Starting phenix.real_space_refine on Tue Sep 24 00:21:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qa8_13880/09_2024/7qa8_13880.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qa8_13880/09_2024/7qa8_13880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qa8_13880/09_2024/7qa8_13880.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qa8_13880/09_2024/7qa8_13880.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qa8_13880/09_2024/7qa8_13880.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qa8_13880/09_2024/7qa8_13880.cif" } resolution = 2.7 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 4235 2.51 5 N 769 2.21 5 O 1087 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6111 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2299 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 290} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 97 Classifications: {'peptide': 12} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NLE:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2302 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 290} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 588 Unusual residues: {'NAG': 2, 'Y01': 16} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 623 Unusual residues: {'NAG': 2, 'Y01': 17} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "K" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Restraints were copied for chains: K Time building chain proxies: 5.01, per 1000 atoms: 0.82 Number of scatterers: 6111 At special positions: 0 Unit cell: (80.84, 93.74, 98.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 1087 8.00 N 769 7.00 C 4235 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 - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 25 " " NAG A 502 " - " ASN A 32 " " NAG B 501 " - " ASN B 32 " " NAG B 502 " - " ASN B 25 " Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 733.3 milliseconds 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1180 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 2 sheets defined 75.2% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 9 through 14 removed outlier: 3.504A pdb=" N ASP A 14 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 72 removed outlier: 3.712A pdb=" N SER A 47 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE A 53 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N MET A 54 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE A 55 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 103 removed outlier: 3.708A pdb=" N LEU A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 114 Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.584A pdb=" N ILE A 120 " --> pdb=" O PRO A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 154 removed outlier: 3.697A pdb=" N VAL A 127 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 195 removed outlier: 3.867A pdb=" N GLY A 163 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 164 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 236 removed outlier: 3.775A pdb=" N SER A 207 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE A 209 " --> pdb=" O ASN A 205 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 251 removed outlier: 4.182A pdb=" N LEU A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.618A pdb=" N TYR A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 272 Processing helix chain 'A' and resid 273 through 297 removed outlier: 3.514A pdb=" N LEU A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) Proline residue: A 290 - end of helix removed outlier: 3.683A pdb=" N MET A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TRP A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 14 removed outlier: 3.504A pdb=" N ASP B 14 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 72 removed outlier: 3.712A pdb=" N SER B 47 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B 53 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N MET B 54 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE B 55 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 103 removed outlier: 3.708A pdb=" N LEU B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE B 89 " --> pdb=" O GLN B 85 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 114 Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.584A pdb=" N ILE B 120 " --> pdb=" O PRO B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 154 removed outlier: 3.698A pdb=" N VAL B 127 " --> pdb=" O GLY B 123 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR B 128 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL B 136 " --> pdb=" O ASN B 132 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE B 154 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 195 removed outlier: 3.866A pdb=" N GLY B 163 " --> pdb=" O PHE B 159 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 164 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET B 165 