Starting phenix.real_space_refine (version: dev) on Sun Feb 19 16:12:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0s_26949/02_2023/7v0s_26949_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0s_26949/02_2023/7v0s_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0s_26949/02_2023/7v0s_26949.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0s_26949/02_2023/7v0s_26949.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0s_26949/02_2023/7v0s_26949_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0s_26949/02_2023/7v0s_26949_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "K TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 403": "OD1" <-> "OD2" Residue "L GLU 25": "OE1" <-> "OE2" Residue "L ASP 119": "OD1" <-> "OD2" Residue "L GLU 161": "OE1" <-> "OE2" Residue "L GLU 201": "OE1" <-> "OE2" Residue "L ASP 208": "OD1" <-> "OD2" Residue "L PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 398": "OD1" <-> "OD2" Residue "Q PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 56": "OD1" <-> "OD2" Residue "Q TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 262": "OE1" <-> "OE2" Residue "Q PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 96": "OE1" <-> "OE2" Residue "J TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 1 Unresolved non-hydrogen chiralities: 24 Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "L" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Chain: "Q" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "J" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ATYR K 34 " occ=0.42 ... (22 atoms not shown) pdb=" OH BTYR K 34 " occ=0.58 residue: pdb=" N APHE K 239 " occ=0.58 ... (20 atoms not shown) pdb=" CZ BPHE K 239 " occ=0.42 residue: pdb=" N ATYR K 242 " occ=0.62 ... (22 atoms not shown) pdb=" OH BTYR K 242 " occ=0.38 Time building chain proxies: 7.96, per 1000 atoms: 0.77 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.82 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... running ksdssp... Secondary structure from input PDB file: 61 helices and 0 sheets defined 69.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'K' and resid 12 through 31 Processing helix chain 'K' and resid 44 through 59 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 61 through 65 Processing helix chain 'K' and resid 73 through 99 removed outlier: 3.816A pdb=" N GLN K 89 " --> pdb=" O ALA K 85 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER K 99 " --> pdb=" O ASP K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 129 removed outlier: 3.523A pdb=" N VAL K 123 " --> pdb=" O SER K 119 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ALA K 129 " --> pdb=" O ILE K 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 160 Processing helix chain 'K' and resid 167 through 185 removed outlier: 3.671A pdb=" N ARG K 170 " --> pdb=" O MET K 167 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR K 173 " --> pdb=" O ARG K 170 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE K 175 " --> pdb=" O PHE K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 223 Proline residue: K 221 - end of helix Processing helix chain 'K' and resid 231 through 255 Processing helix chain 'K' and resid 267 through 280 removed outlier: 3.529A pdb=" N SER K 272 " --> pdb=" O THR K 268 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU K 275 " --> pdb=" O HIS K 271 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA K 276 " --> pdb=" O SER K 272 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLY K 277 " --> pdb=" O ALA K 273 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLY K 278 " --> pdb=" O VAL K 274 " (cutoff:3.500A) Processing helix chain 'K' and resid 291 through 311 Processing helix chain 'K' and resid 327 through 349 removed outlier: 3.589A 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 388 Processing helix chain 'K' and resid 391 through 393 No H-bonds generated for 'chain 'K' and resid 391 through 393' Processing helix chain 'K' and resid 398 through 400 No H-bonds generated for 'chain 'K' and resid 398 through 400' Processing helix chain 'K' and resid 404 through 406 No H-bonds generated for 'chain 'K' and resid 404 through 406' Processing helix chain 'L' and resid 4 through 23 Processing helix chain 'L' and resid 51 through 62 Processing helix chain 'L' and resid 64 through 68 Processing helix chain 'L' and resid 76 through 103 removed outlier: 3.733A pdb=" N GLN L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 132 removed outlier: 3.743A 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 138 through 161 Processing helix chain 'L' and resid 175 through 188 Processing helix chain 'L' and resid 192 through 194 No H-bonds generated for 'chain 'L' and resid 192 through 194' Processing helix chain 'L' and resid 205 through 225 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 234 through 261 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 265 No H-bonds generated for 'chain 'L' and resid 263 through 265' Processing helix chain 'L' and resid 269 through 282 removed outlier: 4.298A