Starting phenix.real_space_refine on Fri Dec 27 20:49:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k7s_36940/12_2024/8k7s_36940.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k7s_36940/12_2024/8k7s_36940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k7s_36940/12_2024/8k7s_36940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k7s_36940/12_2024/8k7s_36940.map" model { file = "/net/cci-nas-00/data/ceres_data/8k7s_36940/12_2024/8k7s_36940.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k7s_36940/12_2024/8k7s_36940.cif" } resolution = 3.51 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= 0.001 sd= 0.057 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 4202 2.51 5 N 1083 2.21 5 O 1333 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6645 Number of models: 1 Model: "" Number of chains: 9 Chain: "F" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2519 Classifications: {'peptide': 316} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 295} Chain: "A" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1372 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain: "E" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2523 Classifications: {'peptide': 317} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 296} Chain: "x" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "y" 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: "z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" 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 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "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: 4.70, per 1000 atoms: 0.71 Number of scatterers: 6645 At special positions: 0 Unit cell: (78.02, 101.26, 126.16, 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 1333 8.00 N 1083 7.00 C 4202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS F 108 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 121 " - pdb=" SG CYS F 180 " distance=2.03 Simple disulfide: pdb=" SG CYS F 196 " - pdb=" SG CYS E 108 " distance=2.03 Simple disulfide: pdb=" SG CYS F 226 " - pdb=" SG CYS F 285 " distance=2.03 Simple disulfide: pdb=" SG CYS F 330 " - pdb=" SG CYS F 392 " distance=2.03 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 E 121 " - pdb=" SG CYS E 180 " distance=2.03 Simple disulfide: pdb=" SG CYS E 226 " - pdb=" SG CYS E 285 " distance=2.03 Simple disulfide: pdb=" SG CYS E 330 " - pdb=" SG CYS E 392 " distance=2.04 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 ALPHA1-3 " BMA x 3 " - " MAN x 4 " " BMA z 3 " - " MAN z 4 " ALPHA1-6 " BMA x 3 " - " MAN x 5 " " BMA z 3 " - " MAN z 5 " BETA1-4 " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " NAG-ASN " NAG A 301 " - " ASN A 160 " " NAG A 302 " - " ASN A 46 " " NAG A 303 " - " ASN A 191 " " NAG E 501 " - " ASN E 238 " " NAG F 501 " - " ASN F 238 " " NAG x 1 " - " ASN F 261 " " NAG y 1 " - " ASN A 67 " " NAG z 1 " - " ASN E 261 " Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 1.0 seconds 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1532 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 17 sheets defined 7.5% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'F' and resid 168 through 173 Processing helix chain 'F' and resid 212 through 218 Processing helix chain 'F' and resid 273 through 280 removed outlier: 3.733A pdb=" N TRP F 277 " --> pdb=" O VAL F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 386 removed outlier: 3.542A pdb=" N GLN F 386 " --> pdb=" O THR F 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'E' and resid 169 through 173 Processing helix chain 'E' and resid 273 through 279 Processing helix chain 'E' and resid 352 through 356 Processing sheet with id=AA1, first strand: chain 'F' and resid 150 through 154 removed outlier: 6.746A pdb=" N SER F 160 " --> pdb=" O ILE F 152 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER F 163 " --> pdb=" O CYS F 121 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLN F 118 " --> pdb=" O SER F 106 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER F 106 " --> pdb=" O GLN F 118 