Starting phenix.real_space_refine on Sat May 10 17:54:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k7s_36940/05_2025/8k7s_36940.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k7s_36940/05_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_36940/05_2025/8k7s_36940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k7s_36940/05_2025/8k7s_36940.map" model { file = "/net/cci-nas-00/data/ceres_data/8k7s_36940/05_2025/8k7s_36940.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k7s_36940/05_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-5687/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: 4.17, per 1000 atoms: 0.63 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: 1.67 Conformation dependent library (CDL) restraints added in 947.7 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: 0.85 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: 1.96 Time building geometry restraints manager: 1.95 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: 0.160 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.850 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.170 ------------------------------------------------------------------------------- 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 6839 Z= 0.093 Angle : 0.535 9.619 9357 Z= 0.269 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 8) link_NAG-ASN : angle 1.02960 ( 24) link_ALPHA1-6 : bond 0.00748 ( 2) link_ALPHA1-6 : angle 1.37275 ( 6) link_BETA1-4 : bond 0.00459 ( 6) link_BETA1-4 : angle 1.33029 ( 18) link_ALPHA1-3 : bond 0.00648 ( 2) link_ALPHA1-3 : angle 1.32711 ( 6) hydrogen bonds : bond 0.11242 ( 222) hydrogen bonds : angle 5.35487 ( 561) SS BOND : bond 0.00261 ( 10) SS BOND : angle 0.82668 ( 20) covalent geometry : bond 0.00212 ( 6811) covalent geometry : angle 0.52790 ( 9283) *********************** 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 : 0.659 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: 0.1943 time to fit residues: 58.0429 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 : 0.737 ------------------------------------------------------------------------------- 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: 0.8980 chunk 20 optimal weight: 0.0000 chunk 39 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 overall best weight: 0.4984 ------------------------------------------------------------------------------- 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 = 0.4329 r_free = 0.4329 target = 0.203997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.176404 restraints weight = 8652.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.175386 restraints weight = 6582.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.176965 restraints weight = 6671.323| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 6839 Z= 0.134 Angle : 0.689 10.781 9357 Z= 0.331 Chirality : 0.047 0.209 1097 Planarity : 0.006 0.123 1157 Dihedral : 5.388 54.458 1215 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.43 % Favored : 92.07 % Rotamer: Outliers : 3.38 % Allowed : 12.18 % 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: 0.00 (0.32), residues: 794 helix: -1.05 (0.79), residues: 42 sheet: 1.06 (0.29), residues: 357 loop : -0.90 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 64 HIS 0.013 0.001 HIS E 289 PHE 0.024 0.002 PHE E 372 TYR 0.013 0.001 TYR E 217 ARG 0.008 0.001 ARG E 307 Details of bonding type rmsd link_NAG-ASN : bond 0.00495 ( 8) link_NAG-ASN : angle 2.63626 ( 24) link_ALPHA1-6 : bond 0.00701 ( 2) link_ALPHA1-6 : angle 1.36313 ( 6) link_BETA1-4 : bond 0.00354 ( 6) link_BETA1-4 : angle 1.48488 ( 18) link_ALPHA1-3 : bond 0.00468 ( 2) link_ALPHA1-3 : angle 1.53350 ( 6) hydrogen bonds : bond 0.02802 ( 222) hydrogen bonds : angle 4.95483 ( 561) SS BOND : bond 0.00287 ( 10) SS BOND : angle 2.43915 ( 20) covalent geometry : bond 0.00323 ( 