dihedral : 6.098 58.319 1615 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.02 % Allowed : 16.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.22), residues: 1301 helix: 1.95 (0.16), residues: 936 sheet: None (None), residues: 0 loop : 0.07 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 220 HIS 0.004 0.001 HIS J 162 PHE 0.020 0.002 PHE Q 54 TYR 0.018 0.002 TYR Q 180 ARG 0.003 0.000 ARG K 70 Details of bonding type rmsd hydrogen bonds : bond 0.05798 ( 728) hydrogen bonds : angle 4.73685 ( 2148) covalent geometry : bond 0.00354 (10370) covalent geometry : angle 0.57839 (14103) *********************** 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: 32 poor density : 191 time to evaluate : 1.063 Fit side-chains REVERT: K 200 GLN cc_start: 0.6996 (OUTLIER) cc_final: 0.6468 (mm-40) REVERT: L 394 GLN cc_start: 0.8051 (pt0) cc_final: 0.7341 (pm20) REVERT: L 404 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8413 (ttpp) REVERT: Q 85 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8710 (tp) REVERT: Q 264 ARG cc_start: 0.7516 (mtp180) cc_final: 0.7272 (mmm160) REVERT: Q 321 LYS cc_start: 0.8366 (mmtm) cc_final: 0.8155 (mmtm) REVERT: Q 323 ARG cc_start: 0.8192 (mpt90) cc_final: 0.7726 (mpt90) REVERT: J 18 ARG cc_start: 0.6254 (OUTLIER) cc_final: 0.5917 (mmm160) REVERT: J 47 ASN cc_start: 0.8248 (p0) cc_final: 0.7992 (p0) REVERT: J 91 ASP cc_start: 0.7030 (OUTLIER) cc_final: 0.6703 (m-30) REVERT: J 128 LYS cc_start: 0.8432 (mtpp) cc_final: 0.7654 (mttp) REVERT: J 145 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.7638 (m-80) outliers start: 32 outliers final: 20 residues processed: 208 average time/residue: 1.2739 time to fit residues: 284.6212 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 : 1.296 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 2 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 117 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Q 83 ASN Q 104 GLN 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 = 0.3189 r_free = 0.3189 target = 0.116436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.092764 restraints weight = 18947.898| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 1.41 r_work: 0.2751 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.0965 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= 0.193 Angle : 0.614 7.787 14103 Z= 0.321 Chirality : 0.043 0.289 1665 Planarity : 0.004 0.050 1726 Dihedral : 6.233 57.812 1615 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.84 % Allowed : 16.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.22), residues: 1301 helix: 1.84 (0.16), residues: 936 sheet: None (None), residues: 0 loop : 0.03 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 220 HIS 0.005 0.001 HIS L 325 PHE 0.022 0.002 PHE L 54 TYR 0.020 0.002 TYR L 180 ARG 0.003 0.000 ARG K 70 Details of bonding type rmsd hydrogen bonds : bond 0.06212 ( 728) hydrogen bonds : angle 4.81641 ( 2148) covalent geometry : bond 0.00429 (10370) covalent geometry : angle 0.61401 (14103) *********************** 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 220 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 1.080 Fit side-chains REVERT: K 200 GLN cc_start: 0.6965 (OUTLIER) cc_final: 0.6437 (mm-40) REVERT: L 394 GLN cc_start: 0.8042 (pt0) cc_final: 0.7387 (pm20) REVERT: L 404 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8371 (ttpp) REVERT: Q 264 ARG cc_start: 0.7500 (mtp180) cc_final: 0.7269 (mmm160) REVERT: Q 321 LYS cc_start: 0.8372 (mmtm) cc_final: 0.8096 (mmtm) REVERT: Q 323 ARG cc_start: 0.8175 (mpt90) cc_final: 0.7946 (mpt-90) REVERT: J 47 ASN cc_start: 0.8306 (p0) cc_final: 0.8040 (p0) REVERT: J 91 ASP cc_start: 0.6985 (OUTLIER) cc_final: 0.6655 (m-30) REVERT: J 145 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.7709 (m-80) outliers start: 30 outliers final: 20 residues processed: 202 average time/residue: 1.3143 time to fit residues: 284.6144 Evaluate side-chains 211 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 74 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 19 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 109 optimal weight: 0.0270 chunk 25 optimal weight: 5.9990 chunk 55 optimal weight: 0.2980 chunk 112 optimal weight: 2.9990 overall best weight: 1.8644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Q 83 ASN Q 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.119751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.094424 restraints weight = 