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR F 124 " --> pdb=" O THR F 100 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N HIS F 105 " --> pdb=" O HIS E 105 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N HIS E 105 " --> pdb=" O HIS F 105 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N CYS E 162 " --> pdb=" O LEU E 151 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU E 151 " --> pdb=" O CYS E 162 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LYS E 164 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N THR E 149 " --> pdb=" O LYS E 164 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ASN E 166 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ALA E 147 " --> pdb=" O ASN E 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 132 through 136 Processing sheet with id=AA3, first strand: chain 'F' and resid 205 through 209 removed outlier: 3.976A pdb=" N ASP F 230 " --> pdb=" O THR F 264 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR F 264 " --> pdb=" O ASP F 230 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 238 through 242 Processing sheet with id=AA5, first strand: chain 'F' and resid 311 through 315 removed outlier: 3.837A pdb=" N THR F 329 " --> pdb=" O PHE F 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 349 through 350 Processing sheet with id=AA7, first strand: chain 'A' and resid 31 through 34 Processing sheet with id=AA8, first strand: chain 'A' and resid 69 through 70 Processing sheet with id=AA9, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AB1, first strand: chain 'A' and resid 121 through 122 removed outlier: 3.657A pdb=" N VAL A 122 " --> pdb=" O THR A 193 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 150 through 157 removed outlier: 6.617A pdb=" N TYR A 145 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR A 154 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL A 143 " --> pdb=" O TYR A 154 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TYR A 156 " --> pdb=" O TYR A 141 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TYR A 141 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL A 143 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR A 177 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TYR A 145 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR A 175 " --> pdb=" O TYR A 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 133 through 137 Processing sheet with id=AB4, first strand: chain 'E' and resid 205 through 209 removed outlier: 3.626A pdb=" N THR E 225 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP E 230 " --> pdb=" O THR E 264 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N THR E 264 " --> pdb=" O ASP E 230 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 238 through 244 removed outlier: 4.132A pdb=" N GLY E 282 " --> pdb=" O GLU E 244 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 311 through 315 removed outlier: 4.005A pdb=" N THR E 329 " --> pdb=" O PHE E 315 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N PHE E 371 " --> pdb=" O ASN E 334 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 311 through 315 removed outlier: 4.005A pdb=" N THR E 329 " --> pdb=" O PHE E 315 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N PHE E 371 " --> pdb=" O ASN E 334 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU E 362 " --> pdb=" O PHE E 372 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 340 through 344 236 hydrogen bonds defined for protein. 