Starting phenix.real_space_refine on Mon Mar 11 03:04:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybv_10774/03_2024/6ybv_10774.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybv_10774/03_2024/6ybv_10774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybv_10774/03_2024/6ybv_10774.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybv_10774/03_2024/6ybv_10774.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybv_10774/03_2024/6ybv_10774.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybv_10774/03_2024/6ybv_10774.pdb" } resolution = 3.8 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= 0.004 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 36 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 77 5.49 5 S 21 5.16 5 C 3877 2.51 5 N 1250 2.21 5 O 1506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "s TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 188": "NH1" <-> "NH2" Residue "s ARG 200": "NH1" <-> "NH2" Residue "s ARG 211": "NH1" <-> "NH2" Residue "s PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 243": "OE1" <-> "OE2" Residue "s ARG 261": "NH1" <-> "NH2" Residue "s PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 268": "OE1" <-> "OE2" Residue "s GLU 277": "OE1" <-> "OE2" Residue "s ARG 285": "NH1" <-> "NH2" Residue "s ASP 288": "OD1" <-> "OD2" Residue "s ASP 294": "OD1" <-> "OD2" Residue "s ARG 296": "NH1" <-> "NH2" Residue "s PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 308": "NH1" <-> "NH2" Residue "r ARG 7": "NH1" <-> "NH2" Residue "r ARG 25": "NH1" <-> "NH2" Residue "r ARG 57": "NH1" <-> "NH2" Residue "r ARG 75": "NH1" <-> "NH2" Residue "r ASP 77": "OD1" <-> "OD2" Residue "r GLU 79": "OE1" <-> "OE2" Residue "r ARG 88": "NH1" <-> "NH2" Residue "r ARG 89": "NH1" <-> "NH2" Residue "r ARG 113": "NH1" <-> "NH2" Residue "r GLU 128": "OE1" <-> "OE2" Residue "r PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 133": "NH1" <-> "NH2" Residue "r ARG 144": "NH1" <-> "NH2" Residue "r ARG 173": "NH1" <-> "NH2" Residue "r ARG 182": "NH1" <-> "NH2" Residue "r ARG 183": "NH1" <-> "NH2" Residue "r ASP 194": "OD1" <-> "OD2" Residue "r GLU 221": "OE1" <-> "OE2" Residue "r ARG 234": "NH1" <-> "NH2" Residue "r ARG 244": "NH1" <-> "NH2" Residue "r ARG 266": "NH1" <-> "NH2" 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: 6731 Number of models: 1 Model: "" Number of chains: 5 Chain: "s" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1123 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "r" Number of atoms: 2215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2215 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 9, 'TRANS': 265} Chain: "w" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1604 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 4, 'rna3p_pur': 34, 'rna3p_pyr': 29} Link IDs: {'rna2p': 12, 'rna3p': 62} Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 2} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {' A%rna2p_pur:plan': 1, ' A%rna2p_pur:plan2': 1, ' A%rna3p_pur:plan2': 2, ' A%rna3p_pur:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "t" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 1750 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 298} Link IDs: {'PTRANS': 15, 'TRANS': 340} Chain breaks: 4 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1009 Unresolved non-hydrogen angles: 1285 Unresolved non-hydrogen dihedrals: 814 Unresolved non-hydrogen chiralities: 125 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 9, 'TYR:plan': 6, 'ASN:plan1': 12, 'TRP:plan': 2, 'HIS:plan': 9, 'PHE:plan': 8, 'GLU:plan': 23, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 445 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ALA t 51 " occ=0.32 ... (3 atoms not shown) pdb=" CB ALA t 51 " occ=0.32 residue: pdb=" N GLN t 206 " occ=0.55 ... (3 atoms not shown) pdb=" CB GLN t 206 " occ=0.55 residue: pdb=" N LEU t 208 " occ=0.35 ... (3 atoms not shown) pdb=" CB LEU t 208 " occ=0.35 residue: pdb=" N ASN t 431 " occ=0.42 ... (3 atoms not shown) pdb=" CB ASN t 431 " occ=0.42 Time building chain proxies: 4.52, per 1000 atoms: 0.67 Number of scatterers: 6731 At special positions: 0 Unit cell: (111.696, 117.066, 106.326, 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 21 16.00 P 77 15.00 O 1506 8.00 N 1250 7.00 C 3877 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 1.1 seconds 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1444 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 