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 236 removed outlier: 3.696A pdb=" N SER B 207 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE B 209 " --> pdb=" O ASN B 205 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG B 234 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE B 235 " --> pdb=" O ARG B 231 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 236 " --> pdb=" O SER B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 251 removed outlier: 4.182A pdb=" N LEU B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 268 removed outlier: 3.617A pdb=" N TYR B 266 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER B 267 " --> pdb=" O ILE B 263 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 272 Processing helix chain 'B' and resid 273 through 297 removed outlier: 3.514A pdb=" N LEU B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 283 " --> pdb=" O THR B 279 " (cutoff:3.500A) Proline residue: B 290 - end of helix removed outlier: 3.683A pdb=" N MET B 294 " --> pdb=" O PRO B 290 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TRP B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 28 removed outlier: 6.477A pdb=" N ILE A 24 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR A 35 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TYR A 26 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A 33 " --> pdb=" O TYR A 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 23 through 28 removed outlier: 6.478A pdb=" N ILE B 24 " --> pdb=" O THR B 35 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR B 35 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TYR B 26 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 33 " --> pdb=" O TYR B 26 " (cutoff:3.500A) 298 hydrogen bonds defined for protein. 864 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 819 1.31 - 1.43: 1417 1.43 - 1.56: 3916 1.56 - 1.68: 55 1.68 - 1.80: 36 Bond restraints: 6243 Sorted by residual: bond pdb=" C7 NAG B 501 " pdb=" N2 NAG B 501 " ideal model delta sigma weight residual 1.346 1.461 -0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" C7 NAG A 502 " pdb=" N2 NAG A 502 " ideal model delta sigma weight residual 1.346 1.461 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C7 NAG B 502 " pdb=" N2 NAG B 502 " ideal model delta sigma weight residual 1.346 1.460 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C7 NAG A 501 " pdb=" N2 NAG A 501 " ideal model delta sigma weight residual 1.346 1.458 -0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.516 -0.110 2.00e-02 2.50e+03 3.05e+01 ... (remaining 6238 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 7731 1.60 - 3.20: 737 3.20 - 4.80: 149 4.80 - 6.40: 58 6.40 - 8.00: 7 Bond angle restraints: 8682 Sorted by residual: angle pdb=" N PHE A 99 " pdb=" CA PHE A 99 " pdb=" C PHE A 99 " ideal model delta sigma weight residual 111.36 105.46 5.90 1.09e+00 8.42e-01 2.93e+01 angle pdb=" N PHE B 99 " pdb=" CA PHE B 99 " pdb=" C PHE B 99 " ideal model delta sigma weight residual 111.36 105.63 5.73 1.09e+00 8.42e-01 2.76e+01 angle pdb=" N PHE A 204 " pdb=" CA PHE A 204 " pdb=" C PHE A 204 " ideal model delta sigma weight residual 113.41 107.33 6.08 1.22e+00 6.72e-01 2.48e+01 angle pdb=" N LYS B 202 " pdb=" CA LYS B 202 " pdb=" C LYS B 202 " ideal model delta sigma weight residual 113.97 107.77 6.20 1.28e+00 6.10e-01 2.35e+01 angle pdb=" N TYR B 106 " pdb=" CA TYR B 106 " pdb=" C TYR B 106 " ideal model delta sigma weight residual 113.28 107.50 5.78 1.22e+00 6.72e-01 2.24e+01 ... (remaining 8677 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.95: 5010 20.95 - 41.90: 261 41.90 - 62.85: 98 62.85 - 83.80: 6 83.80 - 104.75: 5 Dihedral angle restraints: 5380 sinusoidal: 3554 harmonic: 1826 Sorted by residual: dihedral pdb=" C ASP B 275 " pdb=" N ASP B 275 " pdb=" CA ASP B 275 " pdb=" CB ASP B 275 " ideal model delta harmonic sigma weight residual -122.60 -113.06 -9.54 0 2.50e+00 1.60e-01 1.46e+01 dihedral pdb=" C1 NAG A 501 " pdb=" C5 NAG A 501 " pdb=" O5 NAG A 501 " pdb=" C6 NAG A 501 " ideal model delta sinusoidal sigma weight residual 171.16 -84.09 -104.75 1 3.00e+01 1.11e-03 1.34e+01 dihedral pdb=" C1 NAG A 501 " pdb=" C5 NAG A 501 " pdb=" O5 NAG A 501 " pdb=" C4 NAG A 501 " ideal model delta sinusoidal sigma weight residual -64.11 40.38 -104.49 1 3.00e+01 1.11e-03 1.33e+01 ... (remaining 5377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 890 0.062 - 0.124: 172 0.124 - 0.186: 46 0.186 - 0.248: 10 0.248 - 0.310: 4 Chirality restraints: 1122 Sorted by residual: chirality pdb=" CBC Y01 A 518 " pdb=" CAR Y01 A 518 " pdb=" CAV Y01 A 518 " pdb=" OAW Y01 A 518 " both_signs ideal model delta sigma weight residual False -2.54 -2.23 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C1 NAG A 501 " pdb=" ND2 ASN A 25 " pdb=" C2 NAG A 501 " pdb=" O5 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CBC Y01 A 514 " pdb=" CAR Y01 A 514 " pdb=" CAV Y01 A 514 " pdb=" OAW