Starting phenix.real_space_refine on Fri Mar 15 01:43:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0s_26949/03_2024/7v0s_26949_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0s_26949/03_2024/7v0s_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_26949/03_2024/7v0s_26949.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0s_26949/03_2024/7v0s_26949.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0s_26949/03_2024/7v0s_26949_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0s_26949/03_2024/7v0s_26949_updated.pdb" } 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 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 7.42, per 1000 atoms: 0.72 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: 4.43 Conformation dependent library (CDL) restraints added in 2.6 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: 2.03 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: 2.67 Time building geometry restraints manager: 4.76 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: 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: 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 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: 0.870 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: 5.130 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 33.310 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 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:12.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.380 ------------------------------------------------------------------------------- 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= 0.279 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 *********************** 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 : 1.139 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: 1.1891 time to fit residues: 264.7230 Evaluate side-chains 203 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 184 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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: 4.9990 chunk 98 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 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: 0.8658 moved from start: 0.0651 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= 0.298 Angle : 0.611 7.653 14103 Z= 0.321 Chirality : 0.043 0.256 1665 Planarity : 0.005 0.054 1726 Dihedral : 7.197 59.013 1640 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.69 % Allowed : 14.84 % 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: 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 220 HIS 0.006 0.002 HIS Q 263 PHE 0.023 0.002 PHE L 54 TYR 0.022 0.002 TYR Q 180 ARG 0.003 0.000 ARG K 11 *********************** 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 226 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 187 time to evaluate : 1.102 Fit side-chains REVERT: K 189 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7540 (mmmm) REVERT: K 200 GLN cc_start: 0.6590 (OUTLIER) cc_final: 0.6087 (mm-40) REVERT: L 394 GLN cc_start: 0.7622 (pt0) cc_final: 0.7042 (pm20) REVERT: L 404 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8170 (ttpp) REVERT: Q 323 ARG cc_start: 0.7937 (mpt90) cc_final: 0.7639 (mpt-90) REVERT: J 110 LYS cc_start: 0.8293 (mtpt) cc_final: 0.8038 (mtpt) outliers start: 39 outliers final: 18 residues processed: 204 average time/residue: 1.2899 time to fit residues: 281.8128 Evaluate side-chains 204 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 183 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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 248 SER 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 311 CYS 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 60 MET 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 65 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 118 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 233 GLN L 58 HIS Q 83 ASN Q 104 GLN J 103 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 10370 Z= 0.386 Angle : 0.664 8.014 14103 Z= 0.349 Chirality : 0.047 0.284 1665 Planarity : 0.005 0.055 1726 Dihedral : 7.084 58.472 1622 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.31 % Allowed : 15.22 % 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: 1.37 (0.22), residues: 1301 helix: 1.35 (0.16), residues: 932 sheet: None (None), residues: 0 loop : -0.06 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 16 HIS 0.007 0.002 HIS Q 263 PHE 0.025 0.003 PHE L 54 TYR 0.023 0.003 TYR L 180 ARG 0.004 0.001 ARG K 11 *********************** 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 fitting. rotamer outliers: 35 poor density : 191 time to evaluate : 1.152 Fit side-chains REVERT: K 200 GLN cc_start: 0.6594 (OUTLIER) cc_final: 0.6102 (mm-40) REVERT: K 235 LYS cc_start: 0.8171 (ttmt) cc_final: 0.7856 (tttt) REVERT: L 394 GLN cc_start: 0.7648 (pt0) cc_final: 0.7110 (pm20) REVERT: L 404 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8183 (ttpp) REVERT: Q 323 ARG cc_start: 0.7959 (mpt90) cc_final: 0.7704 (mpt-90) REVERT: J 91 ASP cc_start: 0.7112 (OUTLIER) cc_final: 0.6821 (m-30) REVERT: J 92 GLU cc_start: 0.7062 (pm20) cc_final: 0.6861 (pm20) outliers start: 35 outliers final: 20 residues processed: 209 average time/residue: 1.2803 time to fit residues: 286.2830 Evaluate side-chains 208 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 185 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 268 THR Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain L residue 306 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 314 