561 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: 2.15 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2078 1.34 - 1.46: 1588 1.46 - 1.58: 3113 1.58 - 1.70: 0 1.70 - 1.82: 32 Bond restraints: 6811 Sorted by residual: bond pdb=" CB PRO E 197 " pdb=" CG PRO E 197 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.95e+00 bond pdb=" CG PRO E 197 " pdb=" CD PRO E 197 " ideal model delta sigma weight residual 1.503 1.538 -0.035 3.40e-02 8.65e+02 1.03e+00 bond pdb=" CB PRO E 201 " pdb=" CG PRO E 201 " ideal model delta sigma weight residual 1.492 1.543 -0.051 5.00e-02 4.00e+02 1.02e+00 bond pdb=" N ASP E 198 " pdb=" CA ASP E 198 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.87e-01 bond pdb=" CB PRO E 222 " pdb=" CG PRO E 222 " ideal model delta sigma weight residual 1.492 1.534 -0.042 5.00e-02 4.00e+02 7.18e-01 ... (remaining 6806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 9152 1.92 - 3.85: 119 3.85 - 5.77: 9 5.77 - 7.70: 1 7.70 - 9.62: 2 Bond angle restraints: 9283 Sorted by residual: angle pdb=" C2 NAG A 303 " pdb=" N2 NAG A 303 " pdb=" C7 NAG A 303 " ideal model delta sigma weight residual 124.56 134.18 -9.62 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C GLU F 244 " pdb=" CA GLU F 244 " pdb=" CB GLU F 244 " ideal model delta sigma weight residual 110.42 116.18 -5.76 1.99e+00 2.53e-01 8.37e+00 angle pdb=" C PRO E 197 " pdb=" N ASP E 198 " pdb=" CA ASP E 198 " ideal model delta sigma weight residual 121.54 126.86 -5.32 1.91e+00 2.74e-01 7.77e+00 angle pdb=" C HIS F 114 " pdb=" N SER F 115 " pdb=" CA SER F 115 " ideal model delta sigma weight residual 120.82 124.75 -3.93 1.50e+00 4.44e-01 6.88e+00 angle pdb=" C ASP F 288 " pdb=" N HIS F 289 " pdb=" CA HIS F 289 " ideal model delta sigma weight residual 122.15 130.25 -8.10 3.47e+00 8.31e-02 5.45e+00 ... (remaining 9278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.19: 3953 11.19 - 22.37: 271 22.37 - 33.55: 79 33.55 - 44.74: 15 44.74 - 55.92: 10 Dihedral angle restraints: 4328 sinusoidal: 1971 harmonic: 2357 Sorted by residual: dihedral pdb=" CA TRP F 254 " pdb=" C TRP F 254 " pdb=" N TYR F 255 " pdb=" CA TYR F 255 " ideal model delta harmonic sigma weight residual -180.00 -163.60 -16.40 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA CYS F 196 " pdb=" C CYS F 196 " pdb=" N PRO F 197 " pdb=" CA PRO F 197 " ideal model delta harmonic sigma weight residual 180.00 -163.65 -16.35 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA GLU E 321 " pdb=" C GLU E 321 " pdb=" N SER E 322 " pdb=" CA SER E 322 " ideal model delta harmonic sigma weight residual -180.00 -164.62 -15.38 0 5.00e+00 4.00e-02 9.46e+00 ... (remaining 4325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 872 0.047 - 0.093: 145 0.093 - 0.139: 78 0.139 - 0.186: 0 0.186 - 0.232: 2 Chirality restraints: 1097 Sorted by residual: chirality pdb=" C2 NAG A 303 " pdb=" C1 NAG A 303 " pdb=" C3 NAG A 303 " pdb=" N2 NAG A 303 " both_signs ideal model delta sigma weight residual False -2.49 -2.26 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA PRO E 197 " pdb=" N PRO E 197 " pdb=" C PRO E 197 " pdb=" CB PRO E 197 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.21e-01 chirality pdb=" C1 NAG A 303 " pdb=" ND2 ASN A 191 " pdb=" C2 NAG A 303 " pdb=" O5 NAG A 303 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 1094 not shown) Planarity restraints: 1165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS E 196 " 0.078 5.00e-02 4.00e+02 1.19e-01 2.26e+01 pdb=" N PRO E 197 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO E 197 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO E 197 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 155 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.86e+00 pdb=" C GLU E 155 " 0.024 2.00e-02 2.50e+03 pdb=" O GLU E 155 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY E 156 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS E 289 " -0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO E 290 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO E 290 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 290 " -0.019 5.00e-02 4.00e+02 ... (remaining 1162 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1254 2.79 - 3.32: 5928 3.32 - 3.85: 10462 3.85 - 4.37: 11974 4.37 - 4.90: 20724 Nonbonded interactions: 50342 Sorted by model distance: nonbonded pdb=" OD1 ASN F 261 " pdb=" OG1 THR F 263 " model vdw 2.263 3.040 nonbonded pdb=" O ASP A 87 " pdb=" OH TYR A 91 " model vdw 2.287 3.040 nonbonded pdb=" OD1 ASN E 261 " pdb=" OG1 THR E 263 " model vdw 2.311 3.040 nonbonded pdb=" OG SER E 354 " pdb=" OE1 GLN E 355 " model vdw 2.314 3.040 nonbonded pdb=" OE1 GLU F 321 " pdb=" NE2 