Starting phenix.real_space_refine on Sat Aug 3 02:16:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z0t_39033/08_2024/8z0t_39033.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z0t_39033/08_2024/8z0t_39033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z0t_39033/08_2024/8z0t_39033.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z0t_39033/08_2024/8z0t_39033.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z0t_39033/08_2024/8z0t_39033.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z0t_39033/08_2024/8z0t_39033.cif" } resolution = 3.58 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= 0.026 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 27 5.16 5 C 4096 2.51 5 N 1121 2.21 5 O 1312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 139": "OD1" <-> "OD2" Residue "A TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 204": "OD1" <-> "OD2" Residue "D ASP 243": "OD1" <-> "OD2" Residue "D PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 122": "OD1" <-> "OD2" Residue "E TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 293": "OE1" <-> "OE2" Residue "E GLU 396": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6556 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1393 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 162} Chain: "D" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2467 Classifications: {'peptide': 316} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 293} Chain: "E" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2467 Classifications: {'peptide': 316} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 292} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'BMA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.96, per 1000 atoms: 0.76 Number of scatterers: 6556 At special positions: 0 Unit cell: (101.65, 87.74, 116.63, 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 27 16.00 O 1312 8.00 N 1121 7.00 C 4096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 93 " distance=2.03 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 176 " distance=2.03 Simple disulfide: pdb=" SG CYS D 121 " - pdb=" SG CYS E 209 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 193 " distance=2.03 Simple disulfide: pdb=" SG CYS D 209 " - pdb=" SG CYS E 121 " distance=2.03 Simple disulfide: pdb=" SG CYS D 239 " - pdb=" SG CYS D 299 " distance=2.03 Simple disulfide: pdb=" SG CYS D 345 " - pdb=" SG CYS D 405 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 193 " distance=2.03 Simple disulfide: pdb=" SG CYS E 239 " - pdb=" SG CYS E 299 " distance=2.03 Simple disulfide: pdb=" SG CYS E 345 " - pdb=" SG CYS E 405 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " BMA B 3 " - " NAG B 4 " " NAG C 1 " - " NAG C 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A 301 " - " ASN A 46 " " NAG A 302 " - " ASN A 191 " " NAG A 303 " - " ASN A 99 " " NAG A 304 " - " ASN A 165 " " NAG B 1 " - " ASN A 67 " " NAG C 1 " - " ASN A 160 " " NAG E 501 " - " ASN E 252 " " NAG F 1 " - " ASN D 275 " " NAG G 1 " - " ASN E 275 " Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.2 seconds 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1514 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 20 sheets defined 6.7% alpha, 41.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.601A pdb=" N ASP A 87 " --> pdb=" O LYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'D' and resid 181 through 187 removed outlier: 3.523A pdb=" N TRP D 185 " --> pdb=" O SER D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 231 Processing helix chain 'D' and resid 287 through 293 Processing helix chain 'D' and resid 394 through 398 Processing helix chain 'E' and resid 184 through 188 removed outlier: 3.742A pdb=" N ASP E 188 " --> pdb=" O TRP E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 294 Processing helix chain 'E' and resid 393 through 399 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 35 removed outlier: 3.641A pdb=" N VAL A 47 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 42 removed outlier: 6.256A pdb=" N ILE A 41 " --> pdb=" O PHE A 109 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TRP A 64 " --> pdb=" O SER A 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 113 through 117 Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 122 removed outlier: 4.841A pdb=" N LYS A 179 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LYS A 142 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL A 143 " --> pdb=" O TYR A 154 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYR A 154 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TYR A 145 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 150 " --> pdb=" O LYS A 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 121 through 122 Processing sheet with id=AA6, first strand: chain 'D' and resid 113 through 117 removed outlier: 6.023A pdb=" N ALA D 172 " --> pdb=" O GLY D 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 146 through 151 removed outlier: 3.880A pdb=" N ASN D 146 " --> pdb=" O THR D 196 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 218 through 222 removed outlier: 3.786A pdb=" N THR D 238 " --> pdb=" O SER D 222 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP D 243 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU D 278 " --> pdb=" O ASP D 243 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 252 through 257 Processing sheet with id=AB1, first strand: chain 'D' and resid 325 through 329 removed outlier: 5.865A pdb=" N PHE D 384 " --> pdb=" O ASN D 349 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 356 through 360 Processing sheet with id=AB3, first strand: chain 'E' and resid 113 through 118 removed outlier: 5.842A pdb=" N ALA E 172 " --> pdb=" O GLY E 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 113 through 118 Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 151 removed outlier: 3.580A pdb=" N ASP E 204 " --> pdb=" O CYS E 193 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 219 through 222 removed outlier: 3.908A pdb=" N THR E 238 " --> pdb=" O SER E 222 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 219 through 222 removed outlier: 3.908A pdb=" N THR E 238 " --> pdb=" O SER E 222 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 252 through 256 Processing sheet with id=AB9, first strand: chain 'E' and resid 327 through 329 Processing sheet with id=AC1, first strand: chain 'E' and resid 327 through 329 Processing sheet with id=AC2, first strand: chain 'E' and resid 364 through 365 removed outlier: 3.612A pdb=" N CYS E 405 " --> pdb=" O ARG E 420 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL E 418 " --> pdb=" O ALA E 407 " (cutoff:3.500A) 252 hydrogen bonds defined for protein. 624 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2019 1.34 - 1.46: 1572 1.46 - 1.58: 3091 1.58 - 1.70: 1 1.70 - 1.82: 34 Bond restraints: 6717 Sorted by residual: bond pdb=" C1 NAG A 304 " pdb=" O5 NAG A 304 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.21e+00 bond pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " ideal model delta sigma weight residual 1.528 1.575 -0.047 2.00e-02 2.50e+03 5.44e+00 bond pdb=" C1 NAG E 501 " pdb=" O5 NAG E 501 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.39e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 4.96e+00 bond pdb=" C3 BMA B 3 " pdb=" C4 BMA B 3 " ideal model delta sigma weight residual 1.541 1.585 -0.044 2.00e-02 2.50e+03 4.88e+00 ... (remaining 6712 not shown) Histogram of bond angle deviations from ideal: 98.59 - 105.99: 194 105.99 - 113.39: 3825 113.39 - 120.78: 2625 120.78 - 128.18: 2427 128.18 - 135.58: 84 Bond angle restraints: 9155 Sorted by residual: angle pdb=" C ASP E 122 " pdb=" N GLY E 123 " pdb=" CA GLY E 123 " ideal model delta sigma weight residual 121.70 135.58 -13.88 1.80e+00 3.09e-01 5.94e+01 angle pdb=" C HIS E 361 " pdb=" N ASN E 362 " pdb=" CA ASN E 362 " ideal model delta sigma weight residual 121.54 130.68 -9.14 1.91e+00 2.74e-01 2.29e+01 angle pdb=" C PHE E 227 " pdb=" N ASP E 228 " pdb=" CA ASP E 228 " ideal model delta sigma weight residual 121.54 130.54 -9.00 1.91e+00 2.74e-01 2.22e+01 angle pdb=" CA VAL E 242 " pdb=" CB VAL E 242 " pdb=" CG1 VAL E 242 " ideal model delta sigma weight residual 110.40 118.15 -7.75 1.70e+00 3.46e-01 2.08e+01 angle pdb=" CB MET E 351 " pdb=" CG MET E 351 " pdb=" SD MET E 351 " ideal model delta sigma weight residual 112.70 125.96 -13.26 3.00e+00 1.11e-01 1.95e+01 ... (remaining 9150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.71: 3744 21.71 - 43.41: 414 43.41 - 65.12: 67 65.12 - 86.83: 31 86.83 - 108.54: 10 Dihedral angle restraints: 4266 sinusoidal: 1931 harmonic: 2335 Sorted by residual: dihedral pdb=" CB CYS E 135 " pdb=" SG CYS E 135 " pdb=" SG CYS E 193 " pdb=" CB CYS E 193 " ideal model delta sinusoidal sigma weight residual 93.00 28.70 64.30 1 1.00e+01 1.00e-02 5.44e+01 dihedral pdb=" CA VAL E 242 " pdb=" C VAL E 242 " pdb=" N ASP E 243 " pdb=" CA ASP E 243 " ideal model delta harmonic sigma weight residual 180.00 143.82 36.18 0 5.00e+00 4.00e-02 5.24e+01 dihedral pdb=" CB CYS D 121 " pdb=" SG CYS D 121 " pdb=" SG CYS E 209 " pdb=" CB CYS E 209 " ideal model delta sinusoidal sigma weight residual 93.00 146.37 -53.37 1 1.00e+01 1.00e-02 3.87e+01 ... (remaining 4263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 1037 0.133 - 0.266: 30 0.266 - 0.398: 4 0.398 - 0.531: 1 0.531 - 0.664: 1 Chirality restraints: 1073 Sorted by residual: chirality pdb=" C1 NAG A 304 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A 304 " pdb=" O5 NAG A 304 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" C1 NAG A 303 " pdb=" ND2 ASN A 99 " pdb=" C2 NAG A 303 " pdb=" O5 NAG A 303 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.65e+00 chirality pdb=" CB ILE E 116 " pdb=" CA ILE E 116 " pdb=" CG1 ILE E 116 " pdb=" CG2 ILE E 116 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.75e+00 ... (remaining 1070 not shown) Planarity restraints: 1166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 242 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C VAL E 242 " -0.059 2.00e-02 2.50e+03 pdb=" O VAL E 242 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP E 243 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 149 " 0.021 2.00e-02 2.50e+03 1.95e-02 9.53e+00 pdb=" CG TRP D 149 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP D 149 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP D 149 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 149 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 149 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 149 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 149 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 149 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP D 149 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 185 " -0.012 2.00e-02 2.50e+03 1.92e-02 7.38e+00 pdb=" CG TYR A 185 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 185 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 185 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR A 185 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 185 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 185 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 185 " 0.000 2.00e-02 2.50e+03 ... (remaining 1163 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1395 2.79 - 3.32: 5429 3.32 - 3.84: 11037 3.84 - 4.37: 11823 4.37 - 4.90: 21302 Nonbonded interactions: 50986 Sorted by model distance: nonbonded pdb=" O LYS D 183 " pdb=" OG SER D 187 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASP A 170 " pdb=" OH TYR A 174 " model vdw 2.270 3.040 nonbonded pdb=" OG1 THR E 393 " pdb=" OE1 GLU E 396 " model vdw 2.301 3.040 nonbonded pdb=" O THR D 196 " pdb=" OG1 THR D 196 " model vdw 2.318 3.040 nonbonded pdb=" OG SER A 33 " pdb=" OG1 THR A 50 " model vdw 2.348 3.040 ... (remaining 50981 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 'D' selection = (chain 'E' and resid 110 through 425) } ncs_group { reference = chain 'F' selection = chain 'G' } 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 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: 4.880 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: 0.000 Extract box with map and model: 1.160 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 22.130 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 : 0.005 0.057 6717 Z= 0.359 Angle : 0.981 13.878 9155 Z= 0.501 Chirality : 0.062 0.664 1073 Planarity : 0.007 0.057 1157 Dihedral : 19.033 108.536 2722 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.98 % Allowed : 31.47 % Favored : 67.55 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.26 (0.28), residues: 796 helix: -3.15 (0.51), residues: 35 sheet: -0.04 (0.29), residues: 318 loop : -1.25 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP D 149 HIS 0.011 0.001 HIS D 361 PHE 0.040 0.003 PHE A 56 TYR 0.044 0.002 TYR A 185 ARG 0.007 0.000 ARG E 289 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7847 (tppt) cc_final: 0.7600 (mmtt) outliers start: 7 outliers final: 3 residues processed: 102 average time/residue: 0.1651 time to fit residues: 23.2982 Evaluate side-chains 93 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 209 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN D 154 GLN D 361 HIS E 399 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6717 