pdb=" N THR L 276 " --> pdb=" O ILE L 272 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU L 277 " --> pdb=" O GLN L 273 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA L 278 " --> pdb=" O ASN L 274 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLY L 279 " --> pdb=" O ALA L 275 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLY L 280 " --> pdb=" O THR L 276 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL L 281 " --> pdb=" O LEU L 277 " (cutoff:3.500A) Processing helix chain 'L' and resid 292 through 320 removed outlier: 4.457A 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 330 through 333 No H-bonds generated for 'chain 'L' and resid 330 through 333' Processing helix chain 'L' and resid 335 through 350 Processing helix chain 'L' and resid 358 through 383 Processing helix chain 'L' and resid 399 through 401 No H-bonds generated for 'chain 'L' and resid 399 through 401' Processing helix chain 'Q' and resid 4 through 23 Processing helix chain 'Q' and resid 47 through 62 Proline residue: Q 52 - end of helix Processing helix chain 'Q' and resid 64 through 68 Processing helix chain 'Q' and resid 76 through 103 removed outlier: 3.812A pdb=" N GLN Q 92 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 112 through 131 removed outlier: 3.799A pdb=" N ALA Q 131 " --> pdb=" O ILE Q 127 " (cutoff:3.500A) Processing helix chain 'Q' and resid 138 through 161 removed outlier: 3.610A pdb=" N VAL Q 150 " --> pdb=" O ILE Q 146 " (cutoff:3.500A) Processing helix chain 'Q' and resid 175 through 188 Processing helix chain 'Q' and resid 192 through 194 No H-bonds generated for 'chain 'Q' and resid 192 through 194' Processing helix chain 'Q' and resid 205 through 227 Proline residue: Q 223 - end of helix Processing helix chain 'Q' and resid 234 through 261 removed outlier: 3.630A pdb=" N LEU Q 252 " --> pdb=" O ALA Q 248 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 265 No H-bonds generated for 'chain 'Q' and resid 263 through 265' Processing helix chain 'Q' and resid 269 through 282 removed outlier: 4.287A pdb=" N THR Q 276 " --> pdb=" O ILE Q 272 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU Q 277 " --> pdb=" O GLN Q 273 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA Q 278 " --> pdb=" O ASN Q 274 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLY Q 279 " --> pdb=" O ALA Q 275 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLY Q 280 " --> pdb=" O THR Q 276 " (cutoff:3.500A) Processing helix chain 'Q' and resid 293 through 312 Processing helix chain 'Q' and resid 314 through 320 Processing helix chain 'Q' and resid 330 through 333 No H-bonds generated for 'chain 'Q' and resid 330 through 333' Processing helix chain 'Q' and resid 335 through 351 Processing helix chain 'Q' and resid 358 through 383 Processing helix chain 'Q' and resid 399 through 401 No H-bonds generated for 'chain 'Q' and resid 399 through 401' Processing helix chain 'J' and resid 12 through 22 Processing helix chain 'J' and resid 25 through 34 Processing helix chain 'J' and resid 48 through 55 Processing helix chain 'J' and resid 58 through 66 Processing helix chain 'J' and resid 81 through 88 Processing helix chain 'J' and resid 91 through 99 Processing helix chain 'J' and resid 114 through 120 Processing helix chain 'J' and resid 124 through 132 Processing helix chain 'J' and resid 147 through 154 Processing helix chain 'J' and resid 157 through 166 624 hydrogen bonds defined for protein. 1836 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: 3.22 Time building geometry restraints manager: 5.11 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: 95.68 - 103.38: 106 103.38 - 111.08: 4027 111.08 - 118.78: 4407 118.78 - 126.48: 5417 126.48 - 134.19: 146 Bond angle restraints: 14103 Sorted by residual: angle pdb=" C BTYR K 34 " pdb=" N ASP K 35 " pdb=" CA ASP K 35 " ideal model delta sigma weight residual 121.70 129.19 -7.49 1.80e+00 3.09e-01 1.73e+01 angle pdb=" N SER Q 354 " pdb=" CA SER Q 354 " pdb=" C SER Q 354 " ideal model delta sigma weight residual 109.85 116.17 -6.32 1.58e+00 4.01e-01 1.60e+01 angle pdb=" N GLY Q 284 " pdb=" CA GLY Q 284 " pdb=" C GLY Q 284 " ideal model delta sigma weight residual 112.50 116.74 -4.24 1.16e+00 7.43e-01 1.34e+01 angle pdb=" C THR Q 319 " pdb=" N THR Q 320 " pdb=" CA THR Q 320 " ideal model delta sigma weight residual 122.60 116.31 6.29 1.88e+00 2.83e-01 1.12e+01 angle pdb=" CA GLY Q 345 " pdb=" C GLY Q 345 " pdb=" O GLY Q 345 " ideal model delta sigma weight residual 120.75 117.32 3.43 1.03e+00 9.43e-01 1.11e+01 ... (remaining 14098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 5214 17.70 - 35.39: 548 35.39 - 53.09: 134 53.09 - 70.79: 35 70.79 - 88.49: 15 Dihedral angle restraints: 5946 sinusoidal: 2201 harmonic: 3745 Sorted by residual: dihedral pdb=" CA TRP L 403 " pdb=" C TRP L 403 " pdb=" N LYS L 404 " pdb=" CA LYS L 404 " ideal model delta harmonic sigma weight residual 180.00 162.75 17.25 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA TRP Q 403 " pdb=" C TRP Q 403 " pdb=" N LYS Q 404 " pdb=" CA LYS Q 404 " ideal model delta harmonic sigma weight residual 180.00 163.10 16.90 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA PHE L 23 " pdb=" C PHE L 23 " pdb=" N VAL L 24 " pdb=" CA VAL L 24 " ideal model delta harmonic sigma weight residual -180.00 -163.80 -16.20 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 5943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1416 0.063 - 0.125: 230 0.125 - 0.188: 15 0.188 - 0.251: 3 0.251 - 0.314: 1 Chirality restraints: 1665 Sorted by residual: chirality pdb=" CG LEU K 386 " pdb=" CB LEU K 386 " pdb=" CD1 LEU K 386 " pdb=" CD2 LEU K 386 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C11 AJP Q 501 " pdb=" C10 AJP Q 501 " pdb=" C12 AJP Q 501 " pdb=" C16 AJP Q 501 " both_signs ideal model delta sigma weight residual False 2.20 2.45 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" C08 AJP Q 501 " pdb=" C07 AJP Q 501 " pdb=" C10 AJP Q 501 " pdb=" O09 AJP Q 501 " both_signs ideal model delta sigma weight residual False 2.56 2.79 -0.22 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1662 not shown) Planarity restraints: 1726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP K 220 " 0.038 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO K 221 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO K 221 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO K 221 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY Q 352 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.51e+00 pdb=" C GLY Q 352 " -0.032 2.00e-02 2.50e+03 pdb=" O GLY Q 352 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA Q 353 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP Q 222 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO Q 223 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO Q 223 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO Q 223 " 0.025 5.00e-02 4.00e+02 ... (remaining 1723 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1127 2.75 - 3.28: 10907 3.28 - 3.82: 20213 3.82 - 4.36: 23912 4.36 - 4.90: 39610 Nonbonded interactions: 95769 Sorted by model distance: nonbonded pdb=" OE2 GLU Q 202 " pdb=" O HOH Q 601 " model vdw 2.208 2.440 nonbonded pdb=" NH2 ARG K 70 " pdb=" O GLY J 155 " model vdw 2.232 2.520 nonbonded pdb=" O SER Q 367 " pdb=" OG1 THR Q 371 " model vdw 2.263 2.440 nonbonded pdb=" OG SER K 284 " pdb=" O HOH K 501 " model vdw 2.268 2.440 nonbonded pdb=" O HOH L 659 " pdb=" O HOH Q 643 " model vdw 2.271 2.440 ... (remaining 95764 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'L' and resid 1 through 409) selection = (chain 'Q' and (resid 1 through 26 or resid 48 through 409)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 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: 5.930 Check model and map are aligned: 0.160 Process input model: 33.690 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.090 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 10370 Z= 0.279 Angle : 0.729 10.067 14103 Z= 0.424 Chirality : 0.045 0.314 1665 Planarity : 0.005 0.057 1726 Dihedral : 16.592 88.487 3552 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.70 % Favored : 98.22 % Rotamer Outliers : 2.55 % 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 *********************** 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 fitting. rotamer outliers: 26 poor density : 189 time to evaluate : 1.211 Fit side-chains outliers start: 26 outliers final: 18 residues processed: 207 average time/residue: 1.2063 time to fit residues: 268.9037 Evaluate side-chains 208 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 190 time to evaluate : 1.217 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 16 residues processed: 2 average time/residue: 0.8001 time to fit residues: 3.3202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Q 55 GLN Q 104 GLN J 103 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.0669 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= 0.297 Angle : 0.611 7.470 14103 Z= 0.321 Chirality : 0.043 0.254 1665 Planarity : 0.005 0.054 1726 Dihedral : 4.840 38.568 1404 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 4.35 % 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: 1.71 (0.23), residues: 1301 helix: 1.57 (0.16), residues: 937 sheet: None (None), residues: 0 loop : 0.15 (0.32), residues: 364 *********************** 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 239 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 193 time to evaluate : 1.228 Fit side-chains outliers start: 46 outliers final: 25 residues processed: 217 average time/residue: 1.3226 time to fit residues: 308.0922 Evaluate side-chains 208 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 183 time to evaluate : 1.322 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 17 residues processed: 8 average time/residue: 0.2678 time to fit residues: 4.4938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 98 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 118 optimal weight: 0.4980 chunk 127 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 