9 sheets defined 33.7% alpha, 16.4% beta 14 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 's' and resid 176 through 186 Processing helix chain 's' and resid 221 through 229 Processing helix chain 's' and resid 234 through 243 removed outlier: 4.012A pdb=" N ALA s 238 " --> pdb=" O LYS s 234 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE s 239 " --> pdb=" O HIS s 235 " (cutoff:3.500A) Processing helix chain 's' and resid 244 through 246 No H-bonds generated for 'chain 's' and resid 244 through 246' Processing helix chain 's' and resid 263 through 278 Processing helix chain 'r' and resid 58 through 63 removed outlier: 3.609A pdb=" N LEU r 62 " --> pdb=" O SER r 58 " (cutoff:3.500A) Processing helix chain 'r' and resid 91 through 119 Processing helix chain 'r' and resid 123 through 134 Processing helix chain 'r' and resid 134 through 142 Processing helix chain 'r' and resid 146 through 157 Processing helix chain 'r' and resid 161 through 166 removed outlier: 3.694A pdb=" N LEU r 166 " --> pdb=" O LEU r 163 " (cutoff:3.500A) Processing helix chain 'r' and resid 169 through 181 removed outlier: 3.697A pdb=" N ARG r 173 " --> pdb=" O ASN r 169 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU r 174 " --> pdb=" O GLU r 170 " (cutoff:3.500A) Processing helix chain 'r' and resid 203 through 218 Processing helix chain 'r' and resid 243 through 262 removed outlier: 3.720A pdb=" N GLY r 247 " --> pdb=" O GLU r 243 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER r 249 " --> pdb=" O THR r 245 " (cutoff:3.500A) Processing helix chain 't' and resid 53 through 63 Processing helix chain 't' and resid 69 through 76 Processing helix chain 't' and resid 141 through 152 removed outlier: 3.949A pdb=" N MET t 145 " --> pdb=" O LEU t 141 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL t 151 " --> pdb=" O ASN t 147 " (cutoff:3.500A) Processing helix chain 't' and resid 168 through 181 Processing helix chain 't' and resid 196 through 212 Processing helix chain 't' and resid 214 through 219 removed outlier: 4.131A pdb=" N GLY t 218 " --> pdb=" O VAL t 215 " (cutoff:3.500A) Processing helix chain 't' and resid 231 through 243 Processing helix chain 't' and resid 344 through 349 Processing sheet with id=AA1, first strand: chain 's' and resid 218 through 219 removed outlier: 4.107A pdb=" N VAL s 257 " --> pdb=" O SER s 249 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER s 249 " --> pdb=" O VAL s 257 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 's' and resid 291 through 293 removed outlier: 3.693A pdb=" N GLN s 292 " --> pdb=" O PHE s 299 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE s 299 " --> pdb=" O GLN s 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'r' and resid 19 through 24 removed outlier: 8.870A pdb=" N LEU r 85 " --> pdb=" O GLU r 43 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N MET r 45 " --> pdb=" O LEU r 85 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASP r 84 " --> pdb=" O ILE r 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'r' and resid 226 through 229 removed outlier: 3.751A pdb=" N ASN r 228 " --> pdb=" O VAL r 236 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU r 196 " --> pdb=" O ASN r 270 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN r 270 " --> pdb=" O GLU r 196 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 't' and resid 84 through 86 removed outlier: 3.615A pdb=" N ALA t 84 " --> pdb=" O PHE t 132 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE t 44 " --> pdb=" O VAL t 133 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLY t 45 " --> pdb=" O LEU t 156 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU t 158 " --> pdb=" O GLY t 45 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE t 47 " --> pdb=" O LEU t 158 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ALA t 155 " --> pdb=" O LEU t 186 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N LEU t 188 " --> pdb=" O ALA t 155 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU t 157 " --> pdb=" O LEU t 188 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE t 222 " --> pdb=" O ILE t 187 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 't' and resid 283 through 285 removed outlier: 6.429A pdb=" N ARG t 255 " --> pdb=" O LEU t 284 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 't' and resid 279 through 281 removed outlier: 3.777A pdb=" N ALA t 279 " --> pdb=" O VAL t 339 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 