6811) covalent geometry : angle 0.66377 ( 9283) *********************** 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 155 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6350 (m) cc_final: 0.6082 (p) REVERT: F 194 ARG cc_start: 0.6891 (ptt-90) cc_final: 0.6485 (ptm-80) REVERT: F 292 PHE cc_start: 0.6690 (OUTLIER) cc_final: 0.6453 (t80) REVERT: F 298 ARG cc_start: 0.7090 (ttm-80) cc_final: 0.6471 (ttm170) REVERT: F 327 THR cc_start: 0.8516 (p) cc_final: 0.8191 (t) REVERT: A 52 ASN cc_start: 0.7900 (OUTLIER) cc_final: 0.6378 (p0) REVERT: A 64 TRP cc_start: 0.7252 (m100) cc_final: 0.6367 (m100) REVERT: E 198 ASP cc_start: 0.6146 (p0) cc_final: 0.5806 (p0) REVERT: E 205 ILE cc_start: 0.7705 (mt) cc_final: 0.7313 (mt) REVERT: E 376 ARG cc_start: 0.8450 (ttp80) cc_final: 0.7802 (ttt-90) outliers start: 25 outliers final: 15 residues processed: 149 average time/residue: 0.1727 time to fit residues: 34.7101 Evaluate side-chains 115 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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 248 SER Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain A residue 52 ASN 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 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: 0.7980 chunk 63 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 6 optimal weight: 0.3980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.192128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.158984 restraints weight = 8598.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.161773 restraints weight = 6192.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.163328 restraints weight = 4989.015| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 6839 Z= 0.165 Angle : 0.681 9.375 9357 Z= 0.332 Chirality : 0.047 0.241 1097 Planarity : 0.006 0.116 1157 Dihedral : 5.889 55.397 1215 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.43 % Favored : 92.07 % Rotamer: Outliers : 5.41 % Allowed : 13.13 % Favored : 81.46 % 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: -0.12 (0.31), residues: 794 helix: -1.31 (0.79), residues: 42 sheet: 0.89 (0.29), residues: 366 loop : -0.89 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 254 HIS 0.011 0.002 HIS E 289 PHE 0.042 0.003 PHE F 113 TYR 0.016 0.002 TYR F 189 ARG 0.005 0.001 ARG A 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 8) link_NAG-ASN : angle 2.12293 ( 24) link_ALPHA1-6 : bond 0.00696 ( 2) link_ALPHA1-6 : angle 1.60253 ( 6) link_BETA1-4 : bond 0.00189 ( 6) link_BETA1-4 : angle 1.64637 ( 18) link_ALPHA1-3 : bond 0.00460 ( 2) link_ALPHA1-3 : angle 1.50586 ( 6) hydrogen bonds : bond 0.03019 ( 222) hydrogen bonds : angle 5.21749 ( 561) SS BOND : bond 0.00300 ( 10) SS BOND : angle 1.38428 ( 20) covalent geometry : bond 0.00401 ( 6811) covalent geometry : angle 0.66607 ( 9283) *********************** 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 141 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 101 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6361 (m) cc_final: 0.6106 (p) REVERT: F 194 ARG cc_start: 0.6974 (ptt-90) cc_final: 0.6589 (ptm-80) REVERT: F 292 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.6878 (t80) REVERT: F 298 ARG cc_start: 0.6827 (ttm-80) cc_final: 0.6354 (ttm170) REVERT: F 327 THR cc_start: 0.8804 (p) cc_final: 0.8409 (t) REVERT: F 409 ILE cc_start: 0.6644 (tp) cc_final: 0.6410 (pt) REVERT: A 50 THR cc_start: 0.7929 (m) cc_final: 0.7660 (m) REVERT: A 52 ASN cc_start: 0.7768 (OUTLIER) cc_final: 0.6213 (p0) REVERT: A 63 LYS cc_start: 0.7421 (pttt) cc_final: 0.7123 (pttm) REVERT: A 115 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6933 (pt) REVERT: E 205 ILE cc_start: 0.7755 (mt) cc_final: 0.7408 (mt) REVERT: E 376 ARG cc_start: 0.8544 (ttp80) cc_final: 0.7803 (ttt-90) outliers start: 40 outliers final: 25 residues processed: 134 average