Y01 A 514 " both_signs ideal model delta sigma weight residual False -2.54 -2.27 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 1119 not shown) Planarity restraints: 883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 104 " -0.021 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C SER A 104 " 0.075 2.00e-02 2.50e+03 pdb=" O SER A 104 " -0.029 2.00e-02 2.50e+03 pdb=" N ASN A 105 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 104 " 0.020 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C SER B 104 " -0.071 2.00e-02 2.50e+03 pdb=" O SER B 104 " 0.028 2.00e-02 2.50e+03 pdb=" N ASN B 105 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 186 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C VAL B 186 " 0.063 2.00e-02 2.50e+03 pdb=" O VAL B 186 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS B 187 " -0.021 2.00e-02 2.50e+03 ... (remaining 880 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1617 2.84 - 3.35: 5592 3.35 - 3.87: 9104 3.87 - 4.38: 10853 4.38 - 4.90: 18087 Nonbonded interactions: 45253 Sorted by model distance: nonbonded pdb=" O ASN A 46 " pdb=" OG1 THR A 50 " model vdw 2.323 3.040 nonbonded pdb=" O ASN B 46 " pdb=" OG1 THR B 50 " model vdw 2.324 3.040 nonbonded pdb=" OXT TYR K 13 " pdb=" O HOH K 101 " model vdw 2.338 3.040 nonbonded pdb=" O LYS B 151 " pdb=" OG1 THR B 155 " model vdw 2.338 3.040 nonbonded pdb=" O LYS A 151 " pdb=" OG1 THR A 155 " model vdw 2.339 3.040 ... (remaining 45248 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 5 through 157 or (resid 158 and (name N or name CA or name \ C or name O or name CB )) or resid 159 through 303 or resid 501 through 518)) } ncs_group { reference = (chain 'I' and resid 2 through 13) selection = chain 'K' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.150 Find NCS groups from input model: 0.230 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:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.115 6243 Z= 0.511 Angle : 1.114 8.003 8682 Z= 0.597 Chirality : 0.059 0.310 1122 Planarity : 0.009 0.055 879 Dihedral : 13.163 104.748 4200 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.75 % Allowed : 1.50 % Favored : 97.76 % 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: -2.98 (0.28), residues: 610 helix: -1.93 (0.22), residues: 396 sheet: None (None), residues: 0 loop : -1.71 (0.33), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 295 HIS 0.006 0.003 HIS A 94 PHE 0.031 0.003 PHE A 55 TYR 0.022 0.003 TYR B 26 ARG 0.003 0.001 ARG B 231 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.598 Fit side-chains REVERT: A 165 MET cc_start: 0.6585 (ptm) cc_final: 0.6242 (ptm) REVERT: B 165 MET cc_start: 0.6598 (ptm) cc_final: 0.6325 (ptm) outliers start: 4 outliers final: 3 residues processed: 71 average time/residue: 0.9517 time to fit residues: 71.8171 Evaluate side-chains 52 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 274 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 0.0020 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 94 HIS A 118 GLN B 51 GLN B 94 HIS B 118 GLN B 135 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6243 Z= 0.148 Angle : 0.561 9.735 8682 Z= 0.271 Chirality : 0.035 0.200 1122 Planarity : 0.004 0.036 879 Dihedral : 10.248 59.713 3171 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.62 % Allowed : 7.48 % Favored : 89.91 % 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: -0.14 (0.33), residues: 610 helix: 0.55 (0.26), residues: 404 sheet: None (None), residues: 0 loop : -1.30 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 295 HIS 0.005 0.001 HIS A 94 PHE 0.013 0.001 PHE A 204 TYR 0.008 0.001 TYR A 266 ARG 0.001 0.000 ARG B 161 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 0.557 Fit side-chains REVERT: A 165 MET cc_start: 0.6631 (ptm) cc_final: 0.6384 (ptm) REVERT: A 197 SER cc_start: 0.6960 (m) cc_final: 0.6640 (p) REVERT: B 197 SER cc_start: 0.6932 (m) cc_final: 0.6615 (p) outliers start: 14 outliers final: 7 residues processed: 70 average time/residue: 0.8594 time to fit residues: 64.2014 Evaluate side-chains 58 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 164 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.0870 chunk 16 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 135 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6243 Z= 0.311 Angle : 0.793 5.921 8682 Z= 0.364 Chirality : 0.044 0.178 1122 Planarity : 0.005 0.035 879 Dihedral : 11.451 59.650 3170 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.30 % Allowed : 10.09 % Favored : 85.61 % 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: 0.39 (0.33), residues: 610 helix: 1.10 (0.26), residues: 416 sheet: None (None), residues: 0 loop : -1.58 (0.37), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 295 HIS 0.007 0.002 HIS A 94 PHE 0.019 0.003 PHE B 244 TYR 0.011 0.002 TYR B 17 ARG 0.004 0.001 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 48 time