Starting phenix.real_space_refine on Fri Mar 15 02:40:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6snh_10257/03_2024/6snh_10257_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6snh_10257/03_2024/6snh_10257.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6snh_10257/03_2024/6snh_10257_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6snh_10257/03_2024/6snh_10257_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6snh_10257/03_2024/6snh_10257_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6snh_10257/03_2024/6snh_10257.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6snh_10257/03_2024/6snh_10257.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6snh_10257/03_2024/6snh_10257_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6snh_10257/03_2024/6snh_10257_updated.pdb" } resolution = 3.9 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3122 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 31 5.16 5 C 4801 2.51 5 N 1156 2.21 5 O 1326 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "X PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 129": "NH1" <-> "NH2" Residue "X ASP 150": "OD1" <-> "OD2" Residue "X PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 167": "NH1" <-> "NH2" Residue "X TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 250": "NH1" <-> "NH2" Residue "X PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 86": "NH1" <-> "NH2" Residue "H TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 169": "OD1" <-> "OD2" Residue "L TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7315 Number of models: 1 Model: "" Number of chains: 4 Chain: "X" Number of atoms: 3924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3924 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 25, 'TRANS': 453} Chain breaks: 1 Chain: "H" Number of atoms: 1690 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 225, 1684 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 213} Conformer: "B" Number of residues, atoms: 225, 1684 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 213} bond proxies already assigned to first conformer: 1721 Chain: "L" Number of atoms: 1659 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Conformer: "B" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} bond proxies already assigned to first conformer: 1654 Chain: "X" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'LMH': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 5.84, per 1000 atoms: 0.80 Number of scatterers: 7315 At special positions: 0 Unit cell: (110.04, 84.84, 113.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 P 1 15.00 O 1326 8.00 N 1156 7.00 C 4801 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS X 314 " - pdb=" SG CYS X 515 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 205 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.05 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: 2.34 Conformation dependent library (CDL) restraints added in 1.6 seconds 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1736 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 8 sheets defined 38.6% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'X' and resid 41 through 53 removed outlier: 4.335A pdb=" N VAL X 47 " --> pdb=" O PHE X 43 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 81 removed outlier: 3.931A pdb=" N GLN X 81 " --> pdb=" O MET X 77 " (cutoff:3.500A) Processing helix chain 'X' and resid 85 through 87 No H-bonds generated for 'chain 'X' and resid 85 through 87' Processing helix chain 'X' and resid 102 through 118 Processing helix chain 'X' and resid 121 through 123 No H-bonds generated for 'chain 'X' and resid 121 through 123' Processing helix chain 'X' and resid 139 through 153 Processing helix chain 'X' and resid 155 through 169 Processing helix chain 'X' and resid 173 through 185 removed outlier: 4.045A pdb=" N ILE X 183 " --> pdb=" O ALA X 179 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE X 185 " --> pdb=" O SER X 181 " (cutoff:3.500A) Processing helix chain 'X' and resid 187 through 193 Processing helix chain 'X' and resid 200 through 215 Processing helix chain 'X' and resid 219 through 232 removed outlier: 3.818A pdb=" N VAL X 224 " --> pdb=" O ALA X 220 " (cutoff:3.500A) Processing