't' and resid 367 through 368 removed outlier: 3.908A pdb=" N VAL t 433 " --> pdb=" O PHE t 368 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 't' and resid 411 through 413 removed outlier: 3.756A pdb=" N ASN t 407 " --> pdb=" O ALA t 442 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ALA t 442 " --> pdb=" O ASN t 407 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE t 441 " --> pdb=" O TRP t 456 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N TRP t 456 " --> pdb=" O ILE t 441 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU t 443 " --> pdb=" O ILE t 454 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP t 456 " --> pdb=" O PHE t 376 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE t 373 " --> pdb=" O GLY t 425 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY t 425 " --> pdb=" O ILE t 373 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU t 424 " --> pdb=" O VAL t 420 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N VAL t 420 " --> pdb=" O LEU t 424 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LYS t 426 " --> pdb=" O SER t 418 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER t 418 " --> pdb=" O LYS t 426 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL t 428 " --> pdb=" O ARG t 416 " (cutoff:3.500A) 221 hydrogen bonds defined for protein. 624 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1471 1.33 - 1.45: 1866 1.45 - 1.57: 3452 1.57 - 1.70: 150 1.70 - 1.82: 31 Bond restraints: 6970 Sorted by residual: bond pdb=" C VAL r 90 " pdb=" N SER r 91 " ideal model delta sigma weight residual 1.339 1.213 0.126 5.57e-02 3.22e+02 5.13e+00 bond pdb=" C CYS t 311 " pdb=" N LYS t 312 " ideal model delta sigma weight residual 1.335 1.256 0.079 3.59e-02 7.76e+02 4.81e+00 bond pdb=" N GLU t 324 " pdb=" CA GLU t 324 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.64e+00 bond pdb=" C5' G w 10 " pdb=" C4' G w 10 " ideal model delta sigma weight residual 1.508 1.480 0.028 1.50e-02 4.44e+03 3.59e+00 bond pdb=" CB VAL r 71 " pdb=" CG2 VAL r 71 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.58e+00 ... (remaining 6965 not shown) Histogram of bond angle deviations from ideal: 97.09 - 105.55: 504 105.55 - 114.02: 4059 114.02 - 122.48: 4044 122.48 - 130.94: 1201 130.94 - 139.40: 32 Bond angle restraints: 9840 Sorted by residual: angle pdb=" N PRO t 168 " pdb=" CA PRO t 168 " pdb=" C PRO t 168 " ideal model delta sigma weight residual 112.47 124.78 -12.31 2.06e+00 2.36e-01 3.57e+01 angle pdb=" N VAL s 203 " pdb=" CA VAL s 203 " pdb=" C VAL s 203 " ideal model delta sigma weight residual 109.34 97.09 12.25 2.08e+00 2.31e-01 3.47e+01 angle pdb=" N GLY s 252 " pdb=" CA GLY s 252 " pdb=" C GLY s 252 " ideal model delta sigma weight residual 112.18 105.50 6.68 1.34e+00 5.57e-01 2.48e+01 angle pdb=" CA ARG s 272 " pdb=" CB ARG s 272 " pdb=" CG ARG s 272 " ideal model delta sigma weight residual 114.10 124.02 -9.92 2.00e+00 2.50e-01 2.46e+01 angle pdb=" C4' G w 52 " pdb=" C3' G w 52 " pdb=" O3' G w 52 " ideal model delta sigma weight residual 113.00 120.35 -7.35 1.50e+00 4.44e-01 2.40e+01 ... (remaining 9835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.56: 3765 24.56 - 49.11: 386 49.11 - 73.67: 141 73.67 - 98.23: 18 98.23 - 122.78: 2 Dihedral angle restraints: 4312 sinusoidal: 2090 harmonic: 2222 Sorted by residual: dihedral pdb=" O4' C w 73 " pdb=" C1' C w 73 " pdb=" N1 C w 73 " pdb=" C2 C w 73 " ideal model delta sinusoidal sigma weight residual -128.00 -44.83 -83.17 1 1.70e+01 3.46e-03 2.93e+01 dihedral pdb=" O4' A k 17 " pdb=" C2' A k 17 " pdb=" C1' A k 17 " pdb=" C3' A k 17 " ideal model delta sinusoidal sigma weight residual 25.00 -9.51 34.51 1 8.00e+00 1.56e-02 2.64e+01 dihedral pdb=" O4' A k 16 " pdb=" C2' A k 16 " pdb=" C1' A k 16 " pdb=" C3' A k 16 " ideal model delta sinusoidal sigma weight residual 25.00 -9.08 34.08 1 8.00e+00 1.56e-02 2.58e+01 ... (remaining 4309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 883 0.068 - 0.136: 271 0.136 - 0.204: 68 0.204 - 0.272: 9 0.272 - 0.340: 4 Chirality restraints: 1235 Sorted by residual: chirality pdb=" C1' C w 73 " pdb=" O4' C w 73 " pdb=" C2' C w 73 " pdb=" N1 C w 73 " both_signs ideal model delta sigma weight residual False 2.45 2.11 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CB VAL r 34 " pdb=" CA VAL r 34 " pdb=" CG1 VAL r 34 " pdb=" CG2 VAL r 34 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA PRO t 168 " pdb=" N PRO t 168 " pdb=" C PRO