GLN E 333 " model vdw 2.345 3.120 ... (remaining 50337 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 'E' and (resid 98 through 413 or resid 501)) selection = chain 'F' } ncs_group { reference = chain 'x' selection = chain 'z' } 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: 1.790 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: 0.030 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.340 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 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 : 0.002 0.086 6811 Z= 0.145 Angle : 0.528 9.619 9283 Z= 0.268 Chirality : 0.043 0.232 1097 Planarity : 0.005 0.119 1157 Dihedral : 8.555 55.925 2766 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.43 % Favored : 92.19 % Rotamer: Outliers : 0.95 % Allowed : 4.06 % Favored : 94.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.24 (0.32), residues: 794 helix: -0.31 (0.94), residues: 36 sheet: 1.24 (0.30), residues: 360 loop : -0.84 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 254 HIS 0.003 0.001 HIS E 289 PHE 0.010 0.001 PHE E 292 TYR 0.008 0.001 TYR F 255 ARG 0.002 0.000 ARG F 195 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 227 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6410 (m) cc_final: 0.6070 (p) REVERT: F 298 ARG cc_start: 0.6192 (ttm-80) cc_final: 0.5978 (ttm170) REVERT: F 358 THR cc_start: 0.8496 (m) cc_final: 0.8198 (m) REVERT: F 365 ASN cc_start: 0.6597 (m-40) cc_final: 0.6152 (t0) REVERT: A 67 ASN cc_start: 0.7046 (m-40) cc_final: 0.6717 (m-40) REVERT: A 177 THR cc_start: 0.8722 (m) cc_final: 0.8384 (m) REVERT: E 166 ASN cc_start: 0.6322 (m-40) cc_final: 0.6086 (m-40) REVERT: E 205 ILE cc_start: 0.7586 (mt) cc_final: 0.7211 (mt) REVERT: E 376 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7671 (ttt-90) outliers start: 7 outliers final: 3 residues processed: 234 average time/residue: 0.2114 time to fit residues: 63.0239 Evaluate side-chains 118 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain E residue 108 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 0.0000 chunk 39 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 6811 Z= 0.219 Angle : 0.654 9.888 9283 Z= 0.319 Chirality : 0.046 0.212 1097 Planarity : 0.006 0.122 1157 Dihedral : 5.260 54.670 1215 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.06 % Favored : 91.56 % Rotamer: Outliers : 3.11 % Allowed : 12.45 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.06 (0.32), residues: 794 helix: -0.94 (0.80), residues: 42 sheet: 1.14 (0.29), residues: 355 loop : -0.90 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 64 HIS 0.013 0.001 HIS E 289 PHE 0.023 0.002 PHE E 372 TYR 0.012 0.001 TYR E 217 ARG 0.008 0.001 ARG E 307 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6373 (m) cc_final: 0.6091 (p) REVERT: F 173 MET cc_start: 0.7388 (mtt) cc_final: 0.7170 (mtt) REVERT: F 194 ARG cc_start: 0.6924 (ptt-90) cc_final: 0.6527 (ptt90) REVERT: F 327 THR cc_start: 0.8538 (p) cc_final: 0.8178 (t) REVERT: E 198 ASP cc_start: 0.6290 (p0) cc_final: 0.6024 (p0) REVERT: E 205 ILE cc_start: 0.7670 (mt) cc_final: 0.7286 (mt) REVERT: E 376 ARG cc_start: 0.8418 (ttp80) cc_final: 0.7801 (ttt-90) outliers start: 23 outliers final: 15 residues processed: 144 average time/residue: 0.1819 time to fit residues: 35.0932 Evaluate side-chains 115 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 223 LYS Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 327 THR Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain E residue 385 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.0010 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 19 optimal weight: 0.4980 chunk 70 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 53 optimal weight: 9.