to evaluate : 0.413 Fit side-chains REVERT: A 98 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.8610 (t80) REVERT: B 98 TYR cc_start: 0.8875 (OUTLIER) cc_final: 0.8598 (t80) outliers start: 23 outliers final: 10 residues processed: 67 average time/residue: 0.5910 time to fit residues: 42.4705 Evaluate side-chains 57 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 45 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 297 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6243 Z= 0.229 Angle : 0.663 7.087 8682 Z= 0.307 Chirality : 0.039 0.166 1122 Planarity : 0.004 0.035 879 Dihedral : 11.086 59.786 3170 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.74 % Allowed : 11.40 % Favored : 84.86 % 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: 1.21 (0.33), residues: 610 helix: 1.88 (0.26), residues: 414 sheet: None (None), residues: 0 loop : -1.64 (0.36), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 295 HIS 0.004 0.001 HIS B 94 PHE 0.015 0.002 PHE A 244 TYR 0.007 0.001 TYR A 266 ARG 0.003 0.001 ARG B 161 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 45 time to evaluate : 0.503 Fit side-chains REVERT: A 98 TYR cc_start: 0.8871 (OUTLIER) cc_final: 0.8625 (t80) REVERT: B 98 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.8614 (t80) outliers start: 20 outliers final: 13 residues processed: 59 average time/residue: 0.7066 time to fit residues: 44.6821 Evaluate side-chains 58 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 43 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 297 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6243 Z= 0.182 Angle : 0.610 8.105 8682 Z= 0.282 Chirality : 0.037 0.160 1122 Planarity : 0.004 0.033 879 Dihedral : 10.850 59.567 3170 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.67 % Allowed : 11.40 % Favored : 83.93 % 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: 1.75 (0.33), residues: 610 helix: 2.35 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -1.54 (0.36), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 295 HIS 0.003 0.001 HIS A 94 PHE 0.012 0.002 PHE B 81 TYR 0.006 0.001 TYR B 128 ARG 0.003 0.001 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 46 time to evaluate : 0.592 Fit side-chains REVERT: A 98 TYR cc_start: 0.8890 (OUTLIER) cc_final: 0.8688 (t80) REVERT: B 98 TYR cc_start: 0.8887 (OUTLIER) cc_final: 0.8682 (t80) outliers start: 25 outliers final: 18 residues processed: 66 average time/residue: 0.8413 time to fit residues: 59.5480 Evaluate side-chains 64 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 44 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 252 CYS Chi-restraints excluded: chain B residue 297 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 0.0370 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 8.9990 chunk 30 optimal weight: 0.0270 chunk 55 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6243 Z= 0.124 Angle : 0.525 8.360 8682 Z= 0.245 Chirality : 0.034 0.155 1122 Planarity : 0.003 0.030 879 Dihedral : 10.331 59.719 3170 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.55 % Allowed : 13.64 % Favored : 82.80 % 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: 2.33 (0.34), residues: 610 helix: 2.88 (0.25), residues: 406 sheet: None (None), residues: 0 loop : -1.39 (0.36), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 295 HIS 0.002 0.001 HIS A 94 PHE 0.013 0.001 PHE B 81 TYR 0.008 0.001 TYR A 128 ARG 0.001 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 54 time to evaluate : 0.590 Fit side-chains REVERT: A 98 TYR cc_start: 0.8857 (OUTLIER) cc_final: 0.8642 (t80) REVERT: B 98 TYR cc_start: 0.8852 (OUTLIER) cc_final: 0.8633 (t80) REVERT: B 272 GLN cc_start: 0.6837 (mt0) cc_final: 0.6240 (mp10) outliers start: 19 outliers final: 13 residues processed: 70 average time/residue: 0.8050 time to fit residues: 60.5688 Evaluate side-chains 64 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 49 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 252 CYS Chi-restraints excluded: chain B residue 297 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 57 optimal weight: 0.1980 chunk 36 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6243 Z= 0.182 Angle : 0.609 9.805 8682 Z= 0.280 Chirality : 0.037 0.160 1122 Planarity : 0.004 0.032 879 Dihedral : 10.558 59.888 3170 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.30 % Allowed : 13.27 % Favored : 82.43 % 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: 2.31 (0.33), residues: 610 helix: 2.78 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -1.33 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 295 HIS 0.004 0.001 HIS B 94 PHE 0.011 0.001 PHE B 81 TYR 0.006 0.001 TYR A 266 ARG 0.002 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 50 time to evaluate : 0.575 Fit side-chains REVERT: A 98 TYR cc_start: 0.8903 (OUTLIER) cc_final: 0.8634 (t80) REVERT: B 98 TYR cc_start: 0.8900 (OUTLIER) cc_final: 