time/residue: 0.1768 time to fit residues: 31.5607 Evaluate side-chains 118 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 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 34 LEU Chi-restraints excluded: chain A residue 52 ASN 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 217 TYR Chi-restraints excluded: chain E residue 270 LEU 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: 0.5980 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 53 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 116 GLN ** E 199 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 = 0.4175 r_free = 0.4175 target = 0.187117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.156013 restraints weight = 8704.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.155481 restraints weight = 6385.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.156422 restraints weight = 5702.634| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 6839 Z= 0.186 Angle : 0.710 9.355 9357 Z= 0.344 Chirality : 0.047 0.248 1097 Planarity : 0.006 0.120 1157 Dihedral : 5.799 53.533 1214 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.81 % Favored : 91.81 % Rotamer: Outliers : 5.28 % Allowed : 16.10 % Favored : 78.62 % 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: -0.29 (0.31), residues: 794 helix: -1.43 (0.74), residues: 41 sheet: 0.72 (0.28), residues: 369 loop : -0.96 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 254 HIS 0.010 0.002 HIS E 289 PHE 0.033 0.003 PHE F 113 TYR 0.014 0.002 TYR E 283 ARG 0.005 0.001 ARG E 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 8) link_NAG-ASN : angle 1.94070 ( 24) link_ALPHA1-6 : bond 0.00585 ( 2) link_ALPHA1-6 : angle 1.58057 ( 6) link_BETA1-4 : bond 0.00234 ( 6) link_BETA1-4 : angle 1.85856 ( 18) link_ALPHA1-3 : bond 0.00304 ( 2) link_ALPHA1-3 : angle 1.54126 ( 6) hydrogen bonds : bond 0.03048 ( 222) hydrogen bonds : angle 5.24317 ( 561) SS BOND : bond 0.00497 ( 10) SS BOND : angle 2.26898 ( 20) covalent geometry : bond 0.00451 ( 6811) covalent geometry : angle 0.69102 ( 9283) *********************** 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 133 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 94 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6373 (m) cc_final: 0.6087 (p) REVERT: F 194 ARG cc_start: 0.7277 (ptt-90) cc_final: 0.6969 (ptt90) REVERT: F 277 TRP cc_start: 0.7084 (t-100) cc_final: 0.6786 (t-100) REVERT: F 298 ARG cc_start: 0.6563 (ttm-80) cc_final: 0.6219 (ttm170) REVERT: F 327 THR cc_start: 0.8785 (p) cc_final: 0.8393 (t) REVERT: F 355 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7309 (mp10) REVERT: A 52 ASN cc_start: 0.7786 (m110) cc_final: 0.6127 (p0) REVERT: A 63 LYS cc_start: 0.7674 (pttt) cc_final: 0.7263 (pttm) REVERT: A 115 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6827 (pt) REVERT: E 205 ILE cc_start: 0.7868 (mt) cc_final: 0.7584 (mt) REVERT: E 296 ILE cc_start: 0.5830 (OUTLIER) cc_final: 0.5152 (tp) REVERT: E 307 ARG cc_start: 0.8623 (mtt90) cc_final: 0.8276 (mtt90) REVERT: E 376 ARG cc_start: 0.8510 (ttp80) cc_final: 0.7781 (ttt-90) outliers start: 39 outliers final: 26 residues processed: 126 average time/residue: 0.1670 time to fit residues: 28.7039 Evaluate side-chains 110 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 249 VAL Chi-restraints excluded: chain F residue 273 VAL 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 34 LEU Chi-restraints excluded: chain A residue 104 VAL 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 0.2980 chunk 71 optimal weight: 0.0870 chunk 3 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.4162 ------------------------------------------------------------------------------- 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 242 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.185392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.152764 restraints weight = 8815.