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN A 96 GLN ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 HIS E 353 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 6811 Z= 0.221 Angle : 0.626 9.447 9283 Z= 0.309 Chirality : 0.046 0.208 1097 Planarity : 0.005 0.115 1157 Dihedral : 5.635 57.621 1215 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.43 % Favored : 92.07 % Rotamer: Outliers : 4.87 % Allowed : 13.40 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.03 (0.32), residues: 794 helix: -1.25 (0.80), residues: 42 sheet: 0.92 (0.29), residues: 368 loop : -0.80 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 254 HIS 0.011 0.001 HIS E 289 PHE 0.043 0.002 PHE F 113 TYR 0.016 0.002 TYR F 189 ARG 0.004 0.001 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6358 (m) cc_final: 0.6098 (p) REVERT: F 194 ARG cc_start: 0.6928 (ptt-90) cc_final: 0.6538 (ptt90) REVERT: F 292 PHE cc_start: 0.6887 (OUTLIER) cc_final: 0.6639 (t80) REVERT: F 298 ARG cc_start: 0.6773 (ttm-80) cc_final: 0.6562 (ttm-80) REVERT: F 327 THR cc_start: 0.8753 (p) cc_final: 0.8386 (t) REVERT: F 409 ILE cc_start: 0.6570 (tp) cc_final: 0.6267 (pt) REVERT: A 50 THR cc_start: 0.7735 (m) cc_final: 0.7500 (m) REVERT: A 52 ASN cc_start: 0.7678 (OUTLIER) cc_final: 0.6150 (p0) REVERT: A 96 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7598 (tm130) REVERT: A 190 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7739 (tp) REVERT: E 205 ILE cc_start: 0.7655 (mt) cc_final: 0.7329 (mt) REVERT: E 353 ASN cc_start: 0.7031 (OUTLIER) cc_final: 0.6799 (t0) REVERT: E 376 ARG cc_start: 0.8517 (ttp80) cc_final: 0.7839 (ttt-90) outliers start: 36 outliers final: 25 residues processed: 133 average time/residue: 0.1856 time to fit residues: 33.3531 Evaluate side-chains 120 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 223 LYS Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 327 THR Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain E residue 385 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 71 optimal weight: 0.0770 chunk 75 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 6811 Z= 0.434 Angle : 0.792 10.159 9283 Z= 0.397 Chirality : 0.051 0.344 1097 Planarity : 0.007 0.116 1157 Dihedral : 6.476 53.345 1215 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.44 % Favored : 91.18 % Rotamer: Outliers : 6.63 % Allowed : 14.07 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.52 (0.30), residues: 794 helix: -2.19 (0.65), residues: 47 sheet: 0.65 (0.28), residues: 364 loop : -1.08 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP E 254 HIS 0.009 0.002 HIS E 289 PHE 0.031 0.004 PHE F 113 TYR 0.018 0.003 TYR A 175 ARG 0.006 0.001 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 94 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: F 100 THR cc_start: 0.6585 (m) cc_final: 0.6296 (p) REVERT: F 113 PHE cc_start: 0.3158 (p90) cc_final: 0.2897 (p90) REVERT: F 194 ARG cc_start: 0.7299 (ptt-90) cc_final: 0.6986 (ptt90) REVERT: F 287 VAL cc_start: 0.8220 (p) cc_final: 0.7962 (t) REVERT: F 292 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.7170 (t80) REVERT: F 355 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7293 (mp10) REVERT: A 32 VAL cc_start: 0.7997 (OUTLIER) cc_final: 0.7744 (p) REVERT: A 67 ASN cc_start: 0.6712 (m-40) cc_final: 0.6355 (m-40) REVERT: E 205 ILE cc_start: 0.7825 (mt) cc_final: 0.7485 (mt) REVERT: E 296 ILE cc_start: 0.6244 (OUTLIER) cc_final: 0.5473 (tp) REVERT: E 376 ARG cc_start: 0.8494 (ttp80) cc_final: 0.7817 (ttt180) outliers start: 49 outliers final: 29 residues processed: 133 average time/residue: 0.1775 time to fit residues: 32.2330 Evaluate side-chains 108 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 75 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 355 GLN Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain E residue 385 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 9.9990 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 0.0570 chunk 14 optimal weight: 0.