58 HIS Q 83 ASN Q 104 GLN J 103 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.0631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 10370 Z= 0.218 Angle : 0.548 7.407 14103 Z= 0.288 Chirality : 0.040 0.174 1665 Planarity : 0.004 0.053 1726 Dihedral : 4.625 39.329 1404 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer Outliers : 3.12 % 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: 1.82 (0.23), residues: 1301 helix: 1.69 (0.17), residues: 931 sheet: None (None), residues: 0 loop : 0.10 (0.31), residues: 370 *********************** 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 224 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 191 time to evaluate : 1.154 Fit side-chains outliers start: 33 outliers final: 21 residues processed: 210 average time/residue: 1.2767 time to fit residues: 287.8690 Evaluate side-chains 213 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 192 time to evaluate : 1.145 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 3 average time/residue: 0.0995 time to fit residues: 2.1579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Q 83 ASN Q 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.0688 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= 0.227 Angle : 0.554 7.649 14103 Z= 0.291 Chirality : 0.040 0.206 1665 Planarity : 0.004 0.053 1726 Dihedral : 4.624 39.389 1404 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 3.78 % 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: 1.82 (0.23), residues: 1301 helix: 1.69 (0.16), residues: 938 sheet: None (None), residues: 0 loop : 0.07 (0.32), residues: 363 *********************** 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 237 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 197 time to evaluate : 1.245 Fit side-chains outliers start: 40 outliers final: 25 residues processed: 221 average time/residue: 1.3540 time to fit residues: 321.7118 Evaluate side-chains 211 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 186 time to evaluate : 1.140 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 20 residues processed: 5 average time/residue: 0.1344 time to fit residues: 2.6926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 1 optimal weight: 0.2980 chunk 93 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 233 GLN ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 GLN L 58 HIS Q 83 ASN Q 104 GLN J 103 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.0689 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= 0.200 Angle : 0.535 7.827 14103 Z= 0.280 Chirality : 0.039 0.166 1665 Planarity : 0.004 0.053 1726 Dihedral : 4.529 40.075 1404 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 3.59 % 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: 1.90 (0.23), residues: 1301 helix: 1.76 (0.17), residues: 932 sheet: None (None), residues: 0 loop : 0.08 (0.31), residues: 369 *********************** 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 229 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 191 time to evaluate : 1.315 Fit side-chains outliers start: 38 outliers final: 24 residues processed: 218 average time/residue: 1.2279 time to fit residues: 288.3326 Evaluate side-chains 212 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 188 time to evaluate : 1.123 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 21 residues processed: 3 average time/residue: 0.1235 time to fit residues: 2.0697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 10370 Z= 0.224 Angle : 0.555 8.076 14103 Z= 0.290 Chirality : 0.040 0.231 1665 Planarity : 0.004 0.053 1726 Dihedral : 4.578 39.662 1404 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 3.69 % 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: 1.85 (0.23), residues: 1301 helix: 1.71 (0.16), residues: 938 sheet: None (None), residues: 0 loop : 0.07 (0.32), residues: 363 *********************** 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 232 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 193 time to evaluate : 1.120 Fit side-chains outliers start: 39 outliers final: 26 residues processed: 217 average time/residue: 1.3459 time to fit residues: 314.2094 Evaluate side-chains 216 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 190 time to evaluate : 1.222 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 20 residues processed: 6 average time/residue: 0.1187 time to fit residues: 2.8847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 71 optimal weight: 0.0980 chunk 91 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 10370 Z= 0.151 Angle : 0.500 8.091 14103 Z= 0.260 Chirality : 0.038 0.217 1665 Planarity : 0.004 0.052 1726 Dihedral : 4.306 42.412 1404 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 3.