Starting phenix.real_space_refine (version: dev) on Sat Feb 18 01:17:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybv_10774/02_2023/6ybv_10774.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybv_10774/02_2023/6ybv_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_10774/02_2023/6ybv_10774.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybv_10774/02_2023/6ybv_10774.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybv_10774/02_2023/6ybv_10774.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybv_10774/02_2023/6ybv_10774.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 27 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: 4.72, per 1000 atoms: 0.70 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: 3.12 Conformation dependent library (CDL) restraints added in 877.1 milliseconds 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: 1.98 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: 2.23 Time building geometry restraints manager: 3.34 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: 3655 24.56 - 49.11: 332 49.11 - 73.67: 45 73.67 - 98.23: 8 98.23 - 122.78: 2 Dihedral angle restraints: 4042 sinusoidal: 1820 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 4039 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 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. 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: 10.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 26.320 Check model and map are aligned: 0.110 Process input model: 23.780 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.060 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5584 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 : 17.695 122.782 2598 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 % 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 *********************** 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 : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 6 residues processed: 120 average time/residue: 0.2655 time to fit residues: 39.2101 Evaluate side-chains 59 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.688 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0636 time to fit residues: 1.5772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 39 optimal weight: 0.6980 chunk 47 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 181 ASN s 306 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5651 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 6970 Z= 0.225 Angle : 0.696 7.053 9840 Z= 0.376 Chirality : 0.045 0.218 1235 Planarity : 0.005 0.059 1011 Dihedral : 15.054 113.419 1737 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.43 % Favored : 94.17 % Rotamer Outliers : 3.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.27), residues: 755 helix: -0.11 (0.32), residues: 216 sheet: -0.62 (0.43), residues: 136 loop : -2.13 (0.26), residues: 403 *********************** 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 69 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 56 time to evaluate : 0.673 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 67 average time/residue: 0.2282 time to fit residues: 20.1536 Evaluate side-chains 44 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.677 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0614 time to fit residues: 0.9768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 0.0770 chunk 20 optimal weight: 0.0270 chunk 74 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 chunk 66 optimal weight: 30.0000 chunk 73 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 20.0000 overall best weight: 1.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5677 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 6970 Z= 0.192 Angle : 0.645 12.599 9840 Z= 0.339 Chirality : 0.043 0.170 1235 Planarity : 0.004 0.052 1011 Dihedral : 14.850 112.861 1737 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.43 % Favored : 94.30 % Rotamer Outliers : 3.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.28), residues: 755 helix: 0.15 (0.32), residues: 223 sheet: -0.48 (0.47), residues: 112 loop : -1.98 (0.27), residues: 420 *********************** 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 61 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 48 time to evaluate : 0.667 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 60 average time/residue: 0.1823 time to fit residues: 15.3637 Evaluate side-chains 46 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.615 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0626 time to fit residues: 1.4123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 30.0000 chunk 56 optimal weight: 0.0060 chunk 38 optimal weight: 0.7980 chunk 8 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 0.0070 chunk 74 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 70 optimal weight: 0.0770 chunk 21 optimal weight: 4.9990 overall best weight: 0.2172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** r 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5520 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 6970 Z= 0.128 Angle : 0.541 8.793 9840 Z= 0.286 Chirality : 0.041 0.189 1235 Planarity : 0.003 0.038 1011 Dihedral : 14.195 112.888 1737 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.24 % Favored : 95.63 % Rotamer Outliers : 2.40 % 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: -1.04 (0.29), residues: 755 helix: 0.92 (0.34), residues: 224 sheet: -0.49 (0.47), residues: 114 loop : -1.72 (0.28), residues: 417 *********************** 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 63 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 0.601 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 60 average time/residue: 0.1616 time to fit residues: 13.8841 Evaluate side-chains 46 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.637 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0595 time to fit residues: 1.0600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 30.0000 chunk 44 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5992 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.099 6970 Z= 0.523 Angle : 1.056 16.682 9840 Z= 0.540 Chirality : 0.054 0.216 1235 Planarity : 0.007 0.056 1011 Dihedral : 16.422 135.645 1737 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 30.17 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.14 % Favored : 90.46 % Rotamer Outliers : 6.13 % 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: -2.75 (0.27), residues: 755 helix: -1.03 (0.29), residues: 224 sheet: -2.25 (0.50), residues: 86 loop : -2.24 (0.27), residues: 445 *********************** 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 72 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 49 time to evaluate : 0.607 Fit side-chains outliers start: 23 outliers final: 6 residues processed: 68 average time/residue: 0.1775 time to fit residues: 16.9801 Evaluate side-chains 47 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.652 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0638 time to fit residues: 1.4556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 65 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 76 optimal weight: 20.