0.8626 (t80) outliers start: 23 outliers final: 16 residues processed: 69 average time/residue: 0.7855 time to fit residues: 58.5166 Evaluate side-chains 66 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 48 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 252 CYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 297 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6243 Z= 0.225 Angle : 0.668 10.578 8682 Z= 0.305 Chirality : 0.040 0.158 1122 Planarity : 0.004 0.033 879 Dihedral : 10.904 59.444 3170 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.67 % Allowed : 13.83 % Favored : 81.50 % 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: 2.08 (0.33), residues: 610 helix: 2.63 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -1.51 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 295 HIS 0.003 0.001 HIS A 94 PHE 0.011 0.002 PHE B 55 TYR 0.009 0.001 TYR A 203 ARG 0.003 0.001 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 42 time to evaluate : 0.521 Fit side-chains REVERT: A 98 TYR cc_start: 0.8879 (OUTLIER) cc_final: 0.8616 (t80) REVERT: B 98 TYR cc_start: 0.8875 (OUTLIER) cc_final: 0.8608 (t80) outliers start: 25 outliers final: 18 residues processed: 64 average time/residue: 0.7767 time to fit residues: 53.5955 Evaluate side-chains 63 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 43 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 252 CYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 297 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6243 Z= 0.158 Angle : 0.577 9.747 8682 Z= 0.267 Chirality : 0.036 0.157 1122 Planarity : 0.004 0.032 879 Dihedral : 10.479 58.518 3170 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.11 % Allowed : 14.58 % Favored : 81.31 % 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: 2.35 (0.33), residues: 610 helix: 2.90 (0.25), residues: 408 sheet: None (None), residues: 0 loop : -1.43 (0.36), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 295 HIS 0.002 0.001 HIS A 94 PHE 0.012 0.001 PHE B 81 TYR 0.007 0.001 TYR B 128 ARG 0.002 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 48 time to evaluate : 0.568 Fit side-chains REVERT: A 98 TYR cc_start: 0.8891 (OUTLIER) cc_final: 0.8680 (t80) REVERT: A 244 PHE cc_start: 0.6630 (OUTLIER) cc_final: 0.6403 (t80) REVERT: B 98 TYR cc_start: 0.8888 (OUTLIER) cc_final: 0.8673 (t80) outliers start: 22 outliers final: 17 residues processed: 68 average time/residue: 0.7798 time to fit residues: 57.3968 Evaluate side-chains 65 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 45 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 252 CYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 297 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 0.0170 overall best weight: 1.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6243 Z= 0.190 Angle : 0.620 10.785 8682 Z= 0.284 Chirality : 0.038 0.158 1122 Planarity : 0.004 0.032 879 Dihedral : 10.613 59.966 3170 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.11 % Allowed : 14.95 % Favored : 80.93 % 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: 2.26 (0.33), residues: 610 helix: 2.81 (0.25), residues: 408 sheet: None (None), residues: 0 loop : -1.42 (0.36), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 295 HIS 0.003 0.001 HIS A 94 PHE 0.011 0.001 PHE B 81 TYR 0.006 0.001 TYR B 128 ARG 0.002 0.000 ARG B 161 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 45 time to evaluate : 0.641 Fit side-chains REVERT: A 98 TYR cc_start: 0.8907 (OUTLIER) cc_final: 0.8641 (t80) REVERT: B 98 TYR cc_start: 0.8904 (OUTLIER) cc_final: 0.8634 (t80) outliers start: 22 outliers final: 20 residues processed: 64 average time/residue: 0.7877 time to fit residues: 54.4696 Evaluate side-chains 67 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 45 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 252 CYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 297 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 0.0670 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.170992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.121807 restraints weight = 6941.363| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.91 r_work: 0.3265 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6243 Z= 0.140 Angle : 0.549 9.698 8682 Z= 0.255 Chirality : 0.035 0.157 1122 Planarity : 0.003 0.032 879 Dihedral : 10.255 59.788 3170 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.93 % Allowed : 15.33 % Favored : 80.75 % 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: 2.60 (0.34), residues: 610 helix: 3.02 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -1.29 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 295 HIS 0.002 0.001 HIS A 94 PHE 0.012 0.001 PHE B 81 TYR 0.008 0.001 TYR B 128 ARG 0.001 0.000 ARG A 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1826.95 seconds wall clock time: 41 minutes 57.61 seconds (2517.61 seconds total)