t 168 " pdb=" CB PRO t 168 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 1232 not shown) Planarity restraints: 1011 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN s 292 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" CD GLN s 292 " 0.063 2.00e-02 2.50e+03 pdb=" OE1 GLN s 292 " -0.024 2.00e-02 2.50e+03 pdb=" NE2 GLN s 292 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G w 12 " -0.008 2.00e-02 2.50e+03 2.03e-02 1.24e+01 pdb=" N9 G w 12 " 0.037 2.00e-02 2.50e+03 pdb=" C8 G w 12 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G w 12 " -0.004 2.00e-02 2.50e+03 pdb=" C5 G w 12 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G w 12 " 0.009 2.00e-02 2.50e+03 pdb=" O6 G w 12 " -0.004 2.00e-02 2.50e+03 pdb=" N1 G w 12 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G w 12 " 0.033 2.00e-02 2.50e+03 pdb=" N2 G w 12 " -0.017 2.00e-02 2.50e+03 pdb=" N3 G w 12 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G w 12 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA t 323 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C ALA t 323 " -0.056 2.00e-02 2.50e+03 pdb=" O ALA t 323 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU t 324 " 0.019 2.00e-02 2.50e+03 ... (remaining 1008 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 888 2.74 - 3.28: 6205 3.28 - 3.82: 11334 3.82 - 4.36: 12440 4.36 - 4.90: 19659 Nonbonded interactions: 50526 Sorted by model distance: nonbonded pdb=" O6 G w 9 " pdb=" O2' A w 19 " model vdw 2.202 2.440 nonbonded pdb=" O ALA s 196 " pdb=" NH2 ARG s 285 " model vdw 2.245 2.520 nonbonded pdb=" OG1 THR s 246 " pdb=" O LYS s 259 " model vdw 2.251 2.440 nonbonded pdb=" OG1 THR r 220 " pdb=" O MET r 223 " model vdw 2.259 2.440 nonbonded pdb=" O LYS r 104 " pdb=" OG1 THR r 107 " model vdw 2.277 2.440 ... (remaining 50521 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=0.32 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: 6.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 24.000 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.340 Find NCS groups from input model: 0.170 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5583 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 0.126 6970 Z= 0.532 Angle : 1.466 15.017 9840 Z= 0.842 Chirality : 0.071 0.340 1235 Planarity : 0.009 0.069 1011 Dihedral : 21.435 122.782 2868 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.09 % Favored : 93.38 % Rotamer: Outliers : 6.67 % Allowed : 22.67 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.26), residues: 755 helix: -0.78 (0.32), residues: 214 sheet: 0.05 (0.50), residues: 109 loop : -2.41 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.004 TRP r 136 HIS 0.007 0.003 HIS r 155 PHE 0.032 0.005 PHE r 131 TYR 0.030 0.004 TYR s 176 ARG 0.016 0.002 ARG s 285 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 102 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: r 74 ILE cc_start: 0.7523 (mm) cc_final: 0.7291 (mm) REVERT: r 89 ARG cc_start: 0.6209 (OUTLIER) cc_final: 0.4586 (mmt180) REVERT: r 121 TYR cc_start: 0.2630 (OUTLIER) cc_final: 0.1330 (m-80) REVERT: r 182 ARG cc_start: 0.7039 (mtm180) cc_final: 0.6591 (ttp-170) REVERT: r 273 MET cc_start: 0.3052 (mtt) cc_final: 0.0831 (ttt) outliers start: 25 outliers final: 6 residues processed: 120 average time/residue: 0.2665 time to fit residues: 39.0908 Evaluate side-chains 62 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 244 LEU Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 73 VAL Chi-restraints excluded: chain r residue 89 ARG Chi-restraints excluded: chain r residue 121 TYR Chi-restraints excluded: chain r residue 271 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 306 HIS ** r 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 179 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5737 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6970 Z= 0.279 Angle : 0.758 8.207 9840 Z= 0.408 Chirality : 0.047 0.224 1235 Planarity : 0.005 0.064 1011 Dihedral : 21.124 112.814 2021 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.56 % Favored : 94.04 % Rotamer: Outliers : 5.07 % Allowed : 31.20 % Favored : 63.