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 6811 Z= 0.227 Angle : 0.667 10.838 9283 Z= 0.328 Chirality : 0.046 0.213 1097 Planarity : 0.005 0.115 1157 Dihedral : 5.814 53.182 1213 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.68 % Favored : 91.81 % Rotamer: Outliers : 3.52 % Allowed : 18.81 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.43 (0.30), residues: 794 helix: -1.50 (0.73), residues: 41 sheet: 0.66 (0.28), residues: 363 loop : -1.07 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 254 HIS 0.009 0.002 HIS A 95 PHE 0.030 0.002 PHE E 372 TYR 0.013 0.001 TYR E 283 ARG 0.004 0.001 ARG F 195 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: F 100 THR cc_start: 0.6391 (m) cc_final: 0.6154 (p) REVERT: F 194 ARG cc_start: 0.7206 (ptt-90) cc_final: 0.6887 (ptt90) REVERT: F 287 VAL cc_start: 0.8026 (p) cc_final: 0.7778 (t) REVERT: F 292 PHE cc_start: 0.7227 (OUTLIER) cc_final: 0.7005 (t80) REVERT: F 327 THR cc_start: 0.8878 (p) cc_final: 0.8430 (t) REVERT: F 355 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.7230 (mp10) REVERT: A 32 VAL cc_start: 0.7955 (OUTLIER) cc_final: 0.7586 (m) REVERT: A 67 ASN cc_start: 0.6570 (m-40) cc_final: 0.6229 (m-40) REVERT: E 137 MET cc_start: 0.5788 (ttp) cc_final: 0.5491 (ttp) REVERT: E 205 ILE cc_start: 0.7824 (mt) cc_final: 0.7520 (mt) REVERT: E 307 ARG cc_start: 0.8491 (mtt90) cc_final: 0.8088 (mtt90) REVERT: E 376 ARG cc_start: 0.8479 (ttp80) cc_final: 0.7814 (ttt-90) outliers start: 26 outliers final: 19 residues processed: 107 average time/residue: 0.2025 time to fit residues: 28.9948 Evaluate side-chains 98 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 355 GLN Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain E residue 385 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 72 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 GLN ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 GLN E 289 HIS ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6811 Z= 0.309 Angle : 0.709 11.167 9283 Z= 0.348 Chirality : 0.047 0.269 1097 Planarity : 0.006 0.119 1157 Dihedral : 6.018 53.308 1213 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.44 % Favored : 91.06 % Rotamer: Outliers : 4.47 % Allowed : 19.22 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.61 (0.30), residues: 794 helix: -2.05 (0.65), residues: 48 sheet: 0.52 (0.27), residues: 363 loop : -1.09 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 254 HIS 0.006 0.001 HIS F 105 PHE 0.028 0.003 PHE E 372 TYR 0.015 0.002 TYR E 283 ARG 0.008 0.001 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 82 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6582 (m) cc_final: 0.6335 (p) REVERT: F 120 TYR cc_start: 0.7110 (m-80) cc_final: 0.6791 (m-80) REVERT: F 194 ARG cc_start: 0.7223 (ptt-90) cc_final: 0.6853 (ptt90) REVERT: F 321 GLU cc_start: 0.5677 (OUTLIER) cc_final: 0.5130 (pm20) REVERT: F 355 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.7238 (mp10) REVERT: A 32 VAL cc_start: 0.7971 (OUTLIER) cc_final: 0.7706 (p) REVERT: A 67 ASN cc_start: 0.6716 (m-40) cc_final: 0.6310 (m-40) REVERT: E 137 MET cc_start: 0.5916 (ttp) cc_final: 0.5622 (ttp) REVERT: E 205 ILE cc_start: 0.7770 (mt) cc_final: 0.7416 (mt) REVERT: E 296 ILE cc_start: 0.6294 (OUTLIER) cc_final: 0.5618 (tp) REVERT: E 376 ARG cc_start: 0.8476 (ttp80) cc_final: 0.7839 (ttt-90) outliers start: 33 outliers final: 26 residues processed: 113 average time/residue: 0.1943 time to fit residues: 29.7344 Evaluate side-chains 101 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 71 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 248 SER Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 355 GLN Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain E residue 385 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 0.0770 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 HIS ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 HIS ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 6811 Z= 0.265 Angle : 0.686 11.677 9283 Z= 0.336 Chirality : 0.047 0.235 1097 Planarity : 0.006 0.115 1157 Dihedral : 5.904 53.515 1213 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.56 % Favored : 90.93 % Rotamer: Outliers : 5.14 % Allowed : 19.22 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.65 (0.30), residues: 794 helix: -1.43 (0.71), residues: 42 sheet: 0.50 (0.27), residues: 361 loop : -1.22 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 254 HIS 0.007 0.001 HIS F 105 PHE 0.030 