helix chain 'X' and resid 234 through 252 removed outlier: 3.862A pdb=" N TYR X 238 " --> pdb=" O MET X 235 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR X 239 " --> pdb=" O ALA X 236 " (cutoff:3.500A) Proline residue: X 241 - end of helix removed outlier: 4.750A pdb=" N PHE X 244 " --> pdb=" O PRO X 241 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU X 247 " --> pdb=" O PHE X 244 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER X 251 " --> pdb=" O LEU X 248 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU X 252 " --> pdb=" O SER X 249 " (cutoff:3.500A) Processing helix chain 'X' and resid 260 through 281 Proline residue: X 279 - end of helix Processing helix chain 'X' and resid 286 through 297 removed outlier: 3.515A pdb=" N HIS X 295 " --> pdb=" O GLN X 292 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 320 removed outlier: 4.535A pdb=" N VAL X 318 " --> pdb=" O CYS X 314 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE X 319 " --> pdb=" O VAL X 315 " (cutoff:3.500A) Processing helix chain 'X' and resid 322 through 325 No H-bonds generated for 'chain 'X' and resid 322 through 325' Processing helix chain 'X' and resid 329 through 352 removed outlier: 3.545A pdb=" N LEU X 336 " --> pdb=" O GLN X 332 " (cutoff:3.500A) Proline residue: X 345 - end of helix Processing helix chain 'X' and resid 356 through 373 removed outlier: 3.661A pdb=" N LEU X 359 " --> pdb=" O LYS X 356 " (cutoff:3.500A) Proline residue: X 360 - end of helix removed outlier: 3.514A pdb=" N LEU X 363 " --> pdb=" O PRO X 360 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER X 367 " --> pdb=" O ILE X 364 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU X 372 " --> pdb=" O SER X 369 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE X 373 " --> pdb=" O PHE X 370 " (cutoff:3.500A) Processing helix chain 'X' and resid 382 through 392 Proline residue: X 388 - end of helix removed outlier: 4.359A pdb=" N LEU X 392 " --> pdb=" O PRO X 388 " (cutoff:3.500A) Processing helix chain 'X' and resid 398 through 422 removed outlier: 3.536A pdb=" N LEU X 415 " --> pdb=" O ALA X 411 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TRP X 416 " --> pdb=" O LEU X 412 " (cutoff:3.500A) Proline residue: X 417 - end of helix Processing helix chain 'X' and resid 427 through 438 Processing helix chain 'X' and resid 477 through 498 removed outlier: 3.730A pdb=" N PHE X 495 " --> pdb=" O GLY X 491 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU X 496 " --> pdb=" O PHE X 492 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP X 497 " --> pdb=" O TYR X 493 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN X 498 " --> pdb=" O HIS X 494 " (cutoff:3.500A) Processing helix chain 'X' and resid 510 through 535 removed outlier: 3.742A pdb=" N PHE X 519 " --> pdb=" O CYS X 515 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE X 520 " --> pdb=" O ALA X 516 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N CYS X 521 " --> pdb=" O VAL X 517 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 89 No H-bonds generated for 'chain 'H' and resid 87 through 89' Processing helix chain 'H' and resid 102 through 104 No H-bonds generated for 'chain 'H' and resid 102 through 104' Processing helix chain 'H' and resid 195 through 198 No H-bonds generated for 'chain 'H' and resid 195 through 198' Processing helix chain 'L' and resid 124 through 129 Processing helix chain 'L' and resid 185 through 190 Processing sheet with id= A, first strand: chain 'H' and resid 5 through 7 Processing sheet with id= B, first strand: chain 'H' and resid 116 through 118 removed outlier: 3.912A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 129 through 133 removed outlier: 4.278A pdb=" N SER H 188 " --> pdb=" O PHE H 175 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE H 175 " --> pdb=" O SER H 188 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 159 through 163 Processing sheet with id= E, first strand: chain 'L' and resid 5 through 7 Processing sheet with id= F, first strand: chain 'L' and resid 85 through 90 removed outlier: 6.048A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'L' and resid 116 through 120 Processing sheet with id= H, first strand: chain 'L' and resid 146 through 152 306 hydrogen bonds defined for protein. 