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.27), residues: 755 helix: -0.26 (0.32), residues: 217 sheet: -0.18 (0.47), residues: 105 loop : -2.16 (0.25), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP r 136 HIS 0.016 0.003 HIS s 306 PHE 0.012 0.002 PHE s 239 TYR 0.019 0.003 TYR r 235 ARG 0.006 0.001 ARG r 234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 55 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: s 204 MET cc_start: 0.3706 (pmm) cc_final: 0.2818 (pmm) REVERT: r 48 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8430 (tm) REVERT: r 89 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.5627 (mmt180) REVERT: r 121 TYR cc_start: 0.3147 (OUTLIER) cc_final: 0.1595 (m-80) outliers start: 19 outliers final: 6 residues processed: 74 average time/residue: 0.2160 time to fit residues: 20.7877 Evaluate side-chains 51 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 221 ASN Chi-restraints excluded: chain s residue 279 VAL Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 73 VAL Chi-restraints excluded: chain r residue 89 ARG Chi-restraints excluded: chain r residue 121 TYR Chi-restraints excluded: chain r residue 278 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 50 optimal weight: 0.0370 chunk 20 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 40 ASN ** r 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5913 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 6970 Z= 0.360 Angle : 0.858 14.129 9840 Z= 0.449 Chirality : 0.050 0.244 1235 Planarity : 0.006 0.063 1011 Dihedral : 21.420 137.896 2018 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 24.75 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.87 % Favored : 90.86 % Rotamer: Outliers : 7.73 % Allowed : 30.67 % Favored : 61.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.27), residues: 755 helix: -0.61 (0.32), residues: 223 sheet: -0.96 (0.49), residues: 104 loop : -2.39 (0.26), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP r 136 HIS 0.008 0.002 HIS s 306 PHE 0.027 0.003 PHE s 239 TYR 0.023 0.003 TYR r 150 ARG 0.009 0.001 ARG s 231 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 49 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: s 226 CYS cc_start: 0.5767 (t) cc_final: 0.5070 (t) REVERT: r 30 MET cc_start: 0.5452 (ptt) cc_final: 0.5136 (ptm) REVERT: r 48 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8611 (tm) REVERT: r 89 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.5982 (mmt180) outliers start: 29 outliers final: 12 residues processed: 77 average time/residue: 0.2439 time to fit residues: 26.4138 Evaluate side-chains 57 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 43 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 217 THR Chi-restraints excluded: chain s residue 221 ASN Chi-restraints excluded: chain s residue 224 ASP Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 34 VAL Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 73 VAL Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain r residue 89 ARG Chi-restraints excluded: chain r residue 119 LEU Chi-restraints excluded: chain r residue 242 LEU Chi-restraints excluded: chain r residue 268 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 0.2980 chunk 21 optimal weight: 6.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 181 ASN s 221 ASN ** r 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5889 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 6970 Z= 0.290 Angle : 0.744 11.728 9840 Z= 0.391 Chirality : 0.047 0.211 1235 Planarity : 0.005 0.050 1011 Dihedral : 21.334 123.566 2016 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.48 % Favored : 91.26 % Rotamer: Outliers : 6.13 % Allowed : 29.60 % Favored : 64.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.27), residues: 755 helix: -0.56 (0.31), residues: 223 sheet: -1.56 (0.58), residues: 69 loop : -2.31 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP r 136 HIS 0.005 0.002 HIS s 306 PHE 0.018 0.002 PHE s 299 TYR 0.018 0.002 TYR r 150 ARG 0.006 0.001 ARG s 231 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 52 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: r 89 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.5758 (mmt180) outliers start: 23 outliers final: 11 residues processed: 74 average time/residue: 0.1876 time to fit residues: 18.5833 Evaluate side-chains 58 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 250 ILE Chi-restraints excluded: chain s residue 279 VAL Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 73 VAL Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain r residue 89 ARG Chi-restraints excluded: chain r residue 119 LEU Chi-restraints excluded: chain r residue 176 LEU Chi-restraints excluded: chain r residue 229 LEU Chi-restraints excluded: chain r residue 252 SER Chi-restraints excluded: chain r residue 268 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 1 optimal weight: 0.0570 chunk 59 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 overall best weight: 1.