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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: 0.5776 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6970 Z= 0.177 Angle : 0.649 9.254 9840 Z= 0.341 Chirality : 0.044 0.216 1235 Planarity : 0.004 0.037 1011 Dihedral : 15.270 126.019 1737 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.36 % Favored : 93.38 % Rotamer Outliers : 2.67 % 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: -2.02 (0.28), residues: 755 helix: -0.07 (0.32), residues: 226 sheet: -1.62 (0.52), residues: 87 loop : -2.05 (0.27), residues: 442 *********************** 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: 10 poor density : 51 time to evaluate : 0.682 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 59 average time/residue: 0.1956 time to fit residues: 16.0629 Evaluate side-chains 48 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.686 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0697 time to fit residues: 1.1541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 47 optimal weight: 20.0000 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6045 moved from start: 0.5649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.116 6970 Z= 0.543 Angle : 1.073 19.414 9840 Z= 0.545 Chirality : 0.055 0.282 1235 Planarity : 0.007 0.061 1011 Dihedral : 16.736 115.255 1737 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 32.55 Ramachandran Plot: Outliers : 0.40 % Allowed : 12.05 % Favored : 87.55 % Rotamer Outliers : 4.27 % 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: -3.23 (0.26), residues: 755 helix: -1.39 (0.29), residues: 226 sheet: -2.53 (0.53), residues: 73 loop : -2.58 (0.26), residues: 456 *********************** 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 63 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 47 time to evaluate : 0.654 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 61 average time/residue: 0.1900 time to fit residues: 16.2453 Evaluate side-chains 51 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.670 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1041 time to fit residues: 2.0349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 50 optimal weight: 9.9990 chunk 53 optimal weight: 0.0980 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 73 optimal weight: 40.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** r 132 GLN ** 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: 0.5851 moved from start: 0.5543 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= 0.205 Angle : 0.707 12.279 9840 Z= 0.367 Chirality : 0.046 0.224 1235 Planarity : 0.004 0.037 1011 Dihedral : 15.713 105.562 1737 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.34 % Favored : 91.52 % Rotamer Outliers : 1.07 % 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: -2.57 (0.28), residues: 755 helix: -0.43 (0.32), residues: 225 sheet: -2.47 (0.44), residues: 103 loop : -2.29 (0.28), residues: 427 *********************** 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 50 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.592 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 48 average time/residue: 0.1656 time to fit residues: 11.5454 Evaluate side-chains 46 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.706 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0915 time to fit residues: 1.0790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 chunk 73 optimal weight: 0.0270 chunk 48 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 221 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5944 moved from start: 0.5814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 6970 Z= 0.300 Angle : 0.804 15.984 9840 Z= 0.413 Chirality : 0.048 0.232 1235 Planarity : 0.005 0.043 1011 Dihedral : 16.009 111.846 1737 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 23.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.19 % Favored : 87.68 % Rotamer Outliers : 0.53 % 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: -2.79 (0.28), residues: 755 helix: -0.69 (0.32), residues: 224 sheet: -2.75 (0.47), residues: 88 loop : -2.37 (0.27), residues: 443 *********************** 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 48 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.733 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 47 average time/residue: 0.1579 time to fit residues: 11.1587 Evaluate side-chains 45 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.711 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 6 optimal weight: 0.4980 chunk 50 optimal weight: 9.9990 chunk 39 optimal weight: 0.3980 chunk 51 optimal weight: 4.9990 chunk 69 optimal weight: 30.0000 chunk 19 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** r 132 GLN ** 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: 0.5867 moved from start: 0.5880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 6970 Z= 0.219 Angle : 0.715 13.761 9840 Z= 0.366 Chirality : 0.045 0.254 1235 Planarity : 0.004 0.036 1011 Dihedral : 15.577 106.543 1737 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.67 % Favored : 90.20 % Rotamer Outliers : 0.27 % 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: -2.51 (0.28), residues: 755 helix: -0.39 (0.32), residues: 225 sheet: -2.17 (0.45), residues: 103 loop : -2.32 (0.28), residues: 427 ********************** 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 46 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.647 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 0.1994 time to fit residues: 12.7731 Evaluate side-chains 42 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.667 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 0.0970 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** r 132 GLN ** 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 = 0.4276 r_free = 0.4276 target = 0.113793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.107191 restraints weight = 40656.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.107545 restraints weight = 36742.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.107972 restraints weight = 29168.732| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4276 r_free = 0.4276 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4273 r_free = 0.4273 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5929 moved from start: 0.6092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 6970 Z= 0.254 Angle : 0.746 15.697 9840 Z= 0.381 Chirality : 0.046 0.246 1235 Planarity : 0.005 0.044 1011 Dihedral : 15.693 109.591 1737 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.05 % Favored : 87.81 % Rotamer Outliers : 1.07 % 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: -2.54 (0.28), residues: 755 helix: -0.46 (0.32), residues: 225 sheet: -2.13 (0.47), residues: 97 loop : -2.34 (0.28), residues: 433 =============================================================================== Job complete usr+sys time: 1457.83 seconds wall clock time: 27 minutes 29.38 seconds (1649.38 seconds total)