808 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.97 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1506 1.33 - 1.46: 2404 1.46 - 1.58: 3589 1.58 - 1.71: 2 1.71 - 1.84: 44 Bond restraints: 7545 Sorted by residual: bond pdb=" C SER L 10 " pdb=" O SER L 10 " ideal model delta sigma weight residual 1.235 1.344 -0.109 1.18e-02 7.18e+03 8.52e+01 bond pdb=" C33 LMH X 601 " pdb=" C34 LMH X 601 " ideal model delta sigma weight residual 1.419 1.510 -0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C33 LMH X 601 " pdb=" O32 LMH X 601 " ideal model delta sigma weight residual 1.550 1.464 0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C SER L 10 " pdb=" CA ASER L 10 " ideal model delta sigma weight residual 1.520 1.558 -0.038 1.12e-02 7.97e+03 1.15e+01 bond pdb=" C SER L 10 " pdb=" CA BSER L 10 " ideal model delta sigma weight residual 1.520 1.558 -0.038 1.12e-02 7.97e+03 1.15e+01 ... (remaining 7540 not shown) Histogram of bond angle deviations from ideal: 98.30 - 105.45: 166 105.45 - 112.60: 3991 112.60 - 119.75: 2369 119.75 - 126.90: 3639 126.90 - 134.05: 127 Bond angle restraints: 10292 Sorted by residual: angle pdb=" C16 LMH X 601 " pdb=" C17 LMH X 601 " pdb=" C18 LMH X 601 " ideal model delta sigma weight residual 74.50 120.05 -45.55 3.00e+00 1.11e-01 2.31e+02 angle pdb=" C11 LMH X 601 " pdb=" C12 LMH X 601 " pdb=" C13 LMH X 601 " ideal model delta sigma weight residual 74.50 119.89 -45.39 3.00e+00 1.11e-01 2.29e+02 angle pdb=" C06 LMH X 601 " pdb=" C07 LMH X 601 " pdb=" C08 LMH X 601 " ideal model delta sigma weight residual 74.51 119.88 -45.37 3.00e+00 1.11e-01 2.29e+02 angle pdb=" CA SER H 188 " pdb=" C SER H 188 " pdb=" O SER H 188 " ideal model delta sigma weight residual 120.89 131.05 -10.16 1.10e+00 8.26e-01 8.53e+01 angle pdb=" N SER L 10 " pdb=" CA ASER L 10 " pdb=" C SER L 10 " ideal model delta sigma weight residual 108.13 123.32 -15.19 1.72e+00 3.38e-01 7.80e+01 ... (remaining 10287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.94: 4047 19.94 - 39.89: 284 39.89 - 59.83: 52 59.83 - 79.77: 9 79.77 - 99.71: 4 Dihedral angle restraints: 4396 sinusoidal: 1673 harmonic: 2723 Sorted by residual: dihedral pdb=" N HIS X 378 " pdb=" C HIS X 378 " pdb=" CA HIS X 378 " pdb=" CB HIS X 378 " ideal model delta harmonic sigma weight residual 122.80 149.53 -26.73 0 2.50e+00 1.60e-01 1.14e+02 dihedral pdb=" C HIS X 378 " pdb=" N HIS X 378 " pdb=" CA HIS X 378 " pdb=" CB HIS X 378 " ideal model delta harmonic sigma weight residual -122.60 -149.26 26.66 0 2.50e+00 1.60e-01 1.14e+02 dihedral pdb=" CB CYS X 314 " pdb=" SG CYS X 314 " pdb=" SG CYS X 515 " pdb=" CB CYS X 515 " ideal model delta sinusoidal sigma weight residual -86.00 -153.31 67.31 1 1.00e+01 1.00e-02 5.90e+01 ... (remaining 4393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.218: 1137 0.218 - 0.435: 1 0.435 - 0.653: 2 0.653 - 0.871: 0 0.871 - 1.088: 1 Chirality restraints: 1141 Sorted by residual: chirality pdb=" CA HIS X 378 " pdb=" N HIS X 378 " pdb=" C HIS X 378 " pdb=" CB HIS X 378 " both_signs ideal model delta sigma weight residual False 2.51 1.42 1.09 2.00e-01 2.50e+01 2.96e+01 chirality pdb=" CA ASER L 10 " pdb=" N SER L 10 " pdb=" C SER L 10 " pdb=" CB ASER L 10 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" CA BSER L 10 " pdb=" N SER L 10 " pdb=" C SER L 10 " pdb=" CB BSER L 10 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.99e+00 ... (remaining 1138 not shown) Planarity restraints: 1267 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE X 384 " 0.046 5.00e-02 4.00e+02 7.02e-02 7.90e+00 pdb=" N PRO X 385 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO X 385 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO X 385 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL L 165 " 0.013 2.00e-02 2.50e+03 2.47e-02 6.11e+00 pdb=" C VAL L 165 " -0.043 2.00e-02 2.50e+03 pdb=" O VAL L 165 " 0.016 2.00e-02 2.50e+03 pdb=" N THR L 166 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR H 160 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.92e+00 pdb=" C THR H 160 " 0.042 2.00e-02 2.50e+03 pdb=" O THR H 160 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL H 161 " -0.014 2.00e-02 2.50e+03 ... (remaining 