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** r 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5812 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6970 Z= 0.195 Angle : 0.661 10.747 9840 Z= 0.346 Chirality : 0.045 0.216 1235 Planarity : 0.004 0.044 1011 Dihedral : 21.125 115.968 2014 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.42 % Favored : 92.45 % Rotamer: Outliers : 4.00 % Allowed : 30.93 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.28), residues: 755 helix: -0.22 (0.32), residues: 230 sheet: -1.10 (0.53), residues: 85 loop : -2.18 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP r 136 HIS 0.004 0.001 HIS s 230 PHE 0.014 0.002 PHE s 239 TYR 0.018 0.002 TYR r 82 ARG 0.002 0.000 ARG r 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 51 time to evaluate : 0.639 Fit side-chains REVERT: r 89 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.5709 (mmt180) outliers start: 15 outliers final: 9 residues processed: 66 average time/residue: 0.1927 time to fit residues: 17.2243 Evaluate side-chains 56 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 73 VAL Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain r residue 89 ARG Chi-restraints excluded: chain r residue 119 LEU Chi-restraints excluded: chain r residue 242 LEU Chi-restraints excluded: chain r residue 252 SER Chi-restraints excluded: chain r residue 268 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 10.0000 chunk 71 optimal weight: 30.0000 chunk 15 optimal weight: 0.0670 chunk 46 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 65 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 76 optimal weight: 0.0970 overall best weight: 1.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: r 132 GLN ** r 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5786 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6970 Z= 0.177 Angle : 0.618 10.089 9840 Z= 0.324 Chirality : 0.043 0.200 1235 Planarity : 0.004 0.058 1011 Dihedral : 20.962 107.834 2014 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.68 % Favored : 92.19 % Rotamer: Outliers : 4.00 % Allowed : 30.93 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.29), residues: 755 helix: 0.13 (0.33), residues: 225 sheet: -1.28 (0.51), residues: 94 loop : -2.05 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP r 136 HIS 0.002 0.001 HIS s 235 PHE 0.011 0.001 PHE s 239 TYR 0.012 0.002 TYR r 150 ARG 0.004 0.000 ARG s 188 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 46 time to evaluate : 0.645 Fit side-chains REVERT: s 257 VAL cc_start: 0.7809 (t) cc_final: 0.7608 (t) REVERT: r 89 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.5630 (mmt180) outliers start: 15 outliers final: 11 residues processed: 60 average time/residue: 0.1818 time to fit residues: 15.1260 Evaluate side-chains 58 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 224 ASP Chi-restraints excluded: chain s residue 279 VAL Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 73 VAL Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain r residue 89 ARG Chi-restraints excluded: chain r residue 119 LEU Chi-restraints excluded: chain r residue 252 SER Chi-restraints excluded: chain r residue 268 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 20.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** r 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6055 moved from start: 0.5912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 6970 Z= 0.460 Angle : 0.996 19.045 9840 Z= 0.509 Chirality : 0.052 0.227 1235 Planarity : 0.007 0.070 1011 Dihedral : 21.861 115.581 2014 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 29.75 Ramachandran Plot: Outliers : 0.26 % Allowed : 13.38 % Favored : 86.36 % Rotamer: Outliers : 7.20 % Allowed : 29.07 % Favored : 63.