24738.213| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.64 r_work: 0.2778 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 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 = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.0957 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= 0.140 Angle : 0.551 8.074 14103 Z= 0.287 Chirality : 0.040 0.269 1665 Planarity : 0.004 0.048 1726 Dihedral : 5.888 57.668 1615 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.93 % Allowed : 16.16 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.23), residues: 1301 helix: 2.07 (0.16), residues: 935 sheet: None (None), residues: 0 loop : 0.10 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 220 HIS 0.004 0.001 HIS J 162 PHE 0.020 0.002 PHE Q 54 TYR 0.015 0.002 TYR Q 180 ARG 0.002 0.000 ARG K 70 Details of bonding type rmsd hydrogen bonds : bond 0.05304 ( 728) hydrogen bonds : angle 4.64581 ( 2148) covalent geometry : bond 0.00291 (10370) covalent geometry : angle 0.55137 (14103) *********************** 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 225 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 1.279 Fit side-chains REVERT: K 200 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6444 (mm-40) REVERT: L 394 GLN cc_start: 0.8049 (pt0) cc_final: 0.7328 (pm20) REVERT: L 404 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8397 (ttpp) REVERT: Q 264 ARG cc_start: 0.7546 (mtp180) cc_final: 0.7286 (mmm160) REVERT: Q 323 ARG cc_start: 0.8173 (mpt90) cc_final: 0.7760 (mpt90) REVERT: J 18 ARG cc_start: 0.6253 (OUTLIER) cc_final: 0.5923 (mmm160) REVERT: J 47 ASN cc_start: 0.8186 (p0) cc_final: 0.7912 (p0) REVERT: J 91 ASP cc_start: 0.7016 (OUTLIER) cc_final: 0.6675 (m-30) REVERT: J 128 LYS cc_start: 0.8413 (mtpp) cc_final: 0.7624 (mttp) REVERT: J 145 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.7610 (m-80) outliers start: 31 outliers final: 18 residues processed: 211 average time/residue: 1.5314 time to fit residues: 346.4955 Evaluate side-chains 211 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 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 192 SER 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 74 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 62 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 0.0050 chunk 81 optimal weight: 5.9990 chunk 121 optimal weight: 30.0000 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Q 83 ASN Q 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.121397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.096784 restraints weight = 19112.132| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.44 r_work: 0.2822 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10370 Z= 0.129 Angle : 0.542 8.412 14103 Z= 0.279 Chirality : 0.039 0.283 1665 Planarity : 0.004 0.048 1726 Dihedral : 5.697 57.207 1615 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.27 % Allowed : 17.58 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.23), residues: 1301 helix: 2.17 (0.16), residues: 936 sheet: None (None), residues: 0 loop : 0.16 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 220 HIS 0.004 0.001 HIS J 162 PHE 0.018 0.001 PHE Q 54 TYR 0.016 0.002 TYR Q 244 ARG 0.001 0.000 ARG K 70 Details of bonding type rmsd hydrogen bonds : bond 0.04996 ( 728) hydrogen bonds : angle 4.56450 ( 2148) covalent geometry : bond 0.00261 (10370) covalent geometry : angle 0.54197 (14103) *********************** 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 219 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 1.280 Fit side-chains REVERT: K 200 GLN cc_start: 0.6912 (OUTLIER) cc_final: 0.6394 (mm-40) REVERT: L 394 GLN cc_start: 0.8021 (pt0) cc_final: 0.7362 (pm20) REVERT: L 404 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8369 (ttpp) REVERT: Q 85 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8562 (tp) REVERT: Q 264 ARG cc_start: 0.7538 (mtp180) cc_final: 0.7284 (mmm160) REVERT: Q 321 LYS cc_start: 0.8293 (mmtm) cc_final: 0.8020 (mmtm) REVERT: Q 323 ARG cc_start: 0.8117 (mpt90) cc_final: 0.7732 (mpt90) REVERT: J 18 ARG cc_start: 0.6221 (OUTLIER) cc_final: 0.5885 (mmm160) REVERT: J 47 ASN cc_start: 0.8136 (p0) cc_final: 0.7888 (p0) REVERT: J 91 ASP cc_start: 0.6922 (OUTLIER) cc_final: 0.6573 (m-30) REVERT: J 128 LYS cc_start: 0.8374 (mtpp) cc_final: 0.7621 (mttp) REVERT: J 145 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.7561 (m-80) outliers start: 24 outliers final: 14 residues processed: 207 average time/residue: 1.2726 time to fit residues: 282.8253 Evaluate side-chains 213 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 290 SER Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 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 J residue 18 ARG Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 145 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 21 optimal weight: 0.0470 chunk 37 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 overall best weight: 2.