1264 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 653 2.72 - 3.27: 8138 3.27 - 3.81: 11947 3.81 - 4.36: 14257 4.36 - 4.90: 24172 Nonbonded interactions: 59167 Sorted by model distance: nonbonded pdb=" NH1 ARG L 110 " pdb=" O THR L 111 " model vdw 2.181 2.520 nonbonded pdb=" N VAL H 2 " pdb=" O SER H 25 " model vdw 2.212 2.520 nonbonded pdb=" O HIS L 191 " pdb=" NH1 ARG L 213 " model vdw 2.215 2.520 nonbonded pdb=" OH TYR H 59 " pdb=" N ILE H 69 " model vdw 2.230 2.520 nonbonded pdb=" O TYR L 188 " pdb=" OH TYR L 194 " model vdw 2.236 2.440 ... (remaining 59162 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 5.760 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 25.130 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 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 : 0.008 0.109 7545 Z= 0.509 Angle : 1.237 45.552 10292 Z= 0.619 Chirality : 0.062 1.088 1141 Planarity : 0.005 0.070 1267 Dihedral : 14.354 99.714 2645 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.99 % Favored : 88.90 % Rotamer: Outliers : 1.49 % Allowed : 5.96 % Favored : 92.56 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 8.33 % 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: -4.30 (0.23), residues: 918 helix: -1.92 (0.24), residues: 352 sheet: -2.67 (0.29), residues: 202 loop : -3.80 (0.26), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 163 HIS 0.006 0.001 HIS X 194 PHE 0.024 0.002 PHE X 197 TYR 0.021 0.002 TYR X 239 ARG 0.002 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.847 Fit side-chains REVERT: X 189 LEU cc_start: 0.9340 (tp) cc_final: 0.9071 (tp) REVERT: X 190 MET cc_start: 0.8352 (ttm) cc_final: 0.7928 (ttm) REVERT: X 368 MET cc_start: 0.8839 (tpp) cc_final: 0.8632 (tpt) REVERT: X 490 MET cc_start: 0.8787 (mtm) cc_final: 0.8280 (mtm) REVERT: X 519 PHE cc_start: 0.8964 (t80) cc_final: 0.8626 (t80) outliers start: 11 outliers final: 5 residues processed: 67 average time/residue: 0.1649 time to fit residues: 16.3127 Evaluate side-chains 44 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 380 LYS Chi-restraints excluded: chain H residue 136 SER Chi-restraints excluded: chain H residue 138 LYS Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 166 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 82 HIS ** X 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 194 HIS ** X 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 295 HIS X 408 ASN X 441 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 180 GLN L 37 GLN L 79 GLN L 191 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7545 Z= 0.169 Angle : 0.871 25.782 10292 Z= 0.370 Chirality : 0.042 0.167 1141 Planarity : 0.005 0.056 1267 Dihedral : 7.371 87.309 1044 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.12 % Allowed : 10.42 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -2.35 (0.27), residues: 918 helix: -0.10 (0.28), residues: 352 sheet: -1.99 (0.30), residues: 205 loop : -2.71 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 150 HIS 0.004 0.001 HIS X 75 PHE 0.019 0.001 PHE X 432 TYR 0.011 0.001 TYR H 94 ARG 0.002 0.000 ARG X 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.819 Fit side-chains REVERT: X 189 LEU cc_start: 0.9208 (tp) cc_final: 0.8962 (tt) REVERT: X 190 MET cc_start: 0.8302 (ttm) cc_final: 0.8055 (ttm) REVERT: X 193 ASP cc_start: 0.8540 (m-30) cc_final: 0.8183 (m-30) REVERT: X 490 MET cc_start: 0.8701 (mtm) cc_final: 0.8257 (mtm) REVERT: X 519 PHE cc_start: 0.8955 (t80) cc_final: 0.8548 (t80) outliers start: 8 outliers final: 6 residues processed: 58 average time/residue: 0.1596 time to fit residues: 13.8500 Evaluate side-chains 50 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 506 TYR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 138 LYS Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain L residue 196 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 81 optimal weight: 0.1980 chunk 88 optimal weight: 20.0000 chunk 72 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7545 Z= 0.170 Angle : 0.834 22.546 10292 Z= 0.348 Chirality : 0.041 0.175 1141 Planarity : 0.004 0.047 1267 Dihedral : 7.107 104.071 1037 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.36 % Allowed : 13.15 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.56 (0.28), residues: 918 helix: 0.57 (0.29), residues: 353 sheet: -1.43 (0.31), residues: 202 loop : -2.42 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 163 HIS 0.003 0.001 HIS X 75 PHE 0.018 0.001 PHE X 343 TYR 0.011 0.001 TYR H 94 ARG 0.002 0.000 ARG X 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.880 Fit side-chains REVERT: X 189 LEU cc_start: 0.9266 (tp) cc_final: 0.8764 (tt) REVERT: X 190 MET cc_start: 0.8251 (ttm) cc_final: 0.7986 (ttm) REVERT: X 193 ASP cc_start: 0.8447 (m-30) cc_final: 0.8014 (m-30) REVERT: X 490 MET cc_start: 0.8651 (mtm) cc_final: 0.8255 (mtm) REVERT: X 519 PHE cc_start: 0.9006 (t80) cc_final: 0.8620 (t80) outliers start: 10 outliers final: 6 residues processed: 58 average time/residue: 0.1356 time to fit residues: 12.3563 Evaluate side-chains 49 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 382 ILE Chi-restraints excluded: chain X residue 506 TYR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain L residue 196 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 198 GLN X 200 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 7545 Z= 0.368 Angle : 0.900 22.726 10292 Z= 0.389 Chirality : 0.043 0.170 1141 Planarity : 0.005 0.045 1267 Dihedral : 7.314 112.316 1033 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 2.11 % Allowed : 16.00 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.28), residues: 918 helix: 0.48 (0.29), residues: 352 sheet: -1.20 (0.33), residues: 202 loop : -2.36 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 163 HIS 0.004 0.001 HIS X 378 PHE 0.020 0.002 PHE X 343 TYR 0.019 0.002 TYR H 94 ARG 0.002 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 40 time to evaluate : 0.889 Fit side-chains REVERT: X 185 PHE cc_start: 0.7937 (m-80) cc_final: 0.7615 (m-80) REVERT: X 190 MET cc_start: 0.8353 (ttm) cc_final: 0.8054 (ttm) REVERT: X 490 MET cc_start: 0.8728 (mtm) cc_final: 0.8342 (mtm) REVERT: X 519 PHE cc_start: 0.9027 (t80) cc_final: 0.8673 (t80) outliers start: 16 outliers final: 10 residues processed: 51 average time/residue: 0.1419 time to fit residues: 11.5826 Evaluate side-chains 50 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 382 ILE Chi-restraints excluded: chain X residue 506 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain L residue 136 CYS Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 196 CYS Chi-restraints excluded: chain L residue 198 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 35 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7545 Z= 0.252 Angle : 0.857 22.520 10292 Z= 0.362 Chirality : 0.041 0.162 1141 Planarity : 0.004 0.044 1267 Dihedral : 7.218 120.679 1033 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 1.99 % Allowed : 16.75 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.18 (0.28), residues: 918 helix: 0.76 (0.30), residues: 352 sheet: -1.03 (0.34), residues: 200 loop : -2.17 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 163 HIS 0.002 0.001 HIS X 196 PHE 0.018 0.001 PHE X 343 TYR 0.015 0.001 TYR H 94 ARG 0.002 0.000 ARG X 74 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 44 time to evaluate : 0.875 Fit side-chains REVERT: X 185 PHE cc_start: 0.7849 (m-80) cc_final: 0.7598 (m-80) REVERT: X 190 MET cc_start: 0.8311 (ttm) cc_final: 0.7946 (ttm) REVERT: X 490 MET cc_start: 0.8677 (mtm) cc_final: 0.8310 (mtm) REVERT: X 519 PHE cc_start: 0.9003 (t80) cc_final: 0.8653 (t80) outliers start: 15 outliers final: 13 residues processed: 53 average time/residue: 0.1433 time to fit residues: 12.0065 Evaluate side-chains 54 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 41 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 368 MET Chi-restraints excluded: chain X residue 382 ILE Chi-restraints excluded: chain X residue 506 TYR Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain L residue 136 CYS Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 196 CYS Chi-restraints excluded: chain L residue 198 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 72 optimal weight: 0.0670 chunk 40 optimal weight: 0.0040 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 overall best weight: 0.7934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7545 Z= 0.144 Angle : 0.826 22.184 10292 Z= 0.339 Chirality : 0.040 0.167 1141 Planarity : 0.004 0.044 1267 Dihedral : 6.882 124.082 1033 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.74 % Allowed : 17.62 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.74 (0.29), residues: 918 helix: 1.07 (0.30), residues: 349 sheet: -0.47 (0.35), residues: 202 loop : -2.07 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 93 HIS 0.003 0.001 HIS X 75 PHE 0.017 0.001 PHE X 343 TYR 0.009 0.001 TYR H 94 ARG 0.002 0.000 ARG X 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 50 time to evaluate : 0.938 Fit side-chains REVERT: X 190 MET cc_start: 0.8225 (ttm) cc_final: 0.7904 (ttm) REVERT: X 490 MET cc_start: 0.8558 (mtm) cc_final: 0.8239 (mtm) REVERT: X 519 PHE cc_start: 0.9010 (t80) cc_final: 0.8684 (t80) outliers start: 13 outliers final: 11 residues processed: 58 average time/residue: 0.1272 time to fit residues: 11.7865 Evaluate side-chains 55 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 44 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 368 MET Chi-restraints excluded: chain X residue 382 ILE Chi-restraints excluded: chain X residue 506 TYR Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain L residue 136 CYS Chi-restraints excluded: chain L residue 196 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 86 optimal weight: 0.3980 chunk 54 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 40 optimal weight: 0.0970 chunk 53 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7545 Z= 0.141 Angle : 0.827 21.965 10292 Z= 0.340 Chirality : 0.041 0.174 1141 Planarity : 0.004 0.044 1267 Dihedral : 6.764 128.004 1033 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.61 % Allowed : 18.24 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.47 (0.29), residues: 918 helix: 1.20 (0.30), residues: 348 sheet: -0.20 (0.35), residues: 203 loop : -1.88 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 36 HIS 0.003 0.001 HIS X 75 PHE 0.017 0.001 PHE X 343 TYR 0.010 0.001 TYR H 94 ARG 0.001 0.000 ARG X 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 48 time to evaluate : 0.892 Fit side-chains REVERT: X 190 MET cc_start: 0.8129 (ttm) cc_final: 0.7899 (ttm) REVERT: X 490 MET cc_start: 0.8534 (mtm) cc_final: 0.8162 (mtm) outliers start: 12 outliers final: 11 residues processed: 55 average time/residue: 0.1409 time to fit residues: 12.3143 Evaluate side-chains 56 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 368 MET Chi-restraints excluded: chain X residue 382 ILE Chi-restraints excluded: chain X residue 506 TYR Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain L residue 196 CYS Chi-restraints excluded: chain L residue 198 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 78 optimal weight: 0.0370 chunk 83 optimal weight: 0.1980 chunk 75 optimal weight: 7.9990 overall best weight: 1.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 186 GLN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7545 Z= 0.154 Angle : 0.823 21.802 10292 Z= 0.338 Chirality : 0.040 0.185 1141 Planarity : 0.004 0.043 1267 Dihedral : 6.778 132.617 1033 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.86 % Allowed : 18.11 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.29 (0.29), residues: 918 helix: 1.35 (0.30), residues: 345 sheet: -0.04 (0.36), residues: 197 loop : -1.78 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 93 HIS 0.003 0.001 HIS L 200 PHE 0.022 0.001 PHE X 519 TYR 0.011 0.001 TYR H 94 ARG 0.001 0.000 ARG X 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 44 time to evaluate : 0.837 Fit side-chains REVERT: X 190 MET cc_start: 0.8160 (ttm) cc_final: 0.7810 (ttm) REVERT: X 490 MET cc_start: 0.8527 (mtm) cc_final: 0.8127 (mtm) REVERT: X 519 PHE cc_start: 0.8977 (t80) cc_final: 0.8767 (t80) outliers start: 14 outliers final: 12 residues processed: 54 average time/residue: 0.1349 time to fit residues: 11.5131 Evaluate side-chains 52 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 40 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 368 MET Chi-restraints excluded: chain X residue 382 ILE Chi-restraints excluded: chain X residue 506 TYR Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain L residue 196 CYS Chi-restraints excluded: chain L residue 198 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.0370 