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.23), residues: 1301 helix: 1.95 (0.17), residues: 930 sheet: None (None), residues: 0 loop : 0.17 (0.32), residues: 371 *********************** 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 223 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 189 time to evaluate : 1.237 Fit side-chains outliers start: 34 outliers final: 21 residues processed: 214 average time/residue: 1.2046 time to fit residues: 278.5297 Evaluate side-chains 205 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 184 time to evaluate : 1.238 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 20 residues processed: 1 average time/residue: 0.0980 time to fit residues: 1.8369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 3.9990 chunk 74 optimal weight: 0.0770 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 85 optimal weight: 0.0980 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 120 optimal weight: 0.0670 overall best weight: 1.4480 ------------------------------------------------------------------------------- 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 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Q 83 ASN Q 104 GLN J 162 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.0854 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= 0.162 Angle : 0.514 8.158 14103 Z= 0.265 Chirality : 0.038 0.239 1665 Planarity : 0.004 0.052 1726 Dihedral : 4.293 42.118 1404 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 2.74 % 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: 2.20 (0.23), residues: 1301 helix: 1.95 (0.17), residues: 939 sheet: None (None), residues: 0 loop : 0.27 (0.32), residues: 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 188 time to evaluate : 1.503 Fit side-chains outliers start: 29 outliers final: 20 residues processed: 209 average time/residue: 1.2242 time to fit residues: 275.6577 Evaluate side-chains 206 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 1.238 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 20 residues processed: 0 time to fit residues: 1.9789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 50 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 109 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 10370 Z= 0.310 Angle : 0.630 7.990 14103 Z= 0.326 Chirality : 0.044 0.313 1665 Planarity : 0.005 0.056 1726 Dihedral : 4.733 38.434 1404 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 2.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.23), residues: 1301 helix: 1.63 (0.16), residues: 938 sheet: None (None), residues: 0 loop : 0.12 (0.32), residues: 363 *********************** 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 221 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 191 time to evaluate : 1.198 Fit side-chains outliers start: 30 outliers final: 22 residues processed: 216 average time/residue: 1.2724 time to fit residues: 295.6332 Evaluate side-chains 211 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 189 time to evaluate : 1.233 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 21 residues processed: 2 average time/residue: 0.1651 time to fit residues: 2.0584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 109 optimal weight: 0.0770 overall best weight: 3.2146 ------------------------------------------------------------------------------- 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 109 ASN J 103 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.0870 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= 0.241 Angle : 0.587 8.460 14103 Z= 0.303 Chirality : 0.042 0.308 1665 Planarity : 0.004 0.054 1726 Dihedral : 4.645 39.080 1404 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 2.46 % 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: 1.78 (0.23), residues: 1301 helix: 1.65 (0.16), residues: 938 sheet: None (None), residues: 0 loop : 0.10 (0.32), residues: 363 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 189 time to evaluate : 1.407 Fit side-chains outliers start: 26 outliers final: 22 residues processed: 210 average time/residue: 1.3033 time to fit residues: 295.1835 Evaluate side-chains 209 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 187 time to evaluate : 1.151 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 21 residues processed: 2 average time/residue: 0.2170 time to fit residues: 2.1464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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** L 58 HIS Q 83 ASN Q 104 GLN Q 109 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.117410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.092380 restraints weight = 25025.156| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.74 r_work: 0.2730 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 10370 Z= 0.223 Angle : 0.578 8.476 14103 Z= 0.297 Chirality : 0.041 0.298 1665 Planarity : 0.004 0.053 1726 Dihedral : 4.594 39.431 1404 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 2.46 % 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: 1.84 (0.23), residues: 1301 helix: 1.69 (0.16), residues: 938 sheet: None (None), residues: 0 loop : 0.12 (0.32), residues: 363 =============================================================================== Job complete usr+sys time: 5086.81 seconds wall clock time: 91 minutes 25.84 seconds (5485.84 seconds total)