0.002 PHE E 372 TYR 0.016 0.002 TYR F 255 ARG 0.008 0.001 ARG F 298 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 87 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 120 TYR cc_start: 0.7117 (m-80) cc_final: 0.6799 (m-80) REVERT: F 194 ARG cc_start: 0.7210 (ptt-90) cc_final: 0.6832 (ptt90) REVERT: F 321 GLU cc_start: 0.5372 (OUTLIER) cc_final: 0.4893 (pm20) REVERT: F 355 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.7253 (mp10) REVERT: A 32 VAL cc_start: 0.7910 (OUTLIER) cc_final: 0.7637 (p) REVERT: A 67 ASN cc_start: 0.7046 (m-40) cc_final: 0.6653 (m-40) REVERT: E 137 MET cc_start: 0.5970 (ttp) cc_final: 0.5726 (ttp) REVERT: E 205 ILE cc_start: 0.7747 (mt) cc_final: 0.7431 (mt) REVERT: E 296 ILE cc_start: 0.6304 (OUTLIER) cc_final: 0.5645 (tp) REVERT: E 376 ARG cc_start: 0.8451 (ttp80) cc_final: 0.7842 (ttt-90) outliers start: 38 outliers final: 32 residues processed: 122 average time/residue: 0.2002 time to fit residues: 32.7329 Evaluate side-chains 109 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 73 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 248 SER Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 355 GLN Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain E residue 385 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 HIS ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6811 Z= 0.234 Angle : 0.681 12.189 9283 Z= 0.334 Chirality : 0.047 0.216 1097 Planarity : 0.006 0.113 1157 Dihedral : 5.844 53.916 1213 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.31 % Favored : 91.18 % Rotamer: Outliers : 4.74 % Allowed : 20.57 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.60 (0.30), residues: 794 helix: -1.31 (0.72), residues: 42 sheet: 0.52 (0.28), residues: 361 loop : -1.19 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 254 HIS 0.019 0.002 HIS A 95 PHE 0.032 0.002 PHE E 372 TYR 0.014 0.001 TYR E 283 ARG 0.003 0.001 ARG F 298 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 74 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 120 TYR cc_start: 0.7119 (m-80) cc_final: 0.6794 (m-80) REVERT: F 194 ARG cc_start: 0.7204 (ptt-90) cc_final: 0.6829 (ptt90) REVERT: F 321 GLU cc_start: 0.5338 (OUTLIER) cc_final: 0.4811 (pm20) REVERT: F 327 THR cc_start: 0.8901 (p) cc_final: 0.8533 (t) REVERT: F 355 GLN cc_start: 0.7488 (OUTLIER) cc_final: 0.7235 (mp10) REVERT: A 32 VAL cc_start: 0.7863 (OUTLIER) cc_final: 0.7588 (p) REVERT: A 67 ASN cc_start: 0.7002 (m-40) cc_final: 0.6619 (m-40) REVERT: E 137 MET cc_start: 0.5911 (ttp) cc_final: 0.5637 (ttp) REVERT: E 205 ILE cc_start: 0.7768 (mt) cc_final: 0.7444 (mt) REVERT: E 296 ILE cc_start: 0.6612 (OUTLIER) cc_final: 0.5884 (tp) REVERT: E 376 ARG cc_start: 0.8443 (ttp80) cc_final: 0.7840 (ttt-90) outliers start: 35 outliers final: 28 residues processed: 108 average time/residue: 0.1969 time to fit residues: 28.4015 Evaluate side-chains 102 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 248 SER Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 355 GLN Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain E residue 385 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 0.0970 chunk 51 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6811 Z= 0.219 Angle : 0.682 11.555 9283 Z= 0.333 Chirality : 0.047 0.204 1097 Planarity : 0.005 0.113 1157 Dihedral : 5.764 54.275 1213 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.44 % Favored : 90.93 % Rotamer: Outliers : 5.01 % Allowed : 20.43 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.61 (0.30), residues: 794 helix: -1.23 (0.74), residues: 42 sheet: 0.48 (0.28), residues: 361 loop : -1.16 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP E 254 HIS 0.007 0.001 HIS F 105 PHE 0.033 0.002 PHE E 372 TYR 0.017 0.001 TYR F 255 ARG 0.003 0.001 ARG F 195 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 78 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 120 TYR cc_start: 0.7122 (m-80) cc_final: 0.6803 (m-80) REVERT: F 194 ARG cc_start: 0.7194 (ptt-90) cc_final: 0.6813 (ptt90) REVERT: F 321 GLU cc_start: 0.5332 (OUTLIER) cc_final: 