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.151559 restraints weight = 6890.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.153082 restraints weight = 6360.344| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 6839 Z= 0.207 Angle : 0.744 9.929 9357 Z= 0.360 Chirality : 0.049 0.294 1097 Planarity : 0.006 0.115 1157 Dihedral : 6.144 53.546 1214 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.31 % Favored : 91.18 % Rotamer: Outliers : 5.14 % Allowed : 17.86 % Favored : 77.00 % 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: -1.99 (0.66), residues: 48 sheet: 0.62 (0.28), residues: 368 loop : -1.09 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 254 HIS 0.009 0.002 HIS E 289 PHE 0.032 0.003 PHE E 372 TYR 0.018 0.002 TYR E 283 ARG 0.007 0.001 ARG E 195 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 8) link_NAG-ASN : angle 1.97738 ( 24) link_ALPHA1-6 : bond 0.00974 ( 2) link_ALPHA1-6 : angle 1.72840 ( 6) link_BETA1-4 : bond 0.00116 ( 6) link_BETA1-4 : angle 2.00565 ( 18) link_ALPHA1-3 : bond 0.00261 ( 2) link_ALPHA1-3 : angle 1.46368 ( 6) hydrogen bonds : bond 0.03201 ( 222) hydrogen bonds : angle 5.44104 ( 561) SS BOND : bond 0.00385 ( 10) SS BOND : angle 1.78130 ( 20) covalent geometry : bond 0.00499 ( 6811) covalent geometry : angle 0.72806 ( 9283) *********************** 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 126 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 88 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6449 (m) cc_final: 0.6168 (p) REVERT: F 298 ARG cc_start: 0.6765 (ttm-80) cc_final: 0.6526 (ttm170) REVERT: F 355 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7312 (mp10) REVERT: A 52 ASN cc_start: 0.7669 (m110) cc_final: 0.6247 (p0) REVERT: A 63 LYS cc_start: 0.7517 (pttt) cc_final: 0.7086 (pttm) REVERT: A 67 ASN cc_start: 0.7001 (m-40) cc_final: 0.6532 (m-40) REVERT: E 137 MET cc_start: 0.5222 (ttp) cc_final: 0.4919 (ttp) REVERT: E 205 ILE cc_start: 0.7806 (mt) cc_final: 0.7460 (mt) REVERT: E 296 ILE cc_start: 0.6311 (OUTLIER) cc_final: 0.5524 (tp) REVERT: E 376 ARG cc_start: 0.8481 (ttp80) cc_final: 0.7866 (ttt-90) outliers start: 38 outliers final: 27 residues processed: 121 average time/residue: 0.1649 time to fit residues: 27.2505 Evaluate side-chains 108 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 79 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 266 ILE Chi-restraints excluded: chain F residue 273 VAL 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 369 GLN 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 106 LEU 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 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: 0.6980 chunk 21 optimal weight: 0.0040 chunk 54 optimal weight: 7.9990 chunk 75 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS E 242 ASN E 284 GLN E 353 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.187883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.156498 restraints weight = 8601.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.154833 restraints weight = 6931.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.156181 restraints weight = 6243.420| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 6839 Z= 0.129 Angle : 0.656 9.367 9357 Z= 0.317 Chirality : 0.046 0.199 1097 Planarity : 0.005 0.116 1157 Dihedral : 5.734 54.074 1213 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.56 % Favored : 91.94 % Rotamer: Outliers : 4.19 % Allowed : 19.35 % Favored : 76.45 % 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 (0.30), residues: 794 helix: -1.87 (0.67), residues: 48 sheet: 0.63 (0.28), residues: 369 loop : -0.97 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 254 HIS 0.008 0.001 HIS E 289 PHE 0.032 0.002 PHE E 372 TYR 0.013 0.001 TYR E 283 ARG 0.002 0.000 ARG A 