Z= 0.287 Angle : 0.648 6.565 9155 Z= 0.323 Chirality : 0.047 0.368 1073 Planarity : 0.004 0.038 1157 Dihedral : 10.499 60.334 1220 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 4.06 % Allowed : 29.09 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % 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: -0.86 (0.29), residues: 796 helix: -1.57 (0.74), residues: 35 sheet: -0.02 (0.29), residues: 323 loop : -0.87 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 149 HIS 0.004 0.001 HIS D 361 PHE 0.008 0.001 PHE E 350 TYR 0.014 0.001 TYR A 185 ARG 0.003 0.000 ARG D 341 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 96 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 132 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7358 (mp10) outliers start: 29 outliers final: 17 residues processed: 121 average time/residue: 0.1525 time to fit residues: 26.3270 Evaluate side-chains 106 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 374 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 0.3980 chunk 22 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 77 optimal weight: 0.0970 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN D 371 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 6717 Z= 0.260 Angle : 0.610 5.757 9155 Z= 0.304 Chirality : 0.046 0.362 1073 Planarity : 0.004 0.035 1157 Dihedral : 8.930 55.584 1220 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 6.29 % Allowed : 27.83 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % 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: -0.73 (0.29), residues: 796 helix: -1.17 (0.79), residues: 36 sheet: 0.00 (0.29), residues: 323 loop : -0.76 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 149 HIS 0.004 0.001 HIS D 371 PHE 0.006 0.001 PHE E 385 TYR 0.008 0.001 TYR A 175 ARG 0.002 0.000 ARG E 308 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 100 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7805 (tppt) cc_final: 0.7549 (tppt) REVERT: A 94 GLN cc_start: 0.8122 (tt0) cc_final: 0.7870 (tt0) REVERT: D 132 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7452 (mp10) outliers start: 45 outliers final: 27 residues processed: 139 average time/residue: 0.1482 time to fit residues: 29.0793 Evaluate side-chains 119 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 91 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 392 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6717 Z= 0.237 Angle : 0.603 6.330 9155 Z= 0.299 Chirality : 0.046 0.361 1073 Planarity : 0.004 0.033 1157 Dihedral : 7.881 47.020 1218 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 5.03 % Allowed : 28.95 % Favored : 66.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % 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: -0.76 (0.29), residues: 796 helix: -0.41 (0.81), residues: 35 sheet: -0.10 (0.28), residues: 334 loop : -0.78 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 149 HIS 0.004 0.001 HIS D 361 PHE 0.008 0.001 PHE E 387 TYR 0.009 0.001 TYR A 185 ARG 0.002 0.000 ARG D 341 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 97 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7830 (tppt) cc_final: 0.7591 (tppt) REVERT: A 139 ASP cc_start: 0.7760 (p0) cc_final: 0.7556 (p0) REVERT: D 132 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7426 (mp10) REVERT: D 306 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8330 (mp) REVERT: E 184 HIS cc_start: 0.8148 (m90) cc_final: 0.7867 (m90) outliers start: 36 outliers final: 29 residues processed: 130 average time/residue: 0.1440 time to fit residues: 26.3995 Evaluate side-chains 119 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 88 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 305 HIS Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 392 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 6717 Z= 0.321 Angle : 0.620 5.716 9155 Z= 0.310 Chirality : 0.047 0.359 1073 Planarity : 0.004 0.034 1157 Dihedral : 7.754 49.270 1218 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 6.57 % Allowed : 26.71 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.29), residues: 796 helix: -0.39 (0.88), residues: 36 sheet: -0.13 (0.28), residues: 333 loop : -0.70 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 149 HIS 0.004 0.001 HIS D 361 PHE 0.009 0.001 PHE E 387 TYR 0.009 0.001 TYR A 185 ARG 0.002 0.000 ARG D 341 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 91 