Starting phenix.real_space_refine on Wed Feb 14 04:07:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej0_31147/02_2024/7ej0_31147_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej0_31147/02_2024/7ej0_31147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej0_31147/02_2024/7ej0_31147.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej0_31147/02_2024/7ej0_31147.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej0_31147/02_2024/7ej0_31147_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej0_31147/02_2024/7ej0_31147_updated.pdb" } resolution = 3.2 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= -0.024 sd= 0.466 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 59 5.16 5 C 5486 2.51 5 N 1462 2.21 5 O 1593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 209": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "R GLU 122": "OE1" <-> "OE2" Residue "R ARG 202": "NH1" <-> "NH2" Residue "R ARG 240": "NH1" <-> "NH2" Residue "R ARG 383": "NH1" <-> "NH2" Residue "R GLU 384": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8600 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1715 Classifications: {'peptide': 217} Link IDs: {'CIS': 7, 'PTRANS': 4, 'TRANS': 205} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2564 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 3, 'PTRANS': 5, 'TRANS': 326} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 48} Chain: "H" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1794 Classifications: {'peptide': 233} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2109 Unusual residues: {'E5E': 1} Classifications: {'peptide': 260, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 248, None: 1} Not linked: pdbres="CYS R 457 " pdbres="E5E R 501 " Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LYS H 236 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS H 236 " occ=0.00 Time building chain proxies: 4.89, per 1000 atoms: 0.57 Number of scatterers: 8600 At special positions: 0 Unit cell: (90.95, 120.7, 124.1, 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 59 16.00 O 1593 8.00 N 1462 7.00 C 5486 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 121 " - pdb=" SG CYS R 203 " distance=1.82 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: 3.24 Conformation dependent library (CDL) restraints added in 1.6 seconds 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2050 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 22 helices and 11 sheets defined 30.9% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 8 through 30 Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 274 through 281 removed outlier: 3.931A pdb=" N LYS A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 309 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.940A pdb=" N CYS A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 25 Processing helix chain 'G' and resid 10 through 22 Processing helix chain 'G' and resid 30 through 44 Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'R' and resid 47 through 73 Processing helix chain 'R' and resid 84 through 107 removed outlier: 4.809A pdb=" N LEU R 96 " --> pdb=" O SER R 92 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA R 98 " --> pdb=" O ASP R 94 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N THR R 99 " --> pdb=" O ILE R 95 " (cutoff:3.500A) Proline residue: R 103 - end of helix Processing helix chain 'R' and resid 122 through 150 removed outlier: 3.605A pdb=" N SER R 135 " --> pdb=" O PHE R 131 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE R 136 " --> pdb=" O CYS R 132 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N CYS R 140 " --> pdb=" O ILE R 136 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA R 141 " --> pdb=" O VAL R 137 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER R 143 " --> pdb=" O LEU R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 159 removed outlier: 4.044A pdb=" N LEU R 158 " --> pdb=" O ILE R 154 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS R 159 " --> pdb=" O GLU R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 180 Processing helix chain 'R' and resid 209 through 219 removed outlier: 3.891A pdb=" N ILE R 213 " --> pdb=" O LYS R 209 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N SER R 214 " --> pdb=" O TRP R 210 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE R 217 " --> pdb=" O ILE R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 240 removed