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 60 MET Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 91 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 224 ASN ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Q 104 GLN J 103 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 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 : 0.003 0.042 10370 Z= 0.184 Angle : 0.523 7.639 14103 Z= 0.275 Chirality : 0.039 0.215 1665 Planarity : 0.004 0.052 1726 Dihedral : 6.361 58.338 1621 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.21 % Allowed : 15.31 % 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: 1.85 (0.23), residues: 1301 helix: 1.74 (0.17), residues: 932 sheet: None (None), residues: 0 loop : 0.02 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 16 HIS 0.004 0.001 HIS J 162 PHE 0.017 0.001 PHE L 54 TYR 0.016 0.002 TYR Q 244 ARG 0.002 0.000 ARG L 2 *********************** 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 230 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 196 time to evaluate : 1.227 Fit side-chains REVERT: L 394 GLN cc_start: 0.7596 (pt0) cc_final: 0.7037 (pm20) REVERT: L 404 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8151 (ttpp) REVERT: Q 323 ARG cc_start: 0.7939 (mpt90) cc_final: 0.7671 (mpt-90) REVERT: Q 404 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8095 (tppt) REVERT: J 91 ASP cc_start: 0.7075 (OUTLIER) cc_final: 0.6737 (m-30) REVERT: J 92 GLU cc_start: 0.6987 (pm20) cc_final: 0.6782 (pm20) REVERT: J 145 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.7841 (m-80) outliers start: 34 outliers final: 17 residues processed: 214 average time/residue: 1.2527 time to fit residues: 287.5841 Evaluate side-chains 214 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 193 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 248 SER Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 268 THR 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 349 VAL Chi-restraints excluded: chain L residue 357 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 Q residue 404 LYS Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 145 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 86 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Q 83 ASN Q 104 GLN Q 109 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10370 Z= 0.347 Angle : 0.633 7.701 14103 Z= 0.332 Chirality : 0.045 0.268 1665 Planarity : 0.005 0.054 1726 Dihedral : 6.772 57.875 1619 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.50 % Allowed : 14.84 % Favored : 81.66 % 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: 1.51 (0.22), residues: 1301 helix: 1.48 (0.17), residues: 932 sheet: None (None), residues: 0 loop : -0.08 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 220 HIS 0.007 0.002 HIS Q 263 PHE 0.024 0.003 PHE L 54 TYR 0.023 0.003 TYR L 180 ARG 0.004 0.000 ARG K 11 *********************** 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 231 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 194 time to evaluate : 1.341 Fit side-chains REVERT: K 200 GLN cc_start: 0.6586 (OUTLIER) cc_final: 0.6089 (mm-40) REVERT: L 394 GLN cc_start: 0.7644 (pt0) cc_final: 0.7109 (pm20) REVERT: L 404 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8188 (ttpp) REVERT: Q 323 ARG cc_start: 0.7954 (mpt90) cc_final: 0.7723 (mpt-90) REVERT: Q 404 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8104 (tppt) REVERT: J 91 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6817 (m-30) REVERT: J 92 GLU cc_start: 0.7023 (pm20) cc_final: 0.6816 (pm20) outliers start: 37 outliers final: 21 residues processed: 213 average time/residue: 1.2593 time to fit residues: 287.4091 Evaluate side-chains 216 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 191 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 268 THR Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain L residue 306 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 314 LEU Chi-restraints excluded: chain Q residue 384 LYS Chi-restraints excluded: chain Q residue 404 LYS Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 60 MET Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 91 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 125 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 224 ASN ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Q 83 ASN Q 104 GLN J 103 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.0810 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= 0.226 Angle : 0.560 8.232 14103 Z= 0.294 Chirality : 0.041 0.231 1665 Planarity : 0.004 0.052 1726 Dihedral : 6.468 57.997 1619 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.02 % Allowed : 15.50 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.70 (0.23), residues: 1301 helix: 1.63 (0.17), residues: 932 sheet: None (None), residues: 0 loop : -0.05 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 220 HIS 0.005 0.001 HIS Q 263 PHE 0.020 0.002 PHE L 54 TYR 0.018 0.002 TYR Q 180 ARG 0.002 0.000 ARG Q 264 *********************** 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 224 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 192 time to evaluate : 1.151 Fit side-chains REVERT: K 200 GLN cc_start: 0.6585 (OUTLIER) cc_final: 0.6071 (mm-40) REVERT: L 394 GLN cc_start: 0.7619 (pt0) cc_final: 0.7058 (pm20) REVERT: L 404 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8162 (ttpp) REVERT: Q 85 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8726 (tp) REVERT: Q 323 ARG cc_start: 0.7947 (mpt90) cc_final: 0.7677 (mpt-90) REVERT: Q 404 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8097 (tppt) REVERT: J 91 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6812 (m-30) REVERT: J 92 GLU cc_start: 0.6989 (pm20) cc_final: 0.6781 (pm20) outliers start: 32 outliers final: 18 residues processed: 207 average time/residue: 1.2682 time to fit residues: 281.1834 Evaluate side-chains 210 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 187 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 200 GLN Chi-restraints excluded: chain K residue 248 SER Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 404 LYS Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain Q residue 314 LEU Chi-restraints excluded: chain Q residue 384 LYS Chi-restraints excluded: chain Q residue 404 LYS Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 91 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 71 optimal weight: 20.0000 chunk 91 optimal weight: 0.0980 chunk 105 optimal weight: 8.9990 chunk 70 optimal weight: 20.0000 chunk 125 optimal weight: 0.0070 chunk 78 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 overall best weight: 2.2204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 GLN ** 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: 0.8628 moved from start: 0.0782 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= 0.192 Angle : 0.532 8.262 14103 Z= 0.278 Chirality : 0.039 0.215 1665 Planarity : 0.004 0.052 1726 Dihedral : 6.247 57.672 1619 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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: 1.90 (0.23), residues: 1301 helix: 1.78 (0.17), residues: 932 sheet: None (None), residues: 0 loop : 0.03 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 220 HIS 0.005 0.001 HIS Q 263 PHE 0.018 0.002 PHE L 54 TYR 0.016 0.002 TYR Q 180 ARG 0.003 0.000 ARG Q 2 *********************** 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 227 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 194 time to evaluate : 1.077 Fit side-chains REVERT: K 200 GLN cc_start: 0.6581 (OUTLIER) cc_final: 0.6073 (mm-40) REVERT: K 311 CYS cc_start: 0.5237 (OUTLIER) cc_final: 0.4170 (p) REVERT: L 394 GLN cc_start: 0.7594 (pt0) cc_final: 0.7045 (pm20) REVERT: L 404 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8153 (ttpp) REVERT: Q 323 ARG cc_start: 0.7936 (mpt90) cc_final: 0.7407 (mpt90) REVERT: Q 404 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8083 (tppt) REVERT: J 91 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6764 (m-30) REVERT: J 92 GLU cc_start: 0.6970 (pm20) cc_final: 0.6758 (pm20) REVERT: J 145 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.7848 (m-80) outliers start: 33 outliers final: 19 residues processed: 211 average time/residue: 1.2584 time to fit residues: 284.6499 Evaluate side-chains 217 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 192 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 268 THR Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 311 CYS Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 306 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 Q residue 404 LYS Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 145 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 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 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10370 Z= 0.220 Angle : 0.559 8.462 14103 Z= 0.291 Chirality : 0.040 0.225 1665 Planarity : 0.004 0.052 1726 Dihedral : 6.185 57.311 1616 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.02 % Allowed : 15.60 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.72 (0.17), residues: 932 sheet: None (None), residues: 0 loop : 0.05 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 220 HIS 0.005 0.001 HIS Q 263 PHE 0.020 0.002 PHE L 54 TYR 0.018 0.002 TYR Q 180 ARG 0.003 0.000 ARG Q 2 *********************** 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 222 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 190 time to evaluate : 1.102 Fit side-chains REVERT: K 200 GLN cc_start: 0.6575 (OUTLIER) cc_final: 0.6074 (mm-40) REVERT: K 311 CYS cc_start: 0.5231 (OUTLIER) cc_final: 0.4176 (p) REVERT: L 394 GLN cc_start: 0.7607 (pt0) cc_final: 0.7051 (pm20) REVERT: L 404 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8155 (ttpp) REVERT: Q 323 ARG cc_start: 0.7942 (mpt90) cc_final: 0.7412 (mpt90) REVERT: Q 404 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8085 (tppt) REVERT: J 91 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.6817 (m-30) REVERT: J 92 GLU cc_start: 0.6967 (pm20) cc_final: 0.6756 (pm20) REVERT: J 128 LYS cc_start: 0.8427 (mtpp) cc_final: 0.7823 (mttp) REVERT: J 145 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.7851 (m-80) outliers start: 32 outliers final: 20 residues processed: 207 average time/residue: 1.3530 time to fit residues: 299.3267 Evaluate side-chains 215 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 189 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 268 THR Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 311 CYS Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain K residue 391 LYS 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 306 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 Q residue 404 LYS Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 145 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 8.9990 chunk 116 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 70 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Q 83 ASN Q 104 GLN Q 109 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10370 Z= 0.268 Angle : 0.595 8.581 14103 Z= 0.310 Chirality : 0.042 0.243 