0.4782 (pm20) REVERT: F 327 THR cc_start: 0.8915 (p) cc_final: 0.8539 (t) REVERT: F 355 GLN cc_start: 0.7488 (OUTLIER) cc_final: 0.7237 (mp10) REVERT: A 32 VAL cc_start: 0.7814 (OUTLIER) cc_final: 0.7544 (p) REVERT: A 67 ASN cc_start: 0.6975 (m-40) cc_final: 0.6599 (m-40) REVERT: E 198 ASP cc_start: 0.6844 (p0) cc_final: 0.6579 (p0) REVERT: E 205 ILE cc_start: 0.7734 (mt) cc_final: 0.7208 (mt) REVERT: E 296 ILE cc_start: 0.6596 (OUTLIER) cc_final: 0.5864 (tp) REVERT: E 376 ARG cc_start: 0.8436 (ttp80) cc_final: 0.7833 (ttt-90) outliers start: 37 outliers final: 29 residues processed: 113 average time/residue: 0.2021 time to fit residues: 30.4447 Evaluate side-chains 107 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 74 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 248 SER Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 355 GLN Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 385 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.0010 chunk 71 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 0.0980 chunk 9 optimal weight: 0.7980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS E 218 GLN ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6811 Z= 0.197 Angle : 0.667 10.947 9283 Z= 0.326 Chirality : 0.046 0.210 1097 Planarity : 0.005 0.109 1157 Dihedral : 5.631 54.460 1213 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.56 % Favored : 91.81 % Rotamer: Outliers : 3.92 % Allowed : 21.52 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.54 (0.30), residues: 794 helix: -1.16 (0.76), residues: 42 sheet: 0.49 (0.28), residues: 363 loop : -1.09 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 344 HIS 0.006 0.001 HIS F 105 PHE 0.033 0.002 PHE E 372 TYR 0.013 0.001 TYR E 283 ARG 0.004 0.000 ARG F 298 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 120 TYR cc_start: 0.7120 (m-80) cc_final: 0.6799 (m-80) REVERT: F 194 ARG cc_start: 0.7192 (ptt-90) cc_final: 0.6805 (ptt90) REVERT: F 321 GLU cc_start: 0.5298 (OUTLIER) cc_final: 0.4765 (pm20) REVERT: F 327 THR cc_start: 0.8913 (p) cc_final: 0.8541 (t) REVERT: F 355 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.7234 (mp10) REVERT: A 32 VAL cc_start: 0.7693 (OUTLIER) cc_final: 0.7436 (p) REVERT: A 67 ASN cc_start: 0.6952 (m-40) cc_final: 0.6578 (m-40) REVERT: E 205 ILE cc_start: 0.7521 (mt) cc_final: 0.7178 (mt) REVERT: E 296 ILE cc_start: 0.6555 (OUTLIER) cc_final: 0.5876 (tp) REVERT: E 376 ARG cc_start: 0.8427 (ttp80) cc_final: 0.7821 (ttt-90) outliers start: 29 outliers final: 25 residues processed: 103 average time/residue: 0.1741 time to fit residues: 24.7244 Evaluate side-chains 101 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 248 SER Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 355 GLN Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 385 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 63 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 54 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 41 optimal weight: 0.1980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.185501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.153779 restraints weight = 8581.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.152852 restraints weight = 6425.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.154127 restraints weight = 5959.187| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6811 Z= 0.235 Angle : 0.684 11.468 9283 Z= 0.335 Chirality : 0.047 0.214 1097 Planarity : 0.005 0.105 1157 Dihedral : 5.669 54.440 1213 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.31 % Favored : 91.06 % Rotamer: Outliers : 4.47 % Allowed : 21.38 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.58 (0.30), residues: 794 helix: -1.22 (0.74), residues: 42 sheet: 0.50 (0.27), residues: 361 loop : -1.14 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 254 HIS 0.009 0.001 HIS A 95 PHE 0.031 0.002 PHE E 372 TYR 0.016 0.001 TYR F 255 ARG 0.005 0.001 ARG F 298 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1695.90 seconds wall clock time: 33 minutes 8.70 seconds (1988.70 seconds total)