outlier: 3.936A pdb=" N LEU R 225 " --> pdb=" O PHE R 221 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE R 226 " --> pdb=" O ALA R 222 " (cutoff:3.500A) Processing helix chain 'R' and resid 380 through 411 removed outlier: 3.803A pdb=" N LYS R 385 " --> pdb=" O GLN R 381 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG R 386 " --> pdb=" O ASN R 382 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR R 388 " --> pdb=" O GLU R 384 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE R 389 " --> pdb=" O LYS R 385 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE R 398 " --> pdb=" O VAL R 394 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL R 399 " --> pdb=" O ILE R 395 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N CYS R 401 " --> pdb=" O VAL R 397 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TRP R 402 " --> pdb=" O PHE R 398 " (cutoff:3.500A) Proline residue: R 404 - end of helix Processing helix chain 'R' and resid 422 through 442 removed outlier: 3.731A pdb=" N TRP R 428 " --> pdb=" O PHE R 425 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN R 433 " --> pdb=" O GLY R 430 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN R 437 " --> pdb=" O SER R 434 " (cutoff:3.500A) Proline residue: R 438 - end of helix removed outlier: 4.146A pdb=" N TYR R 441 " --> pdb=" O PRO R 438 " (cutoff:3.500A) Processing helix chain 'R' and resid 446 through 456 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.754A pdb=" N ILE A 265 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N HIS A 322 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU A 267 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL A 226 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N CYS A 225 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 34 " --> pdb=" O HIS A 196 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 61 through 63 removed outlier: 3.501A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.107A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.975A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 295 through 298 removed outlier: 3.869A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 46 through 51 removed outlier: 4.133A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 150 through 153 removed outlier: 6.477A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.648A pdb=" N THR H 69 " --> pdb=" O GLN H 82 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 115 through 117 removed outlier: 3.633A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR H 50 " --> pdb=" O TYR H 59 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 128 through 130 Processing sheet with id= K, first strand: chain 'H' and resid 162 through 167 318 hydrogen bonds defined for protein. 891 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: 2.48 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1380 1.29 - 1.42: 2378 1.42 - 1.55: 4936 1.55 - 1.68: 5 1.68 - 1.81: 81 Bond restraints: 8780 Sorted by residual: bond pdb=" CA ASN R 437 " pdb=" C ASN R 437 " ideal model delta sigma weight residual 1.522 1.406 0.116 1.29e-02 6.01e+03 8.02e+01 bond pdb=" N PRO R 223 " pdb=" CD PRO R 223 " ideal model delta sigma weight residual 1.473 1.360 0.113 1.40e-02 5.10e+03 6.49e+01 bond pdb=" N ARG A 349 " pdb=" CA ARG A 349 " ideal model delta sigma weight residual 1.459 1.363 0.096 1.25e-02 6.40e+03 5.89e+01 bond pdb=" CA LEU R 125 " pdb=" C LEU R 125 " ideal model delta sigma weight residual 1.524 1.429 0.095 1.27e-02 6.20e+03 5.54e+01 bond pdb=" C SER R 135 " pdb=" O SER R 135 " ideal model delta sigma weight residual 1.236 1.155 0.082 1.15e-02 7.56e+03 5.03e+01 ... (remaining 8775 not shown) Histogram of bond angle deviations from ideal: 98.41 - 105.53: 166 105.53 - 112.66: 4518 112.66 - 119.79: 2821 119.79 - 126.91: 4282 126.91 - 134.04: 107 Bond angle restraints: 11894 Sorted by residual: angle pdb=" N LEU R 436 " pdb=" CA LEU R 436 " pdb=" C LEU R 436 " ideal model delta sigma weight residual 111.36 126.23 -14.87 1.09e+00 8.42e-01 1.86e+02 angle pdb=" N CYS R 224 " pdb=" CA CYS R 224 " pdb=" C CYS R 224 " ideal model delta sigma weight residual 111.36 98.77 12.59 1.09e+00 8.42e-01 1.33e+02 angle pdb=" N LEU A 348 " pdb=" CA LEU A 348 " pdb=" C LEU A 348 " ideal model delta sigma weight residual 111.71 98.51 13.20 1.15e+00 7.56e-01 1.32e+02 angle pdb=" N THR R 442 " pdb=" CA THR R 442 " pdb=" C THR R 442 " ideal model delta sigma weight residual 