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.27), residues: 755 helix: -1.18 (0.30), residues: 224 sheet: -2.58 (0.57), residues: 73 loop : -2.51 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP r 136 HIS 0.008 0.002 HIS s 306 PHE 0.015 0.003 PHE s 239 TYR 0.031 0.003 TYR r 150 ARG 0.005 0.001 ARG s 231 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 48 time to evaluate : 0.613 Fit side-chains REVERT: s 296 ARG cc_start: 0.5118 (OUTLIER) cc_final: 0.4723 (tpm170) REVERT: r 89 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.6209 (mmt180) outliers start: 27 outliers final: 15 residues processed: 72 average time/residue: 0.1917 time to fit residues: 18.6164 Evaluate side-chains 63 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 46 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 224 ASP Chi-restraints excluded: chain s residue 258 ILE Chi-restraints excluded: chain s residue 278 TYR Chi-restraints excluded: chain s residue 279 VAL Chi-restraints excluded: chain s residue 296 ARG Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 73 VAL Chi-restraints excluded: chain r residue 89 ARG Chi-restraints excluded: chain r residue 91 SER Chi-restraints excluded: chain r residue 119 LEU Chi-restraints excluded: chain r residue 137 VAL Chi-restraints excluded: chain r residue 229 LEU Chi-restraints excluded: chain r residue 242 LEU Chi-restraints excluded: chain r residue 252 SER Chi-restraints excluded: chain r residue 268 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 73 optimal weight: 40.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 301 GLN ** r 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6091 moved from start: 0.6451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.131 6970 Z= 0.478 Angle : 1.008 19.193 9840 Z= 0.515 Chirality : 0.054 0.293 1235 Planarity : 0.007 0.062 1011 Dihedral : 21.982 110.776 2014 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 29.92 Ramachandran Plot: Outliers : 0.26 % Allowed : 13.91 % Favored : 85.83 % Rotamer: Outliers : 7.47 % Allowed : 29.87 % Favored : 62.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.27), residues: 755 helix: -1.64 (0.28), residues: 223 sheet: -3.00 (0.48), residues: 95 loop : -2.71 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP r 136 HIS 0.010 0.003 HIS s 306 PHE 0.019 0.003 PHE s 239 TYR 0.021 0.003 TYR r 150 ARG 0.006 0.001 ARG s 211 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 45 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: r 89 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.6113 (mmt180) REVERT: r 209 LYS cc_start: 0.3587 (OUTLIER) cc_final: 0.2798 (mmtt) outliers start: 28 outliers final: 15 residues processed: 70 average time/residue: 0.2183 time to fit residues: 19.9974 Evaluate side-chains 61 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 44 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 216 LYS Chi-restraints excluded: chain s residue 217 THR Chi-restraints excluded: chain s residue 278 TYR Chi-restraints excluded: chain s residue 279 VAL Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 30 MET Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 73 VAL Chi-restraints excluded: chain r residue 89 ARG Chi-restraints excluded: chain r residue 91 SER Chi-restraints excluded: chain r residue 119 LEU Chi-restraints excluded: chain r residue 209 LYS Chi-restraints excluded: chain r residue 229 LEU Chi-restraints excluded: chain r residue 242 LEU Chi-restraints excluded: chain r residue 252 SER Chi-restraints excluded: chain r residue 274 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 73 optimal weight: 30.0000 chunk 48 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 301 GLN ** r 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.6550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 6970 Z= 0.353 Angle : 0.867 20.477 9840 Z= 0.443 Chirality : 0.049 0.244 1235 Planarity : 0.006 0.062 1011 Dihedral : 21.795 108.925 2014 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 24.92 Ramachandran Plot: Outliers : 0.26 % Allowed : 14.44 % Favored : 85.30 % Rotamer: Outliers : 6.13 % Allowed : 30.40 % Favored : 63.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.28), residues: 755 helix: -1.34 (0.30), residues: 229 sheet: -3.03 (0.47), residues: 97 loop : -2.59 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP r 136 HIS 0.007 0.002 HIS s 306 PHE 0.018 0.002 PHE s 239 TYR 0.021 0.003 TYR r 150 ARG 0.005 0.001 ARG s 296 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 49 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: r 89 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.6078 (mmt180) REVERT: r 209 LYS cc_start: 0.3325 (OUTLIER) cc_final: 0.2545 (mmtt) outliers start: 23 outliers final: 19 residues processed: 67 average time/residue: 0.2078 time to fit residues: 18.9456 Evaluate side-chains 67 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 46 