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 8) link_NAG-ASN : angle 1.68754 ( 24) link_ALPHA1-6 : bond 0.00748 ( 2) link_ALPHA1-6 : angle 1.51817 ( 6) link_BETA1-4 : bond 0.00313 ( 6) link_BETA1-4 : angle 1.76459 ( 18) link_ALPHA1-3 : bond 0.00512 ( 2) link_ALPHA1-3 : angle 1.32023 ( 6) hydrogen bonds : bond 0.02765 ( 222) hydrogen bonds : angle 5.20839 ( 561) SS BOND : bond 0.00298 ( 10) SS BOND : angle 1.22455 ( 20) covalent geometry : bond 0.00311 ( 6811) covalent geometry : angle 0.64415 ( 9283) *********************** 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 127 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6446 (m) cc_final: 0.6175 (p) REVERT: F 194 ARG cc_start: 0.7254 (ptt-90) cc_final: 0.6850 (ptt90) REVERT: F 298 ARG cc_start: 0.6662 (ttm-80) cc_final: 0.6293 (ttm170) REVERT: F 321 GLU cc_start: 0.5482 (OUTLIER) cc_final: 0.4760 (pm20) REVERT: F 327 THR cc_start: 0.8797 (p) cc_final: 0.8393 (t) REVERT: F 355 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7284 (mp10) REVERT: A 63 LYS cc_start: 0.7419 (pttt) cc_final: 0.7023 (pttm) REVERT: A 67 ASN cc_start: 0.7108 (m-40) cc_final: 0.6717 (m-40) REVERT: E 205 ILE cc_start: 0.7825 (mt) cc_final: 0.7527 (mt) REVERT: E 296 ILE cc_start: 0.6501 (OUTLIER) cc_final: 0.5837 (tp) REVERT: E 307 ARG cc_start: 0.8461 (mtt90) cc_final: 0.8039 (mtt90) REVERT: E 353 ASN cc_start: 0.6842 (OUTLIER) cc_final: 0.6232 (t0) REVERT: E 376 ARG cc_start: 0.8461 (ttp80) cc_final: 0.7862 (ttt-90) outliers start: 31 outliers final: 22 residues processed: 122 average time/residue: 0.1916 time to fit residues: 30.8269 Evaluate side-chains 104 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 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 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 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 A residue 34 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 6 optimal weight: 8.9990 chunk 71 optimal weight: 0.2980 chunk 38 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.183818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.150728 restraints weight = 8728.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.150176 restraints weight = 6904.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.151386 restraints weight = 6399.758| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 6839 Z= 0.225 Angle : 0.751 11.782 9357 Z= 0.364 Chirality : 0.049 0.270 1097 Planarity : 0.006 0.120 1157 Dihedral : 6.119 53.589 1213 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.82 % Favored : 90.55 % Rotamer: Outliers : 5.01 % Allowed : 19.49 % Favored : 75.51 % 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: -0.63 (0.30), residues: 794 helix: -1.28 (0.71), residues: 42 sheet: 0.52 (0.28), residues: 358 loop : -1.23 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 254 HIS 0.021 0.002 HIS A 95 PHE 0.035 0.003 PHE A 56 TYR 0.018 0.002 TYR E 283 ARG 0.005 0.001 ARG E 195 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 8) link_NAG-ASN : angle 1.95520 ( 24) link_ALPHA1-6 : bond 0.00411 ( 2) link_ALPHA1-6 : angle 1.64110 ( 6) link_BETA1-4 : bond 0.00169 ( 6) link_BETA1-4 : angle 2.02628 ( 18) link_ALPHA1-3 : bond 0.00241 ( 2) link_ALPHA1-3 : angle 1.54877 ( 6) hydrogen bonds : bond 0.03272 ( 222) hydrogen bonds : angle 5.48871 ( 561) SS BOND : bond 0.00312 ( 10) SS BOND : angle 1.93348 ( 20) covalent geometry : bond 0.00545 ( 6811) covalent geometry : angle 0.73480 ( 9283) *********************** 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 113 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 76 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6555 (m) cc_final: 0.6342 (p) REVERT: F 194 ARG cc_start: 0.7303 (ptt-90) cc_final: 0.6853 (ptt90) REVERT: F 298 ARG cc_start: 0.6719 (ttm-80) cc_final: 0.6499 (ttm170) REVERT: F 321 GLU cc_start: 0.5428 (OUTLIER) cc_final: 0.4661 (pm20) REVERT: F 355 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7278 (mp10) REVERT: A 63 LYS cc_start: 0.7402 (pttt) cc_final: 0.7044 (pttm) REVERT: A 67 ASN cc_start: 0.7016 (m-40) cc_final: 0.6548 (m-40) REVERT: A 94 GLN cc_start: 0.4850 (tt0) cc_final: 0.4367 (tt0) REVERT: E 205 ILE cc_start: 0.7837 (mt) cc_final: 0.7268 (mt) REVERT: E 296 ILE cc_start: 0.6388 (OUTLIER) cc_final: 0.5651 (tp) REVERT: E 376 ARG cc_start: 0.8488 (ttp80) cc_final: 0.7909 (ttt-90) outliers start: 37 outliers final: 26 residues processed: 110 average time/residue: 0.1678 time to fit residues: 25.3040 Evaluate side-chains 99 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 273 VAL Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 321 GLU 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 369 GLN Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain A residue 34 LEU 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 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 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: 0.3980 chunk 52 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 58 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 289 HIS 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 = 0.185122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.151980 restraints weight = 8669.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.151908 restraints weight = 6813.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.153440 restraints weight = 5941.256| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6839 Z= 0.139 Angle : 0.696 10.416 9357 Z= 0.334 Chirality : 0.047 0.226 1097 Planarity : 0.006 0.117 1157 Dihedral : 5.903 54.105 1213 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.81 % Favored : 91.56 % Rotamer: Outliers : 4.06 % Allowed : 20.97 % 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: -1.25 (0.72), residues: 42 sheet: 0.50 (0.28), residues: 358 loop : -1.12 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 254 HIS 0.009 0.001 HIS A 95 PHE 0.034 0.002 PHE E 372 TYR 0.014 0.001 TYR E 283 ARG 0.003 0.001 ARG E 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 8) link_NAG-ASN : angle 1.74852 ( 24) link_ALPHA1-6 : bond 0.00651 ( 2) link_ALPHA1-6 : angle 1.53559 ( 6) link_BETA1-4 : bond 0.00284 ( 6) link_BETA1-4 : angle 1.81382 ( 18) link_ALPHA1-3 : bond 0.00456 ( 2) link_ALPHA1-3 : angle 1.34887 ( 6) hydrogen bonds : bond 0.02850 ( 222) hydrogen bonds : angle 5.32533 ( 561) SS BOND : bond 0.00304 ( 10) SS BOND : angle 1.34332 ( 20) covalent geometry : bond 0.00335 ( 6811) covalent geometry : angle 0.68331 ( 9283) *********************** 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 105 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6327 (m) cc_final: 0.6101 (p) REVERT: F 194 ARG cc_start: 0.7386 (ptt-90) cc_final: 0.6878 (ptt90) REVERT: F 298 ARG cc_start: 0.6747 (ttm-80) cc_final: 0.6385 (ttm170) REVERT: F 321 GLU cc_start: 0.5507 (OUTLIER) cc_final: 0.4765 (pm20) REVERT: F 327 THR cc_start: 0.8833 (p) cc_final: 0.8437 (t) REVERT: F 355 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.7293 (mp10) REVERT: A 32 VAL cc_start: 0.7517 (OUTLIER) cc_final: 0.7147 (m) REVERT: A 63 LYS cc_start: 0.7282 (pttt) cc_final: 0.6968 (pttm) REVERT: A 67 ASN cc_start: 0.7270 (m-40) cc_final: 0.6820 (m-40) REVERT: E 296 ILE cc_start: 0.6598 (OUTLIER) cc_final: 0.5834 (tp) REVERT: E 376 ARG cc_start: 0.8459 (ttp80) cc_final: 0.7838 (ttt-90) outliers start: 30 outliers final: 19 residues processed: 103 average time/residue: 0.1937 time to fit residues: 26.3232 Evaluate side-chains 92 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 A residue 32 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 104 VAL 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 273 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: 2.9990 chunk 65 optimal weight: 0.9980 chunk 48 optimal weight: 20.0000 chunk 68 optimal weight: 0.0470 chunk 6 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 69 optimal weight: 0.0980 chunk 71 optimal weight: 0.9990 overall best weight: 0.