112.23 124.38 -12.15 1.26e+00 6.30e-01 9.30e+01 angle pdb=" N ALA R 238 " pdb=" CA ALA R 238 " pdb=" C ALA R 238 " ideal model delta sigma weight residual 113.16 103.92 9.24 1.24e+00 6.50e-01 5.55e+01 ... (remaining 11889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 4686 17.55 - 35.11: 400 35.11 - 52.66: 88 52.66 - 70.21: 11 70.21 - 87.77: 8 Dihedral angle restraints: 5193 sinusoidal: 2014 harmonic: 3179 Sorted by residual: dihedral pdb=" C TYR R 231 " pdb=" N TYR R 231 " pdb=" CA TYR R 231 " pdb=" CB TYR R 231 " ideal model delta harmonic sigma weight residual -122.60 -140.36 17.76 0 2.50e+00 1.60e-01 5.05e+01 dihedral pdb=" N TYR R 231 " pdb=" C TYR R 231 " pdb=" CA TYR R 231 " pdb=" CB TYR R 231 " ideal model delta harmonic sigma weight residual 122.80 138.80 -16.00 0 2.50e+00 1.60e-01 4.09e+01 dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 146.60 -53.60 1 1.00e+01 1.00e-02 3.90e+01 ... (remaining 5190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.167: 1312 0.167 - 0.334: 26 0.334 - 0.501: 8 0.501 - 0.668: 5 0.668 - 0.836: 1 Chirality restraints: 1352 Sorted by residual: chirality pdb=" CA TYR R 231 " pdb=" N TYR R 231 " pdb=" C TYR R 231 " pdb=" CB TYR R 231 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.84 2.00e-01 2.50e+01 1.75e+01 chirality pdb=" CA ARG A 349 " pdb=" N ARG A 349 " pdb=" C ARG A 349 " pdb=" CB ARG A 349 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.67e+00 chirality pdb=" CA PRO R 223 " pdb=" N PRO R 223 " pdb=" C PRO R 223 " pdb=" CB PRO R 223 " both_signs ideal model delta sigma weight residual False 2.72 2.17 0.55 2.00e-01 2.50e+01 7.56e+00 ... (remaining 1349 not shown) Planarity restraints: 1501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA R 222 " -0.084 5.00e-02 4.00e+02 1.45e-01 3.35e+01 pdb=" N PRO R 223 " 0.251 5.00e-02 4.00e+02 pdb=" CA PRO R 223 " -0.089 5.00e-02 4.00e+02 pdb=" CD PRO R 223 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 226 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C ILE R 226 " 0.067 2.00e-02 2.50e+03 pdb=" O ILE R 226 " -0.025 2.00e-02 2.50e+03 pdb=" N MET R 227 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 142 " 0.019 2.00e-02 2.50e+03 3.88e-02 1.50e+01 pdb=" C ILE R 142 " -0.067 2.00e-02 2.50e+03 pdb=" O ILE R 142 " 0.025 2.00e-02 2.50e+03 pdb=" N SER R 143 " 0.022 2.00e-02 2.50e+03 ... (remaining 1498 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 423 2.70 - 3.25: 8742 3.25 - 3.80: 12991 3.80 - 4.35: 16250 4.35 - 4.90: 26981 Nonbonded interactions: 65387 Sorted by model distance: nonbonded pdb=" OD1 ASP R 94 " pdb=" OG SER R 434 " model vdw 2.150 2.440 nonbonded pdb=" O THR R 133 " pdb=" CG2 VAL R 137 " model vdw 2.157 3.460 nonbonded pdb=" O HIS R 446 " pdb=" C ASP R 447 " model vdw 2.162 3.270 nonbonded pdb=" OG SER R 89 " pdb=" NE2 HIS R 138 " model vdw 2.195 2.520 nonbonded pdb=" O HIS R 446 " pdb=" N ARG R 449 " model vdw 2.235 2.520 ... (remaining 65382 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=0.00 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: 0.760 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: 4.080 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.980 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 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 : 0.009 0.116 8780 Z= 0.599 Angle : 1.116 23.392 11894 Z= 0.716 Chirality : 0.075 0.836 1352 Planarity : 0.006 0.145 1501 Dihedral : 13.818 87.768 3131 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.43 % Allowed : 1.93 % Favored : 97.65 % Cbeta Deviations : 0.68 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.32 % 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: -0.98 (0.25), residues: 1078 helix: 0.48 (0.30), residues: 333 sheet: 0.22 (0.34), residues: 231 loop : -1.87 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP R 428 HIS 0.004 0.001 HIS R 138 PHE 0.038 0.002 PHE R 220 TYR 0.033 0.002 TYR R 431 ARG 0.006 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 277 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 LYS cc_start: 0.8024 (tppp) cc_final: 0.7765 (ttmt) REVERT: G 46 LYS cc_start: 0.8841 (tptp) cc_final: 0.8471 (tppt) REVERT: R 208 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7545 (mt0) REVERT: R 425 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8572 (m-10) REVERT: R 445 ASN cc_start: 0.7983 (t0) cc_final: 0.7774 (t0) outliers start: 4 outliers final: 3 residues processed: 280 average time/residue: 0.1920 time to fit residues: 74.0304 Evaluate side-chains 202 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 198 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 423 PHE Chi-restraints excluded: chain R residue 425 PHE Chi-restraints excluded: chain R residue 436 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.0470 chunk 84 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 overall best weight: 1.