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 216 LYS Chi-restraints excluded: chain s residue 217 THR Chi-restraints excluded: chain s residue 224 ASP Chi-restraints excluded: chain s residue 250 ILE Chi-restraints excluded: chain s residue 258 ILE Chi-restraints excluded: chain s residue 278 TYR Chi-restraints excluded: chain s residue 279 VAL Chi-restraints excluded: chain s residue 284 CYS Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 30 MET Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 73 VAL Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain r residue 89 ARG Chi-restraints excluded: chain r residue 91 SER Chi-restraints excluded: chain r residue 119 LEU Chi-restraints excluded: chain r residue 209 LYS Chi-restraints excluded: chain r residue 229 LEU Chi-restraints excluded: chain r residue 242 LEU Chi-restraints excluded: chain r residue 252 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 6 optimal weight: 0.0670 chunk 50 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 69 optimal weight: 20.0000 chunk 19 optimal weight: 0.0870 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 301 GLN ** r 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5798 moved from start: 0.6431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6970 Z= 0.162 Angle : 0.657 14.343 9840 Z= 0.337 Chirality : 0.043 0.223 1235 Planarity : 0.004 0.066 1011 Dihedral : 21.096 105.613 2014 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.15 % Favored : 92.72 % Rotamer: Outliers : 3.73 % Allowed : 33.33 % Favored : 62.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.30), residues: 755 helix: -0.21 (0.33), residues: 228 sheet: -1.86 (0.58), residues: 86 loop : -2.31 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP r 136 HIS 0.004 0.001 HIS s 235 PHE 0.012 0.002 PHE s 239 TYR 0.013 0.001 TYR r 82 ARG 0.004 0.000 ARG s 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 50 time to evaluate : 0.697 Fit side-chains REVERT: s 257 VAL cc_start: 0.7974 (t) cc_final: 0.7732 (t) REVERT: r 89 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.5648 (mmt180) outliers start: 14 outliers final: 12 residues processed: 62 average time/residue: 0.1716 time to fit residues: 14.8682 Evaluate side-chains 58 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 45 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 224 ASP Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 30 MET Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 73 VAL Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain r residue 89 ARG Chi-restraints excluded: chain r residue 119 LEU Chi-restraints excluded: chain r residue 242 LEU Chi-restraints excluded: chain r residue 252 SER Chi-restraints excluded: chain r residue 274 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 8 optimal weight: 0.4980 chunk 12 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 3 optimal weight: 0.0370 chunk 47 optimal weight: 20.0000 overall best weight: 3.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** r 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 181 ASN ** 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 = 0.4250 r_free = 0.4250 target = 0.112138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.104520 restraints weight = 40176.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.105233 restraints weight = 35058.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.105845 restraints weight = 26021.109| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4133 r_free = 0.4133 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4130 r_free = 0.4130 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.6584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 6970 Z= 0.300 Angle : 0.772 19.584 9840 Z= 0.395 Chirality : 0.047 0.226 1235 Planarity : 0.005 0.063 1011 Dihedral : 21.430 108.520 2014 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 22.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.58 % Favored : 87.28 % Rotamer: Outliers : 4.00 % Allowed : 34.13 % Favored : 61.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.29), residues: 755 helix: -0.70 (0.32), residues: 231 sheet: -2.17 (0.53), residues: 95 loop : -2.37 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP r 136 HIS 0.005 0.001 HIS s 306 PHE 0.025 0.002 PHE s 239 TYR 0.015 0.002 TYR s 278 ARG 0.005 0.001 ARG s 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1638.06 seconds wall clock time: 30 minutes 47.47 seconds (1847.47 seconds total)