Starting phenix.real_space_refine on Tue Mar 11 20:59:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k7s_36940/03_2025/8k7s_36940.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k7s_36940/03_2025/8k7s_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_36940/03_2025/8k7s_36940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k7s_36940/03_2025/8k7s_36940.map" model { file = "/net/cci-nas-00/data/ceres_data/8k7s_36940/03_2025/8k7s_36940.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k7s_36940/03_2025/8k7s_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-5624/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: 4.31, per 1000 atoms: 0.65 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: 2.01 Conformation dependent library (CDL) restraints added in 871.8 milliseconds 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: 0.88 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: 1.81 Time building geometry restraints manager: 2.19 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: 0.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.030 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.520 ------------------------------------------------------------------------------- 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 : 0.721 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: 0.2026 time to fit residues: 60.6977 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 : 0.710 ------------------------------------------------------------------------------- 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: 0.6980 chunk 45 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.204476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.176264 restraints weight = 8663.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.175482 restraints weight = 7068.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.177523 restraints weight = 6227.411| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.2505 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= 0.215 Angle : 0.659 10.383 9283 Z= 0.322 Chirality : 0.046 0.212 1097 Planarity : 0.006 0.123 1157 Dihedral : 5.304 54.559 1215 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.68 % Favored : 91.81 % Rotamer: Outliers : 2.98 % Allowed : 12.58 % 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: 0.03 (0.32), residues: 794 helix: -0.99 (0.80), residues: 42 sheet: 1.09 (0.29), residues: 357 loop : -0.89 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 64 HIS 0.012 0.001 HIS E 289 PHE 0.023 0.002 PHE E 372 TYR 0.013 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 152 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6342 (m) cc_final: 0.6052 (p) REVERT: F 194 ARG cc_start: 0.6978 (ptt-90) cc_final: 0.6566 (ptm-80) REVERT: F 298 ARG cc_start: 0.7103 (ttm-80) cc_final: 0.6472 (ttm170) REVERT: F 327 THR cc_start: 0.8489 (p) cc_final: 0.8168 (t) REVERT: E 198 ASP cc_start: 0.6172 (p0) cc_final: 0.5874 (p0) REVERT: E 205 ILE cc_start: 0.7711 (mt) cc_final: 0.7318 (mt) REVERT: E 376 ARG cc_start: 0.8428 (ttp80) cc_final: 0.7796 (ttt-90) outliers start: 22 outliers final: 15 residues processed: 144 average time/residue: 0.1682 time to fit residues: 32.7720 Evaluate side-chains 116 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 37 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 GLN ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 HIS E 289 HIS E 353 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.188925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.156948 restraints weight = 8706.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.155139 restraints weight = 7051.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.156473 restraints weight = 6474.801| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 6811 Z= 0.358 Angle : 0.743 9.304 9283 Z= 0.369 Chirality : 0.050 0.307 1097 Planarity : 0.006 0.112 1157 Dihedral : 6.377 53.456 1215 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.31 % Favored : 91.18 % Rotamer: Outliers : 5.82 % Allowed : 13.13 % Favored : 81.06 % 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 (0.31), residues: 794 helix: -1.51 (0.76), residues: 42 sheet: 0.85 (0.29), residues: 364 loop : -1.00 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP E 254 HIS 0.011 0.002 HIS E 289 PHE 0.039 0.004 PHE F 113 TYR 0.020 0.003 TYR F 313 ARG 0.007 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 138 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 95 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6454 (m) cc_final: 0.6196 (p) REVERT: F 292 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.6995 (t80) REVERT: F 298 ARG cc_start: 0.6890 (ttm-80) cc_final: 0.6465 (ttm170) REVERT: F 365 ASN cc_start: 0.7033 (m-40) cc_final: 0.6540 (t0) REVERT: A 32 VAL cc_start: 0.8170 (OUTLIER) cc_final: 0.7889 (p) REVERT: A 50 THR cc_start: 0.8078 (m) cc_final: 0.7722 (m) REVERT: A 52 ASN cc_start: 0.7752 (OUTLIER) cc_final: 0.6107 (p0) REVERT: A 96 GLN cc_start: 0.8335 (tm130) cc_final: 0.8067 (tm-30) REVERT: A 115 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6936 (pt) REVERT: E 205 ILE cc_start: 0.7744 (mt) cc_final: 0.7383 (mt) REVERT: E 327 THR cc_start: 0.7397 (OUTLIER) cc_final: 0.7177 (t) REVERT: E 376 ARG cc_start: 0.8582 (ttp80) cc_final: 0.7835 (ttt-90) outliers start: 43 outliers final: 31 residues processed: 133 average time/residue: 0.1724 time to fit residues: 31.0428 Evaluate side-chains 119 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 83 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 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 248 SER Chi-restraints excluded: chain F residue 249 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 382 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 115 LEU 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 270 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 299 SER 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 17 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 70 optimal weight: 0.5980 chunk 48 optimal weight: 20.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 258 HIS A 116 GLN ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.186781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.154047 restraints weight = 8818.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.153223 restraints weight = 7043.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.154165 restraints weight = 6646.470| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 6811 Z= 0.311 Angle : 0.705 11.995 9283 Z= 0.345 Chirality : 0.048 0.245 1097 Planarity : 0.006 0.117 1157 Dihedral : 6.040 52.946 1214 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.31 % Favored : 91.18 % Rotamer: Outliers : 6.09 % Allowed : 15.56 % Favored : 78.35 % 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: -0.42 (0.31), residues: 794 helix: -1.53 (0.75), residues: 42 sheet: 0.65 (0.28), residues: 368 loop : -1.07 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 254 HIS 0.009 0.002 HIS E 289 PHE 0.028 0.003 PHE E 372 TYR 0.015 0.002 TYR E 283 ARG 0.004 0.001 ARG E 195 *********************** 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 137 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 92 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6386 (m) cc_final: 0.6087 (p) REVERT: F 194 ARG cc_start: 0.7317 (ptt-90) cc_final: 0.6945 (ptt90) REVERT: F 292 PHE cc_start: 0.7341 (OUTLIER) cc_final: 0.7111 (t80) REVERT: F 298 ARG cc_start: 0.6531 (ttm-80) cc_final: 0.5996 (ttm-80) REVERT: F 327 THR cc_start: 0.8789 (p) cc_final: 0.8373 (t) REVERT: F 355 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7228 (mp10) REVERT: E 205 ILE cc_start: 0.7814 (mt) cc_final: 0.7481 (mt) REVERT: E 296 ILE cc_start: 0.6244 (OUTLIER) cc_final: 0.5480 (tp) REVERT: E 331 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8076 (tt) REVERT: E 376 ARG cc_start: 0.8477 (ttp80) cc_final: 0.7799 (ttt-90) outliers start: 45 outliers final: 26 residues processed: 131 average time/residue: 0.1732 time to fit residues: 31.0686 Evaluate side-chains 105 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 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 258 HIS 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 34 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 111 ASP 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 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 58 optimal weight: 0.5980 chunk 71 optimal weight: 0.1980 chunk 3 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 111 ASN F 253 GLN ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.184544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.151154 restraints weight = 8845.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.150322 restraints weight = 7027.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.151310 restraints weight = 6392.848| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 6811 Z= 0.347 Angle : 0.720 13.412 9283 Z= 0.353 Chirality : 0.049 0.300 1097 Planarity : 0.006 0.117 1157 Dihedral : 6.174 53.096 1213 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.94 % Favored : 90.55 % Rotamer: Outliers : 5.82 % Allowed : 16.91 % Favored : 77.27 % 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: -0.73 (0.30), residues: 794 helix: -2.03 (0.67), residues: 48 sheet: 0.44 (0.27), residues: 377 loop : -1.24 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 254 HIS 0.014 0.002 HIS F 258 PHE 0.028 0.003 PHE E 372 TYR 0.016 0.002 TYR E 283 ARG 0.003 0.001 ARG E 194 *********************** 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 129 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 86 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6470 (m) cc_final: 0.6180 (p) REVERT: F 298 ARG cc_start: 0.6748 (ttm-80) cc_final: 0.6241 (ttm-80) REVERT: F 321 GLU cc_start: 0.5835 (OUTLIER) cc_final: 0.4919 (pm20) REVERT: F 355 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7241 (mp10) REVERT: A 67 ASN cc_start: 0.6970 (m-40) cc_final: 0.6515 (m-40) REVERT: E 137 MET cc_start: 0.5468 (ttp) cc_final: 0.5129 (ttp) REVERT: E 205 ILE cc_start: 0.7837 (mt) cc_final: 0.7490 (mt) REVERT: E 296 ILE cc_start: 0.6382 (OUTLIER) cc_final: 0.5656 (tp) REVERT: E 376 ARG cc_start: 0.8528 (ttp80) cc_final: 0.7901 (ttt-90) outliers start: 43 outliers final: 31 residues processed: 125 average time/residue: 0.1686 time to fit residues: 28.8092 Evaluate side-chains 109 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 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 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 339 ASP 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 F residue 383 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain E residue 108 CYS 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 272 VAL 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 379 VAL 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 76 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 HIS E 289 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.186356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.152990 restraints weight = 8714.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.152298 restraints weight = 7235.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.153993 restraints weight = 6448.620| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6811 Z= 0.235 Angle : 0.673 11.841 9283 Z= 0.329 Chirality : 0.047 0.230 1097 Planarity : 0.006 0.115 1157 Dihedral : 5.930 53.490 1213 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.68 % Favored : 91.69 % Rotamer: Outliers : 4.47 % Allowed : 18.13 % Favored : 77.40 % 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: -1.43 (0.72), residues: 42 sheet: 0.57 (0.28), residues: 367 loop : -1.28 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 254 HIS 0.012 0.001 HIS A 95 PHE 0.032 0.002 PHE E 372 TYR 0.014 0.001 TYR E 283 ARG 0.005 0.000 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 119 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 86 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6494 (m) cc_final: 0.6206 (p) REVERT: F 194 ARG cc_start: 0.7288 (ptt-90) cc_final: 0.6915 (ptt90) REVERT: F 298 ARG cc_start: 0.6675 (ttm-80) cc_final: 0.6183 (ttm-80) REVERT: F 321 GLU cc_start: 0.5556 (OUTLIER) cc_final: 0.4781 (pm20) REVERT: F 327 THR cc_start: 0.8808 (p) cc_final: 0.8434 (t) REVERT: F 355 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7244 (mp10) REVERT: A 52 ASN cc_start: 0.7591 (m110) cc_final: 0.6045 (p0) REVERT: A 67 ASN cc_start: 0.6884 (m-40) cc_final: 0.6473 (m-40) REVERT: E 137 MET cc_start: 0.5434 (ttp) cc_final: 0.5136 (ttp) REVERT: E 205 ILE cc_start: 0.7779 (mt) cc_final: 0.7432 (mt) REVERT: E 296 ILE cc_start: 0.6557 (OUTLIER) cc_final: 0.5787 (tp) REVERT: E 376 ARG cc_start: 0.8506 (ttp80) cc_final: 0.7918 (ttt-90) outliers start: 33 outliers final: 26 residues processed: 117 average time/residue: 0.1797 time to fit residues: 28.2755 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 : 0.704 ------------------------------------------------------------------------------- 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 248 SER 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 F residue 383 LEU Chi-restraints excluded: chain A residue 34 LEU 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 217 TYR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 296 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 6 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 55 optimal weight: 0.0770 chunk 28 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- 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 284 GLN E 289 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.183150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.150479 restraints weight = 8748.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.149503 restraints weight = 7013.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.150531 restraints weight = 6581.125| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 6811 Z= 0.324 Angle : 0.724 13.148 9283 Z= 0.355 Chirality : 0.049 0.265 1097 Planarity : 0.006 0.114 1157 Dihedral : 6.136 53.339 1213 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.63 % Allowed : 9.19 % Favored : 90.18 % Rotamer: Outliers : 5.68 % Allowed : 18.94 % Favored : 75.37 % 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: -0.71 (0.30), residues: 794 helix: -1.38 (0.72), residues: 42 sheet: 0.48 (0.28), residues: 357 loop : -1.28 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 254 HIS 0.011 0.002 HIS A 95 PHE 0.031 0.003 PHE E 372 TYR 0.017 0.002 TYR E 283 ARG 0.006 0.001 ARG A 131 *********************** 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 119 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 77 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6349 (m) cc_final: 0.6125 (p) REVERT: F 116 THR cc_start: 0.3786 (OUTLIER) cc_final: 0.3586 (p) REVERT: F 194 ARG cc_start: 0.7312 (ptt-90) cc_final: 0.6879 (ptt90) REVERT: F 298 ARG cc_start: 0.6690 (ttm-80) cc_final: 0.6244 (ttm-80) REVERT: F 355 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7268 (mp10) REVERT: A 52 ASN cc_start: 0.7345 (m110) cc_final: 0.5856 (p0) REVERT: A 67 ASN cc_start: 0.6990 (m-40) cc_final: 0.6509 (m-40) REVERT: E 137 MET cc_start: 0.5517 (ttp) cc_final: 0.5208 (ttp) REVERT: E 205 ILE cc_start: 0.7828 (mt) cc_final: 0.7298 (mt) REVERT: E 296 ILE cc_start: 0.6623 (OUTLIER) cc_final: 0.5852 (tp) REVERT: E 376 ARG cc_start: 0.8472 (ttp80) cc_final: 0.7868 (ttt-90) outliers start: 42 outliers final: 29 residues processed: 118 average time/residue: 0.1880 time to fit residues: 30.6529 Evaluate side-chains 103 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 71 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 152 ILE Chi-restraints excluded: chain F residue 177 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 272 VAL Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 339 ASP 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 F residue 383 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain E residue 108 CYS 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 287 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 58 optimal weight: 0.0770 chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 0.0370 chunk 29 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 72 optimal weight: 0.2980 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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** A 96 GLN ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.185983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.153512 restraints weight = 8665.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.153225 restraints weight = 6712.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.153711 restraints weight = 6024.410| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.5324 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= 0.209 Angle : 0.688 12.248 9283 Z= 0.336 Chirality : 0.047 0.209 1097 Planarity : 0.006 0.112 1157 Dihedral : 5.842 54.154 1213 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.56 % Favored : 91.81 % Rotamer: Outliers : 3.65 % Allowed : 21.38 % Favored : 74.97 % 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: -0.57 (0.30), residues: 794 helix: -1.24 (0.75), residues: 42 sheet: 0.52 (0.28), residues: 358 loop : -1.13 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP E 254 HIS 0.009 0.001 HIS A 95 PHE 0.035 0.002 PHE E 372 TYR 0.025 0.001 TYR F 189 ARG 0.002 0.000 ARG E 195 *********************** 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 106 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6282 (m) cc_final: 0.6023 (p) REVERT: F 194 ARG cc_start: 0.7253 (ptt-90) cc_final: 0.6854 (ptt90) REVERT: F 298 ARG cc_start: 0.6713 (ttm-80) cc_final: 0.6295 (ttm170) REVERT: F 327 THR cc_start: 0.8796 (p) cc_final: 0.8419 (t) REVERT: F 355 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7227 (mp10) REVERT: A 52 ASN cc_start: 0.7191 (m110) cc_final: 0.5726 (p0) REVERT: A 67 ASN cc_start: 0.7216 (m-40) cc_final: 0.6778 (m-40) REVERT: E 205 ILE cc_start: 0.7301 (mt) cc_final: 0.7097 (mt) REVERT: E 296 ILE cc_start: 0.6553 (OUTLIER) cc_final: 0.5865 (tp) REVERT: E 376 ARG cc_start: 0.8438 (ttp80) cc_final: 0.7857 (ttt-90) outliers start: 27 outliers final: 19 residues processed: 103 average time/residue: 0.1942 time to fit residues: 26.8159 Evaluate side-chains 91 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 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 355 GLN Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain A residue 34 LEU 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 237 VAL Chi-restraints excluded: chain E residue 296 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 75 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 6 optimal weight: 0.2980 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.184624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.151904 restraints weight = 8662.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.151342 restraints weight = 7807.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.153047 restraints weight = 6936.389| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.5444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6811 Z= 0.228 Angle : 0.680 12.126 9283 Z= 0.334 Chirality : 0.047 0.205 1097 Planarity : 0.005 0.109 1157 Dihedral : 5.726 54.241 1213 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.76 % Allowed : 8.19 % Favored : 91.06 % Rotamer: Outliers : 3.11 % Allowed : 22.33 % 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: -0.57 (0.30), residues: 794 helix: -1.23 (0.76), residues: 42 sheet: 0.50 (0.28), residues: 365 loop : -1.14 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP E 254 HIS 0.006 0.001 HIS F 105 PHE 0.032 0.002 PHE E 372 TYR 0.018 0.001 TYR F 189 ARG 0.002 0.000 ARG A 131 *********************** 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 95 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6724 (m) cc_final: 