chunk 83 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7545 Z= 0.244 Angle : 0.855 22.194 10292 Z= 0.358 Chirality : 0.042 0.211 1141 Planarity : 0.004 0.046 1267 Dihedral : 6.940 135.892 1033 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.99 % Allowed : 17.74 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.38 (0.29), residues: 918 helix: 1.17 (0.30), residues: 346 sheet: -0.02 (0.36), residues: 196 loop : -1.76 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 163 HIS 0.003 0.001 HIS X 378 PHE 0.018 0.001 PHE X 343 TYR 0.016 0.001 TYR H 94 ARG 0.001 0.000 ARG X 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 43 time to evaluate : 0.858 Fit side-chains REVERT: X 190 MET cc_start: 0.8151 (ttm) cc_final: 0.7911 (ttm) REVERT: X 490 MET cc_start: 0.8614 (mtm) cc_final: 0.8200 (mtm) REVERT: X 519 PHE cc_start: 0.9014 (t80) cc_final: 0.8808 (t80) outliers start: 15 outliers final: 15 residues processed: 53 average time/residue: 0.1493 time to fit residues: 12.2917 Evaluate side-chains 58 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 43 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 140 THR Chi-restraints excluded: chain X residue 235 MET Chi-restraints excluded: chain X residue 368 MET Chi-restraints excluded: chain X residue 382 ILE Chi-restraints excluded: chain X residue 506 TYR Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain L residue 196 CYS Chi-restraints excluded: chain L residue 198 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.0570 chunk 59 optimal weight: 4.9990 chunk 89 optimal weight: 0.0070 chunk 82 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.0170 chunk 56 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 overall best weight: 0.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7545 Z= 0.151 Angle : 0.840 21.825 10292 Z= 0.343 Chirality : 0.041 0.199 1141 Planarity : 0.004 0.043 1267 Dihedral : 6.878 136.462 1033 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.74 % Allowed : 17.74 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.20 (0.29), residues: 918 helix: 1.30 (0.30), residues: 345 sheet: -0.05 (0.35), residues: 206 loop : -1.59 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 93 HIS 0.003 0.001 HIS X 75 PHE 0.018 0.001 PHE X 519 TYR 0.010 0.001 TYR H 94 ARG 0.002 0.000 ARG X 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 46 time to evaluate : 0.926 Fit side-chains REVERT: X 185 PHE cc_start: 0.7610 (m-80) cc_final: 0.7403 (m-80) REVERT: X 190 MET cc_start: 0.8201 (ttm) cc_final: 0.7869 (ttm) REVERT: X 490 MET cc_start: 0.8468 (mtm) cc_final: 0.8097 (mtm) REVERT: X 519 PHE cc_start: 0.9030 (t80) cc_final: 0.8816 (t80) outliers start: 13 outliers final: 12 residues processed: 55 average time/residue: 0.1396 time to fit residues: 12.2382 Evaluate side-chains 56 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 140 THR Chi-restraints excluded: chain X residue 235 MET Chi-restraints excluded: chain X residue 368 MET Chi-restraints excluded: chain X residue 382 ILE Chi-restraints excluded: chain X residue 506 TYR Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain L residue 196 CYS Chi-restraints excluded: chain L residue 198 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.062497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.048635 restraints weight = 101255.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.050813 restraints weight = 34584.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.052342 restraints weight = 18632.740| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7545 Z= 0.179 Angle : 0.832 22.005 10292 Z= 0.343 Chirality : 0.041 0.196 1141 Planarity : 0.004 0.044 1267 Dihedral : 6.874 138.427 1033 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.74 % Allowed : 17.87 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.19 (0.29), residues: 918 helix: 1.30 (0.30), residues: 345 sheet: 0.05 (0.36), residues: 200 loop : -1.61 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 93 HIS 0.002 0.001 HIS L 200 PHE 0.017 0.001 PHE X 343 TYR 0.012 0.001 TYR H 94 ARG 0.001 0.000 ARG X 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1552.93 seconds wall clock time: 29 minutes 14.50 seconds (1754.50 seconds total)