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 199 HIS A 95 HIS E 289 HIS E 353 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.185797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.152251 restraints weight = 8724.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.152820 restraints weight = 6658.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.153547 restraints weight = 5745.126| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6839 Z= 0.147 Angle : 0.691 12.489 9357 Z= 0.334 Chirality : 0.047 0.217 1097 Planarity : 0.005 0.113 1157 Dihedral : 5.833 54.231 1213 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.76 % Allowed : 8.06 % Favored : 91.18 % Rotamer: Outliers : 4.06 % Allowed : 20.97 % 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: -0.55 (0.30), residues: 794 helix: -1.19 (0.73), residues: 42 sheet: 0.58 (0.28), residues: 354 loop : -1.17 (0.31), residues: 398 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 0.015 0.002 TYR E 283 ARG 0.003 0.000 ARG A 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 8) link_NAG-ASN : angle 1.70582 ( 24) link_ALPHA1-6 : bond 0.00595 ( 2) link_ALPHA1-6 : angle 1.57815 ( 6) link_BETA1-4 : bond 0.00298 ( 6) link_BETA1-4 : angle 1.90427 ( 18) link_ALPHA1-3 : bond 0.00381 ( 2) link_ALPHA1-3 : angle 1.39137 ( 6) hydrogen bonds : bond 0.02897 ( 222) hydrogen bonds : angle 5.34666 ( 561) SS BOND : bond 0.00278 ( 10) SS BOND : angle 1.14920 ( 20) covalent geometry : bond 0.00362 ( 6811) covalent geometry : angle 0.67883 ( 9283) *********************** 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 106 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6622 (m) cc_final: 0.6385 (p) REVERT: F 194 ARG cc_start: 0.7467 (ptt-90) cc_final: 0.6884 (ptt90) REVERT: F 298 ARG cc_start: 0.6761 (ttm-80) cc_final: 0.6400 (ttm170) REVERT: F 321 GLU cc_start: 0.5564 (OUTLIER) cc_final: 0.4846 (pm20) REVERT: F 355 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7407 (mp10) REVERT: A 32 VAL cc_start: 0.7616 (OUTLIER) cc_final: 0.7217 (m) REVERT: A 63 LYS cc_start: 0.7342 (pttt) cc_final: 0.7045 (pttm) REVERT: A 67 ASN cc_start: 0.7294 (m-40) cc_final: 0.6832 (m-40) REVERT: E 198 ASP cc_start: 0.6967 (p0) cc_final: 0.6741 (p0) REVERT: E 202 ARG cc_start: 0.6953 (mmm160) cc_final: 0.6057 (mmm160) REVERT: E 288 ASP cc_start: 0.6811 (t0) cc_final: 0.6569 (t70) REVERT: E 296 ILE cc_start: 0.6484 (OUTLIER) cc_final: 0.5760 (tp) REVERT: E 376 ARG cc_start: 0.8455 (ttp80) cc_final: 0.7839 (ttt-90) outliers start: 30 outliers final: 23 residues processed: 105 average time/residue: 0.1894 time to fit residues: 26.3772 Evaluate side-chains 97 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 292 PHE Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 355 GLN Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 34 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 273 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 332 ILE 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: 2.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 67 optimal weight: 0.0060 chunk 59 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 199 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 = 0.185790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.153321 restraints weight = 8865.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.152481 restraints weight = 6666.