0.6371 (p) REVERT: F 194 ARG cc_start: 0.7246 (ptt-90) cc_final: 0.6855 (ptt90) REVERT: F 298 ARG cc_start: 0.6590 (ttm-80) cc_final: 0.6235 (ttm170) REVERT: F 327 THR cc_start: 0.8826 (p) cc_final: 0.8451 (t) REVERT: F 355 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7261 (mp10) REVERT: A 67 ASN cc_start: 0.7247 (m-40) cc_final: 0.6766 (m-40) REVERT: E 205 ILE cc_start: 0.7302 (mt) cc_final: 0.7100 (mt) REVERT: E 296 ILE cc_start: 0.6652 (OUTLIER) cc_final: 0.5912 (tp) REVERT: E 353 ASN cc_start: 0.6827 (OUTLIER) cc_final: 0.6158 (t0) REVERT: E 376 ARG cc_start: 0.8439 (ttp80) cc_final: 0.7831 (ttt180) outliers start: 23 outliers final: 20 residues processed: 94 average time/residue: 0.1946 time to fit residues: 24.5647 Evaluate side-chains 89 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 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 270 LEU 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 383 LEU Chi-restraints excluded: chain A residue 34 LEU 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 237 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 327 THR Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain E residue 381 LYS 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 25 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** 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 = 0.4134 r_free = 0.4134 target = 0.182472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.149095 restraints weight = 8778.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.148990 restraints weight = 8229.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.150453 restraints weight = 6965.189| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.5627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6811 Z= 0.292 Angle : 0.725 12.618 9283 Z= 0.356 Chirality : 0.049 0.225 1097 Planarity : 0.006 0.109 1157 Dihedral : 5.947 53.826 1213 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.81 % Favored : 91.44 % Rotamer: Outliers : 4.06 % Allowed : 22.06 % Favored : 73.88 % 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: -0.68 (0.30), residues: 794 helix: -1.38 (0.73), residues: 42 sheet: 0.43 (0.28), residues: 363 loop : -1.19 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 254 HIS 0.007 0.002 HIS F 105 PHE 0.029 0.003 PHE E 372 TYR 0.017 0.002 TYR E 283 ARG 0.005 0.001 ARG E 195 ********************** 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 97 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: F 100 THR cc_start: 0.6689 (m) cc_final: 0.6460 (p) REVERT: F 194 ARG cc_start: 0.7268 (ptt-90) cc_final: 0.6847 (ptt90) REVERT: F 298 ARG cc_start: 0.6509 (ttm-80) cc_final: 0.6306 (ttm170) REVERT: F 355 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7264 (mp10) REVERT: A 52 ASN cc_start: 0.7246 (OUTLIER) cc_final: 0.5902 (p0) REVERT: A 67 ASN cc_start: 0.7385 (m-40) cc_final: 0.6882 (m-40) REVERT: E 288 ASP cc_start: 0.6747 (t0) cc_final: 0.6506 (t70) REVERT: E 296 ILE cc_start: 0.6614 (OUTLIER) cc_final: 0.5846 (tp) REVERT: E 376 ARG cc_start: 0.8464 (ttp80) cc_final: 0.7900 (ttt-90) outliers start: 30 outliers final: 22 residues processed: 94 average time/residue: 0.1905 time to fit residues: 24.1398 Evaluate side-chains 89 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 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 270 LEU 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 383 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 133 VAL 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 327 THR Chi-restraints excluded: chain E residue 381 LYS 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 73 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 14 optimal weight: 0.4980 chunk 70 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 69 optimal weight: 0.1980 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 199 HIS E 218 GLN ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.185310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.152485 restraints weight = 8713.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.152507 restraints weight = 7277.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.153724 restraints weight = 6204.182| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.5666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6811 Z= 0.206 Angle : 0.689 11.429 9283 Z= 0.337 Chirality : 0.047 0.213 1097 Planarity : 0.005 0.104 1157 Dihedral : 5.695 54.388 1213 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.76 % Allowed : 8.06 % Favored : 91.18 % Rotamer: Outliers : 2.98 % Allowed : 23.14 % Favored : 73.88 % 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: -1.24 (0.76), residues: 42 sheet: 0.47 (0.28), residues: 365 loop : -1.06 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP E 254 HIS 0.006 0.001 HIS F 105 PHE 0.031 0.002 PHE E 372 TYR 0.016 0.001 TYR F 189 ARG 0.004 0.000 ARG E 195 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2217.59 seconds wall clock time: 39 minutes 29.33 seconds (2369.33 seconds total)