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN A 331 ASN A 347 ASN B 13 GLN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN H 157 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8780 Z= 0.224 Angle : 0.683 10.168 11894 Z= 0.350 Chirality : 0.046 0.197 1352 Planarity : 0.004 0.077 1501 Dihedral : 5.882 54.359 1202 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.57 % Allowed : 14.01 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.32 % 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: -0.81 (0.25), residues: 1078 helix: 0.99 (0.29), residues: 341 sheet: -0.03 (0.34), residues: 242 loop : -1.96 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 428 HIS 0.004 0.001 HIS B 311 PHE 0.018 0.002 PHE B 241 TYR 0.012 0.001 TYR R 231 ARG 0.007 0.001 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 208 time to evaluate : 1.004 Fit side-chains TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 53 MET cc_start: 0.7185 (ppp) cc_final: 0.6488 (pmm) REVERT: A 291 TYR cc_start: 0.7132 (t80) cc_final: 0.6902 (t80) REVERT: A 349 ARG cc_start: 0.8017 (tpp80) cc_final: 0.7483 (ttm110) REVERT: G 27 ARG cc_start: 0.6553 (ptt-90) cc_final: 0.6277 (ptt90) REVERT: G 46 LYS cc_start: 0.8851 (tptp) cc_final: 0.8467 (tppt) REVERT: H 62 ASP cc_start: 0.8679 (p0) cc_final: 0.8467 (p0) REVERT: H 141 GLU cc_start: 0.8005 (tp30) cc_final: 0.7774 (tp30) REVERT: R 155 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8324 (tp30) REVERT: R 208 GLN cc_start: 0.8212 (mm-40) cc_final: 0.7484 (mt0) REVERT: R 236 GLN cc_start: 0.8618 (mm110) cc_final: 0.8222 (mt0) REVERT: R 425 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.8215 (m-10) REVERT: R 445 ASN cc_start: 0.8543 (t0) cc_final: 0.8267 (t0) outliers start: 24 outliers final: 15 residues processed: 219 average time/residue: 0.1959 time to fit residues: 59.6229 Evaluate side-chains 203 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 187 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 400 VAL Chi-restraints excluded: chain R residue 425 PHE Chi-restraints excluded: chain R residue 440 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 106 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 239 ASN B 293 ASN R 437 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8780 Z= 0.196 Angle : 0.641 10.276 11894 Z= 0.331 Chirality : 0.044 0.168 1352 Planarity : 0.004 0.054 1501 Dihedral : 5.395 47.240 1198 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.14 % Allowed : 17.75 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.32 % 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: -0.68 (0.25), residues: 1078 helix: 1.34 (0.29), residues: 339 sheet: 0.07 (0.35), residues: 230 loop : -2.03 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 169 HIS 0.004 0.001 HIS B 311 PHE 0.019 0.001 PHE B 241 TYR 0.012 0.001 TYR R 231 ARG 0.003 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 215 time to evaluate : 0.994 Fit side-chains TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 53 MET cc_start: 0.7122 (ppp) cc_final: 0.6424 (pmm) REVERT: A 291 TYR cc_start: 0.7057 (t80) cc_final: 0.6617 (t80) REVERT: A 349 ARG cc_start: 0.8104 (tpp80) cc_final: 0.7671 (ttm110) REVERT: B 175 GLN cc_start: 0.8094 (pm20) cc_final: 0.7515 (pm20) REVERT: B 259 GLN cc_start: 0.6719 (mm-40) cc_final: 0.6193 (mm110) REVERT: G 27 ARG cc_start: 0.6612 (ptt-90) cc_final: 0.6281 (ptt90) REVERT: G 46 LYS cc_start: 0.8829 (tptp) cc_final: 0.8445 (tppt) REVERT: H 62 ASP cc_start: 0.8677 (p0) cc_final: 0.8467 (p0) REVERT: H 83 MET cc_start: 0.8377 (mmp) cc_final: 0.8155 (mmp) REVERT: H 141 GLU cc_start: 0.8097 (tp30) cc_final: 0.7808 (tp30) REVERT: R 155 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8298 (tp30) REVERT: R 208 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7795 (mm-40) REVERT: R 236 GLN cc_start: 0.8538 (mm110) cc_final: 0.8261 (mt0) REVERT: R 425 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.8276 (m-10) REVERT: R 428 TRP cc_start: 0.8504 (m100) cc_final: 0.6336 (m-10) REVERT: R 445 ASN cc_start: 0.8461 (t0) cc_final: 0.8148 (t0) outliers start: 20 outliers final: 14 residues processed: 225 average time/residue: 0.1901 time to fit residues: 59.8374 Evaluate side-chains 209 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 194 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 391 LEU Chi-restraints excluded: chain R residue 400 VAL Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 425 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 ASN B 13 GLN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 293 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8780 Z= 0.319 Angle : 0.696 9.572 11894 Z= 0.363 Chirality : 0.046 0.182 1352 Planarity : 0.004 0.046 1501 Dihedral : 5.444 41.159 1198 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 4.28 % Allowed : 19.25 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.32 % 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: -0.78 (0.26), residues: 1078 helix: 1.37 (0.29), residues: 342 sheet: -0.27 (0.34), residues: 238 loop : -2.08 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 428 HIS 0.006 0.002 HIS B 311 PHE 0.016 0.002 PHE R 181 TYR 0.011 0.001 TYR H 178 ARG 0.004 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 188 time to evaluate : 1.010 Fit side-chains TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. REVERT: A 53 MET cc_start: 0.7356 (ppp) cc_final: 0.6612 (pmm) REVERT: A 349 ARG cc_start: 0.8118 (tpp80) cc_final: 0.7617 (ttm110) REVERT: B 175 GLN cc_start: 0.8258 (pm20) cc_final: 0.7625 (pm20) REVERT: B 259 GLN cc_start: 0.6951 (mm-40) cc_final: 0.6377 (mm110) REVERT: B 262 MET cc_start: 0.8996 (mmm) cc_final: 0.8552 (mmp) REVERT: G 27 ARG cc_start: 0.6985 (ptt-90) cc_final: 0.6096 (ptt90) REVERT: G 46 LYS cc_start: 0.8846 (tptp) cc_final: 0.8431 (tppt) REVERT: H 1 ASP cc_start: 0.8065 (m-30) cc_final: 0.7783 (t0) REVERT: H 62 ASP cc_start: 0.8734 (p0) cc_final: 0.8523 (p0) REVERT: H 141 GLU cc_start: 0.8114 (tp30) cc_final: 0.7800 (tp30) REVERT: H 218 MET cc_start: 0.8021 (tmm) cc_final: 0.7771 (tmm) REVERT: R 155 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8336 (tp30) REVERT: R 166 LYS cc_start: 0.7866 (mttm) cc_final: 0.7634 (mmtt) REVERT: R 224 CYS cc_start: 0.8777 (t) cc_final: 0.8452 (t) REVERT: R 236 GLN cc_start: 0.8583 (mm110) cc_final: 0.8335 (mt0) REVERT: R 428 TRP cc_start: 0.8363 (m100) cc_final: 0.6585 (m-10) REVERT: R 445 ASN cc_start: 0.8601 (t0) cc_final: 0.8326 (t0) outliers start: 40 outliers final: 31 residues processed: 211 average time/residue: 0.1904 time to fit residues: 56.3280 Evaluate side-chains 208 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 177 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 391 LEU Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 399 VAL Chi-restraints excluded: chain R residue 400 VAL Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 440 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 77 optimal weight: 0.0000 chunk 43 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 437 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8780 Z= 0.226 Angle : 0.663 11.201 11894 Z= 0.343 Chirality : 0.045 0.175 1352 Planarity : 0.003 0.039 1501 Dihedral : 5.128 35.607 1196 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.17 % Allowed : 20.53 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.32 % 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: -0.80 (0.26), residues: 1078 helix: 1.45 (0.29), residues: 341 sheet: -0.35 (0.34), residues: 242 loop : -2.12 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.004 0.001 HIS B 311 PHE 0.021 0.001 PHE B 241 TYR 0.008 0.001 TYR H 178 ARG 0.003 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 190 time to evaluate : 1.025 Fit side-chains TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. REVERT: A 53 MET cc_start: 0.7325 (ppp) cc_final: 0.6570 (pmm) REVERT: A 349 ARG cc_start: 0.8090 (tpp80) cc_final: 0.7613 (ttm110) REVERT: B 175 GLN cc_start: 0.8149 (pm20) cc_final: 0.7494 (pm20) REVERT: B 220 GLN cc_start: 0.8526 (mp10) cc_final: 0.8315 (mm-40) REVERT: B 259 GLN cc_start: 0.6786 (mm-40) cc_final: 0.6153 (mm110) REVERT: G 27 ARG cc_start: 0.7001 (ptt-90) cc_final: 0.6232 (ptt90) REVERT: G 46 LYS cc_start: 0.8843 (tptp) cc_final: 0.8458 (tppt) REVERT: H 1 ASP cc_start: 0.8086 (m-30) cc_final: 0.7782 (t0) REVERT: H 62 ASP cc_start: 0.8671 (p0) cc_final: 0.8452 (p0) REVERT: H 141 GLU cc_start: 0.8140 (tp30) cc_final: 0.7824 (tp30) REVERT: H 218 MET cc_start: 0.8014 (tmm) cc_final: 0.7764 (tmm) REVERT: R 155 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8334 (tp30) REVERT: R 224 CYS cc_start: 0.8736 (t) cc_final: 0.8406 (t) REVERT: R 233 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8022 (tpt90) REVERT: R 236 GLN cc_start: 0.8536 (mm110) cc_final: 0.8301 (mt0) REVERT: R 428 TRP cc_start: 0.8312 (m100) cc_final: 0.6433 (m-10) REVERT: R 445 ASN cc_start: 0.8557 (t0) cc_final: 0.8288 (t0) outliers start: 39 outliers final: 30 residues processed: 215 average time/residue: 0.1942 time to fit residues: 58.4927 Evaluate side-chains 208 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 177 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 222 GLU Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain R residue 391 LEU Chi-restraints excluded: chain R residue 399 VAL Chi-restraints excluded: chain R residue 400 VAL Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 104 optimal weight: 0.0010 chunk 86 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8780 Z= 0.228 Angle : 0.654 9.845 11894 Z= 0.339 Chirality : 0.045 0.172 1352 Planarity : 0.003 0.035 1501 Dihedral : 5.129 35.720 1196 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.28 % Allowed : 20.96 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.32 % 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: -0.81 (0.26), residues: 1078 helix: 1.43 (0.29), residues: 347 sheet: -0.35 (0.34), residues: 241 loop : -2.17 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 47 HIS 0.004 0.001 HIS B 311 PHE 0.044 0.001 PHE B 235 TYR 0.008 0.001 TYR H 178 ARG 0.004 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 189 time to evaluate : 1.056 Fit side-chains TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. REVERT: A 53 MET cc_start: 0.7296 (ppp) cc_final: 0.6523 (pmm) REVERT: A 349 ARG cc_start: 0.8130 (tpp80) cc_final: 0.7674 (ttm110) REVERT: B 175 GLN cc_start: 0.8179 (pm20) cc_final: 0.7514 (pm20) REVERT: B 213 VAL cc_start: 0.9081 (t) cc_final: 0.8879 (m) REVERT: B 259 GLN cc_start: 0.6750 (mm-40) cc_final: 0.6435 (mm110) REVERT: G 46 LYS cc_start: 0.8841 (tptp) cc_final: 0.8449 (tppt) REVERT: H 1 ASP cc_start: 0.8116 (m-30) cc_final: 0.7747 (t0) REVERT: H 62 ASP cc_start: 0.8674 (p0) cc_final: 0.8438 (p0) REVERT: H 141 GLU cc_start: 0.8139 (tp30) cc_final: 0.7824 (tp30) REVERT: H 218 MET cc_start: 0.8006 (tmm) cc_final: 0.7749 (tmm) REVERT: R 155 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8309 (tp30) REVERT: R 224 CYS cc_start: 0.8807 (t) cc_final: 0.8492 (t) REVERT: R 233 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8084 (tpt90) REVERT: R 236 GLN cc_start: 0.8532 (mm110) cc_final: 0.8306 (mt0) REVERT: R 428 TRP cc_start: 0.8317 (m100) cc_final: 0.6379 (m-10) REVERT: R 445 ASN cc_start: 0.8543 (t0) cc_final: 0.8286 (t0) outliers start: 40 outliers final: 33 residues processed: 215 average time/residue: 0.1904 time to fit residues: 57.6095 Evaluate side-chains 209 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 175 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 222 GLU Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 232 VAL Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain R residue 391 LEU Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 399 VAL Chi-restraints excluded: chain R residue 400 VAL Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 10.0000 chunk 11 optimal weight: 0.3980 chunk 59 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 58 optimal weight: 0.0770 chunk 104 optimal weight: 7.9990 chunk 65 optimal weight: 0.0980 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8780 Z= 0.168 Angle : 0.641 12.382 11894 Z= 0.329 Chirality : 0.044 0.175 1352 Planarity : 0.003 0.034 1501 Dihedral : 4.901 35.178 1196 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.89 % Allowed : 23.21 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.32 % 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: -0.72 (0.26), residues: 1078 helix: 1.54 (0.29), residues: 346 sheet: -0.22 (0.35), residues: 233 loop : -2.16 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 47 HIS 0.004 0.001 HIS B 54 PHE 0.042 0.001 PHE B 235 TYR 0.007 0.001 TYR R 231 ARG 0.007 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 190 time to evaluate : 1.106 Fit side-chains TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. REVERT: A 20 GLU cc_start: 0.8721 (tp30) cc_final: 0.8291 (tp30) REVERT: A 53 MET cc_start: 0.7267 (ppp) cc_final: 0.6498 (pmm) REVERT: A 349 ARG cc_start: 0.8129 (tpp80) cc_final: 0.7680 (ttm110) REVERT: B 175 GLN cc_start: 0.8176 (pm20) cc_final: 0.7532 (pm20) REVERT: B 259 GLN cc_start: 0.6673 (mm-40) cc_final: 0.6421 (mm110) REVERT: G 46 LYS cc_start: 0.8841 (tptp) cc_final: 0.8444 (tppt) REVERT: H 1 ASP cc_start: 0.8107 (m-30) cc_final: 0.7740 (t0) REVERT: H 73 ASP cc_start: 0.7482 (t0) cc_final: 0.7270 (t0) REVERT: H 141 GLU cc_start: 0.8085 (tp30) cc_final: 0.7768 (tp30) REVERT: H 218 MET cc_start: 0.7985 (tmm) cc_final: 0.7727 (tmm) REVERT: R 155 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8271 (tp30) REVERT: R 224 CYS cc_start: 0.8765 (t) cc_final: 0.8472 (t) REVERT: R 428 TRP cc_start: 0.8266 (m100) cc_final: 0.6351 (m-10) REVERT: R 445 ASN cc_start: 0.8481 (t0) cc_final: 0.8204 (t0) outliers start: 27 outliers final: 21 residues processed: 209 average time/residue: 0.1841 time to fit residues: 53.9528 Evaluate side-chains 202 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 181 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 134 SER Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 232 VAL Chi-restraints excluded: chain R residue 391 LEU Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8780 Z= 0.176 Angle : 0.646 11.424 11894 Z= 0.330 Chirality : 0.044 0.188 1352 Planarity : 0.003 0.033 1501 Dihedral : 4.792 34.881 1196 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.89 % Allowed : 23.53 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.32 % 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: -0.68 (0.26), residues: 1078 helix: 1.62 (0.28), residues: 344 sheet: -0.22 (0.35), residues: 233 loop : -2.15 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 47 HIS 0.004 0.001 HIS B 54 PHE 0.044 0.001 PHE B 235 TYR 0.007 0.001 TYR R 231 ARG 0.004 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 189 time to evaluate : 1.045 Fit side-chains TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. REVERT: A 20 GLU cc_start: 0.8710 (tp30) cc_final: 0.8274 (tp30) REVERT: A 33 ASP cc_start: 0.8568 (m-30) cc_final: 0.8337 (t0) REVERT: A 53 MET cc_start: 0.7248 (ppp) cc_final: 0.6481 (pmm) REVERT: A 349 ARG cc_start: 0.8157 (tpp80) cc_final: 0.7821 (ttm110) REVERT: B 175 GLN cc_start: 0.8165 (pm20) cc_final: 0.7511 (pm20) REVERT: G 46 LYS cc_start: 0.8841 (tptp) cc_final: 0.8439 (tppt) REVERT: H 1 ASP cc_start: 0.8058 (m-30) cc_final: 0.7683 (t0) REVERT: H 73 ASP cc_start: 0.7512 (t0) cc_final: 0.7302 (t0) REVERT: H 141 GLU cc_start: 0.8076 (tp30) cc_final: 0.7753 (tp30) REVERT: H 218 MET cc_start: 0.7960 (tmm) cc_final: 0.7700 (tmm) REVERT: R 106 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8977 (mm) REVERT: R 155 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8261 (tp30) REVERT: R 224 CYS cc_start: 0.8731 (t) cc_final: 0.8464 (t) REVERT: R 428 TRP cc_start: 0.8269 (m100) cc_final: 0.6331 (m-10) REVERT: R 445 ASN cc_start: 0.8471 (t0) cc_final: 0.8194 (t0) outliers start: 27 outliers final: 22 residues processed: 208 average time/residue: 0.1857 time to fit residues: 54.4519 Evaluate side-chains 204 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 181 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 134 SER Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 232 VAL Chi-restraints excluded: chain R residue 391 LEU Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 0.0040 chunk 42 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 0.1980 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN B 13 GLN B 54 HIS B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8780 Z= 0.160 Angle : 0.650 11.297 11894 Z= 0.329 Chirality : 0.043 0.188 1352 Planarity : 0.003 0.033 1501 Dihedral : 4.653 34.365 1196 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.21 % Allowed : 23.64 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.32 % 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: -0.62 (0.26), residues: 1078 helix: 1.66 (0.28), residues: 343 sheet: -0.16 (0.35), residues: 233 loop : -2.11 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 47 HIS 0.004 0.001 HIS B 311 PHE 0.043 0.001 PHE B 235 TYR 0.007 0.001 TYR R 231 ARG 0.004 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 195 time to evaluate : 1.003 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. REVERT: A 20 GLU cc_start: 0.8699 (tp30) cc_final: 0.8274 (tp30) REVERT: A 53 MET cc_start: 0.7214 (ppp) cc_final: 0.6455 (pmm) REVERT: A 349 ARG cc_start: 0.8160 (tpp80) cc_final: 0.7843 (ttm110) REVERT: B 175 GLN cc_start: 0.8160 (pm20) cc_final: 0.7487 (pm20) REVERT: G 46 LYS cc_start: 0.8857 (tptp) cc_final: 0.8453 (tppt) REVERT: H 1 ASP cc_start: 0.8064 (m-30) cc_final: 0.7682 (t0) REVERT: H 73 ASP cc_start: 0.7465 (t0) cc_final: 0.7248 (t0) REVERT: H 141 GLU cc_start: 0.8127 (tp30) cc_final: 0.7804 (tp30) REVERT: R 106 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8964 (mm) REVERT: R 155 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8244 (tp30) REVERT: R 224 CYS cc_start: 0.8731 (t) cc_final: 0.8467 (t) REVERT: R 428 TRP cc_start: 0.8232 (m100) cc_final: 0.6270 (m-10) REVERT: R 445 ASN cc_start: 0.8406 (t0) cc_final: 0.8137 (t0) outliers start: 30 outliers final: 24 residues processed: 215 average time/residue: 0.1797 time to fit residues: 54.4580 Evaluate side-chains 210 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 185 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 134 SER Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 232 VAL Chi-restraints excluded: chain R residue 391 LEU Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 8 optimal weight: 0.0570 chunk 66 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8780 Z= 0.181 Angle : 0.658 11.026 11894 Z= 0.333 Chirality : 0.044 0.189 1352 Planarity : 0.003 0.033 1501 Dihedral : 4.628 34.458 1196 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.78 % Allowed : 23.96 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.32 % 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: -0.62 (0.26), residues: 1078 helix: 1.69 (0.28), residues: 345 sheet: -0.08 (0.35), residues: 224 loop : -2.16 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 47 HIS 0.005 0.001 HIS B 311 PHE 0.042 0.001 PHE B 235 TYR 0.008 0.001 TYR H 102 ARG 0.004 0.000 ARG A 313 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 188 time to evaluate : 1.033 Fit side-chains TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. REVERT: A 20 GLU cc_start: 0.8689 (tp30) cc_final: 0.8260 (tp30) REVERT: A 53 MET cc_start: 0.7227 (ppp) cc_final: 0.6457 (pmm) REVERT: A 349 ARG cc_start: 0.8107 (tpp80) cc_final: 0.7777 (ttm110) REVERT: B 175 GLN cc_start: 0.8185 (pm20) cc_final: 0.7503 (pm20) REVERT: G 46 LYS cc_start: 0.8855 (tptp) cc_final: 0.8453 (tppt) REVERT: H 1 ASP cc_start: 0.8056 (m-30) cc_final: 0.7679 (t0) REVERT: H 73 ASP cc_start: 0.7478 (t0) cc_final: 0.7276 (t0) REVERT: H 141 GLU cc_start: 0.8118 (tp30) cc_final: 0.7798 (tp30) REVERT: R 106 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8966 (mm) REVERT: R 155 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8250 (tp30) REVERT: R 224 CYS cc_start: 0.8750 (t) cc_final: 0.8486 (t) REVERT: R 428 TRP cc_start: 0.8239 (m100) cc_final: 0.6242 (m-10) REVERT: R 445 ASN cc_start: 0.8394 (t0) cc_final: 0.8116 (t0) outliers start: 26 outliers final: 24 residues processed: 204 average time/residue: 0.1988 time to fit residues: 57.4187 Evaluate side-chains 210 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 185 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 134 SER Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 232 VAL Chi-restraints excluded: chain R residue 391 LEU Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 0.0980 chunk 23 optimal weight: 0.0970 chunk 85 optimal weight: 0.0980 chunk 35 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN B 239 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.127902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.102630 restraints weight = 18064.107| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.69 r_work: 0.3364 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8780 Z= 0.155 Angle : 0.650 11.626 11894 Z= 0.326 Chirality : 0.043 0.185 1352 Planarity : 0.003 0.033 1501 Dihedral : 4.456 33.842 1196 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.35 % Allowed : 24.49 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.32 % 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: -0.54 (0.26), residues: 1078 helix: 1.71 (0.28), residues: 343 sheet: -0.01 (0.35), residues: 226 loop : -2.09 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 47 HIS 0.005 0.001 HIS B 311 PHE 0.042 0.001 PHE B 235 TYR 0.008 0.001 TYR R 231 ARG 0.004 0.000 ARG G 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2352.25 seconds wall clock time: 43 minutes 25.52 seconds (2605.52 seconds total)