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7917 (tppt) cc_final: 0.7693 (tppt) REVERT: D 132 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7506 (mp10) REVERT: D 306 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8541 (mp) REVERT: E 398 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6369 (mp0) outliers start: 47 outliers final: 37 residues processed: 130 average time/residue: 0.1588 time to fit residues: 29.3386 Evaluate side-chains 125 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 85 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 299 CYS Chi-restraints excluded: chain E residue 305 HIS Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain E residue 398 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.0370 chunk 76 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6717 Z= 0.217 Angle : 0.590 6.463 9155 Z= 0.294 Chirality : 0.046 0.343 1073 Planarity : 0.004 0.033 1157 Dihedral : 7.230 45.048 1218 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 6.01 % Allowed : 27.27 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.63 (0.30), residues: 796 helix: 0.24 (0.90), residues: 34 sheet: -0.05 (0.29), residues: 333 loop : -0.72 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 149 HIS 0.003 0.001 HIS D 361 PHE 0.009 0.001 PHE D 385 TYR 0.011 0.001 TYR A 185 ARG 0.002 0.000 ARG D 341 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 100 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7905 (tppt) cc_final: 0.7689 (tppt) REVERT: A 94 GLN cc_start: 0.8120 (tt0) cc_final: 0.7872 (tt0) REVERT: D 132 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7473 (mp10) REVERT: D 306 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8383 (mp) REVERT: E 184 HIS cc_start: 0.8122 (m90) cc_final: 0.7854 (m90) REVERT: E 221 LEU cc_start: 0.8467 (tp) cc_final: 0.8162 (tp) outliers start: 43 outliers final: 35 residues processed: 135 average time/residue: 0.1461 time to fit residues: 27.8475 Evaluate side-chains 131 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 94 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 299 CYS Chi-restraints excluded: chain E residue 305 HIS Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 392 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 6717 Z= 0.277 Angle : 0.603 5.537 9155 Z= 0.301 Chirality : 0.046 0.341 1073 Planarity : 0.004 0.033 1157 Dihedral : 7.177 43.664 1218 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 6.01 % Allowed : 28.11 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.63 (0.30), residues: 796 helix: 0.29 (0.91), residues: 34 sheet: -0.07 (0.28), residues: 333 loop : -0.70 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 149 HIS 0.003 0.001 HIS A 66 PHE 0.008 0.001 PHE D 385 TYR 0.012 0.001 TYR A 185 ARG 0.002 0.000 ARG D 341 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 100 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8201 (tt0) cc_final: 0.7980 (tt0) REVERT: D 132 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7498 (mp10) REVERT: D 306 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8543 (mp) REVERT: E 184 HIS cc_start: 0.8108 (m90) cc_final: 0.7788 (m90) outliers start: 43 outliers final: 37 residues processed: 135 average time/residue: 0.1492 time to fit residues: 28.3611 Evaluate side-chains 134 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 95 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 299 CYS Chi-restraints excluded: chain E residue 305 HIS Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 392 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.0470 chunk 69 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.0270 chunk 42 optimal weight: 0.8980 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6717 Z= 0.198 Angle : 0.586 5.830 9155 Z= 0.291 Chirality : 0.045 0.329 1073 Planarity : 0.004 0.033 1157 Dihedral : 6.744 39.791 1218 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 5.59 % Allowed : 27.69 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.30), residues: 796 helix: 0.24 (0.90), residues: 34 sheet: -0.01 (0.29), residues: 336 loop : -0.63 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 64 HIS 0.002 0.001 HIS D 409 PHE 0.009 0.001 PHE D 385 TYR 0.015 0.001 TYR A 185 ARG 0.002 0.000 ARG E 232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 99 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 TYR cc_start: 0.9092 (p90) cc_final: 0.8872 (p90) REVERT: D 132 