1665 Planarity : 0.004 0.053 1726 Dihedral : 6.342 57.320 1616 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.93 % Allowed : 15.50 % Favored : 81.57 % 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 (0.23), residues: 1301 helix: 1.62 (0.16), residues: 938 sheet: None (None), residues: 0 loop : 0.02 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 220 HIS 0.005 0.001 HIS Q 263 PHE 0.022 0.002 PHE Q 54 TYR 0.020 0.002 TYR L 180 ARG 0.003 0.000 ARG Q 2 *********************** 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 218 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 187 time to evaluate : 1.260 Fit side-chains REVERT: K 200 GLN cc_start: 0.6592 (OUTLIER) cc_final: 0.6082 (mm-40) REVERT: K 311 CYS cc_start: 0.5255 (OUTLIER) cc_final: 0.4209 (p) REVERT: L 394 GLN cc_start: 0.7623 (pt0) cc_final: 0.7056 (pm20) REVERT: L 404 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8175 (ttpp) REVERT: Q 323 ARG cc_start: 0.7950 (mpt90) cc_final: 0.7682 (mpt-90) REVERT: Q 404 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8122 (tppt) REVERT: J 91 ASP cc_start: 0.7106 (OUTLIER) cc_final: 0.6828 (m-30) REVERT: J 92 GLU cc_start: 0.6979 (pm20) cc_final: 0.6768 (pm20) outliers start: 31 outliers final: 21 residues processed: 205 average time/residue: 1.2994 time to fit residues: 285.2182 Evaluate side-chains 212 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 186 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 200 GLN Chi-restraints excluded: chain K residue 248 SER 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 311 CYS Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain K residue 391 LYS 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 306 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 314 LEU Chi-restraints excluded: chain Q residue 384 LYS Chi-restraints excluded: chain Q residue 404 LYS Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 91 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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** ** K 405 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.0804 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= 0.202 Angle : 0.556 8.810 14103 Z= 0.288 Chirality : 0.040 0.220 1665 Planarity : 0.004 0.052 1726 Dihedral : 6.144 57.261 1616 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.74 % Allowed : 15.69 % Favored : 81.57 % 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: 1.75 (0.17), residues: 938 sheet: None (None), residues: 0 loop : 0.09 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 220 HIS 0.005 0.001 HIS Q 263 PHE 0.021 0.002 PHE Q 54 TYR 0.017 0.002 TYR Q 180 ARG 0.003 0.000 ARG Q 2 ********************** 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 220 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 191 time to evaluate : 1.181 Fit side-chains REVERT: K 200 GLN cc_start: 0.6579 (OUTLIER) cc_final: 0.6074 (mm-40) REVERT: K 262 GLN cc_start: 0.6705 (OUTLIER) cc_final: 0.6305 (pm20) REVERT: K 311 CYS cc_start: 0.5240 (OUTLIER) cc_final: 0.4182 (p) REVERT: L 394 GLN cc_start: 0.7597 (pt0) cc_final: 0.7044 (pm20) REVERT: L 404 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8156 (ttpp) REVERT: Q 85 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8729 (tp) REVERT: Q 323 ARG cc_start: 0.7930 (mpt90) cc_final: 0.7409 (mpt90) REVERT: J 91 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.6821 (m-30) REVERT: J 92 GLU cc_start: 0.6969 (pm20) cc_final: 0.6756 (pm20) REVERT: J 128 LYS cc_start: 0.8417 (mtpp) cc_final: 0.7813 (mttp) outliers start: 29 outliers final: 20 residues processed: 207 average time/residue: 1.2763 time to fit residues: 283.2000 Evaluate side-chains 215 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 189 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 200 GLN Chi-restraints excluded: chain K residue 248 SER Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 262 GLN Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 311 CYS Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain K residue 391 LYS 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 306 VAL Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 404 LYS Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain Q residue 314 LEU Chi-restraints excluded: chain Q residue 384 LYS Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 91 ASP 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: 2.9990 chunk 103 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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** ** K 405 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 = 0.3225 r_free = 0.3225 target = 0.119199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.094470 restraints weight = 25632.481| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.75 r_work: 0.2755 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.0822 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= 0.175 Angle : 0.534 9.110 14103 Z= 0.275 Chirality : 0.039 0.206 1665 Planarity : 0.004 0.051 1726 Dihedral : 5.964 57.058 1616 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.36 % Allowed : 16.16 % 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: 2.05 (0.23), residues: 1301 helix: 1.86 (0.17), residues: 932 sheet: None (None), residues: 0 loop : 0.15 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 220 HIS 0.004 0.001 HIS Q 263 PHE 0.019 0.002 PHE Q 54 TYR 0.016 0.002 TYR Q 244 ARG 0.004 0.000 ARG Q 2 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5212.99 seconds wall clock time: 92 minutes 11.07 seconds (5531.07 seconds total)