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Q 83 ASN Q 104 GLN Q 109 ASN J 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.119241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.093245 restraints weight = 29169.236| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.94 r_work: 0.2742 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- 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 = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.0962 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= 0.153 Angle : 0.580 8.896 14103 Z= 0.299 Chirality : 0.041 0.293 1665 Planarity : 0.004 0.049 1726 Dihedral : 5.848 56.822 1615 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.17 % Allowed : 17.67 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.23), residues: 1301 helix: 2.05 (0.16), residues: 936 sheet: None (None), residues: 0 loop : 0.15 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 220 HIS 0.004 0.001 HIS J 162 PHE 0.019 0.002 PHE L 54 TYR 0.017 0.002 TYR Q 180 ARG 0.002 0.000 ARG K 70 Details of bonding type rmsd hydrogen bonds : bond 0.05558 ( 728) hydrogen bonds : angle 4.66428 ( 2148) covalent geometry : bond 0.00328 (10370) covalent geometry : angle 0.57988 (14103) ********************** 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 214 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 1.059 Fit side-chains REVERT: K 200 GLN cc_start: 0.6994 (OUTLIER) cc_final: 0.6482 (mm-40) REVERT: L 394 GLN cc_start: 0.8089 (pt0) cc_final: 0.7357 (pm20) REVERT: L 404 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8451 (ttpp) REVERT: Q 85 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8701 (tp) REVERT: Q 264 ARG cc_start: 0.7587 (mtp180) cc_final: 0.7316 (mmm160) REVERT: Q 321 LYS cc_start: 0.8317 (mmtm) cc_final: 0.8006 (mmtm) REVERT: Q 323 ARG cc_start: 0.8187 (mpt90) cc_final: 0.7762 (mpt90) REVERT: J 47 ASN cc_start: 0.8250 (p0) cc_final: 0.7974 (p0) REVERT: J 128 LYS cc_start: 0.8433 (mtpp) cc_final: 0.7662 (mttp) REVERT: J 145 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.7603 (m-80) outliers start: 23 outliers final: 15 residues processed: 202 average time/residue: 1.3420 time to fit residues: 291.3244 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 : 1.379 ------------------------------------------------------------------------------- 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 248 SER Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 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 J residue 58 VAL Chi-restraints excluded: chain J residue 74 THR 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 3 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 59 optimal weight: 0.1980 chunk 101 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 90 optimal weight: 0.5980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Q 83 ASN Q 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.121801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.096172 restraints weight = 26145.722| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.70 r_work: 0.2802 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1086 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= 0.129 Angle : 0.545 9.025 14103 Z= 0.280 Chirality : 0.039 0.270 1665 Planarity : 0.004 0.048 1726 Dihedral : 5.655 56.597 1615 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.08 % Allowed : 17.96 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.23), residues: 1301 helix: 2.17 (0.16), residues: 935 sheet: None (None), residues: 0 loop : 0.19 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 220 HIS 0.004 0.001 HIS J 162 PHE 0.018 0.001 PHE Q 54 TYR 0.015 0.002 TYR Q 244 ARG 0.001 0.000 ARG Q 195 Details of bonding type rmsd hydrogen bonds : bond 0.04975 ( 728) hydrogen bonds : angle 4.56783 ( 2148) covalent geometry : bond 0.00262 (10370) covalent geometry : angle 0.54464 (14103) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12754.11 seconds wall clock time: 224 minutes 46.94 seconds (13486.94 seconds total)