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7452 (mp10) REVERT: D 306 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8472 (mp) REVERT: E 184 HIS cc_start: 0.8053 (m90) cc_final: 0.7718 (m90) REVERT: E 221 LEU cc_start: 0.8513 (tp) cc_final: 0.8239 (tp) outliers start: 40 outliers final: 34 residues processed: 133 average time/residue: 0.1389 time to fit residues: 26.3791 Evaluate side-chains 132 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 96 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 299 CYS Chi-restraints excluded: chain E residue 305 HIS Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 392 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 6717 Z= 0.352 Angle : 0.635 5.501 9155 Z= 0.317 Chirality : 0.047 0.342 1073 Planarity : 0.004 0.034 1157 Dihedral : 7.241 41.922 1218 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 5.59 % Allowed : 27.69 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.52 (0.30), residues: 796 helix: 0.17 (0.92), residues: 35 sheet: 0.14 (0.29), residues: 323 loop : -0.73 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 149 HIS 0.003 0.001 HIS D 303 PHE 0.008 0.001 PHE E 350 TYR 0.013 0.002 TYR A 185 ARG 0.002 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 97 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8196 (tt0) cc_final: 0.7996 (tm-30) REVERT: D 132 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7529 (mp10) REVERT: D 306 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8559 (mp) outliers start: 40 outliers final: 36 residues processed: 130 average time/residue: 0.1463 time to fit residues: 26.8603 Evaluate side-chains 129 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 91 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 299 CYS Chi-restraints excluded: chain E residue 305 HIS Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 392 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 6717 Z= 0.244 Angle : 0.608 5.415 9155 Z= 0.303 Chirality : 0.046 0.324 1073 Planarity : 0.004 0.033 1157 Dihedral : 6.932 40.766 1218 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 5.87 % Allowed : 27.41 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.58 (0.30), residues: 796 helix: 0.05 (0.91), residues: 34 sheet: -0.04 (0.29), residues: 334 loop : -0.63 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 149 HIS 0.002 0.001 HIS D 409 PHE 0.008 0.001 PHE D 385 TYR 0.034 0.001 TYR A 185 ARG 0.002 0.000 ARG E 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 98 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 TYR cc_start: 0.9127 (p90) cc_final: 0.8887 (p90) REVERT: D 132 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7492 (mp10) REVERT: D 306 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8546 (mp) REVERT: E 184 HIS cc_start: 0.8014 (m90) cc_final: 0.7798 (m90) outliers start: 42 outliers final: 36 residues processed: 130 average time/residue: 0.1249 time to fit residues: 23.0913 Evaluate side-chains 134 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 96 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 299 CYS Chi-restraints excluded: chain E residue 305 HIS Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 392 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 64 optimal weight: 0.0170 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 0.0070 chunk 3 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 GLN A 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.139453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.104186 restraints weight = 10589.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.107330 restraints weight = 6290.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.109380 restraints weight = 4590.273| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6717 Z= 0.198 Angle : 0.607 8.644 9155 Z= 0.301 Chirality : 0.046 0.320 1073 Planarity : 0.004 0.054 1157 Dihedral : 6.582 39.982 1218 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 5.73 % Allowed : 28.11 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.52 (0.30), residues: 796 helix: -0.10 (0.88), residues: 34 sheet: 0.01 (0.29), residues: 333 loop : -0.59 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 149 HIS 0.002 0.001 HIS D 409 PHE 0.009 0.001 PHE D 385 TYR 0.014 0.001 TYR A 185 ARG 0.006 0.000 ARG E 289 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1639.98 seconds wall clock time: 33 minutes 12.61 seconds (1992.61 seconds total)