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.153656 restraints weight = 6030.063| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.5493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 6839 Z= 0.143 Angle : 0.690 12.264 9357 Z= 0.333 Chirality : 0.047 0.202 1097 Planarity : 0.005 0.111 1157 Dihedral : 5.746 54.244 1213 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.76 % Allowed : 8.31 % Favored : 90.93 % Rotamer: Outliers : 3.65 % Allowed : 21.65 % 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: -0.52 (0.30), residues: 794 helix: -1.18 (0.74), residues: 42 sheet: 0.57 (0.28), residues: 356 loop : -1.11 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 254 HIS 0.006 0.001 HIS F 105 PHE 0.034 0.002 PHE E 372 TYR 0.015 0.001 TYR E 283 ARG 0.003 0.000 ARG A 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 8) link_NAG-ASN : angle 1.68574 ( 24) link_ALPHA1-6 : bond 0.00605 ( 2) link_ALPHA1-6 : angle 1.56534 ( 6) link_BETA1-4 : bond 0.00287 ( 6) link_BETA1-4 : angle 1.85973 ( 18) link_ALPHA1-3 : bond 0.00404 ( 2) link_ALPHA1-3 : angle 1.36796 ( 6) hydrogen bonds : bond 0.02871 ( 222) hydrogen bonds : angle 5.29192 ( 561) SS BOND : bond 0.00315 ( 10) SS BOND : angle 1.09832 ( 20) covalent geometry : bond 0.00351 ( 6811) covalent geometry : angle 0.67816 ( 9283) ********************** 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 100 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6626 (m) cc_final: 0.6323 (p) REVERT: F 194 ARG cc_start: 0.7584 (ptt-90) cc_final: 0.7065 (ptt90) REVERT: F 298 ARG cc_start: 0.6587 (ttm-80) cc_final: 0.6223 (ttm170) REVERT: F 321 GLU cc_start: 0.5550 (OUTLIER) cc_final: 0.4826 (pm20) REVERT: F 355 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7415 (mp10) REVERT: A 32 VAL cc_start: 0.7605 (OUTLIER) cc_final: 0.7211 (m) REVERT: A 63 LYS cc_start: 0.7391 (pttt) cc_final: 0.7090 (pttm) REVERT: A 67 ASN cc_start: 0.7344 (m-40) cc_final: 0.6892 (m-40) REVERT: E 198 ASP cc_start: 0.6967 (p0) cc_final: 0.6639 (p0) REVERT: E 202 ARG cc_start: 0.6971 (mmm160) cc_final: 0.6085 (mmm160) REVERT: E 296 ILE cc_start: 0.6468 (OUTLIER) cc_final: 0.5771 (tp) REVERT: E 376 ARG cc_start: 0.8462 (ttp80) cc_final: 0.7847 (ttt-90) outliers start: 27 outliers final: 22 residues processed: 97 average time/residue: 0.1986 time to fit residues: 25.1836 Evaluate side-chains 95 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 292 PHE Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 355 GLN Chi-restraints excluded: chain F residue 378 GLU 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 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 273 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: 1.9990 chunk 34 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 199 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 = 0.4157 r_free = 0.4157 target = 0.184853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.151651 restraints weight = 8774.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.150973 restraints weight = 7347.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.152509 restraints weight = 6717.416| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6839 Z= 0.136 Angle : 0.698 12.036 9357 Z= 0.336 Chirality : 0.047 0.206 1097 Planarity : 0.005 0.112 1157 Dihedral : 5.754 54.451 1213 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.56 % Favored : 90.81 % Rotamer: Outliers : 3.65 % Allowed : 22.06 % Favored : 74.29 % 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: -0.51 (0.30), residues: 794 helix: -1.12 (0.76), residues: 42 sheet: 0.52 (0.27), residues: 366 loop : -1.10 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 254 HIS 0.006 0.001 HIS F 105 PHE 0.033 0.002 PHE E 372 TYR 0.023 0.001 TYR F 189 ARG 0.004 0.000 ARG E 195 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 8) link_NAG-ASN : angle 1.75914 ( 24) link_ALPHA1-6 : bond 0.00596 ( 2) link_ALPHA1-6 : angle 1.55090 ( 6) link_BETA1-4 : bond 0.00315 ( 6) link_BETA1-4 : angle 1.83059 ( 18) link_ALPHA1-3 : bond 0.00426 ( 2) link_ALPHA1-3 : angle 1.36256 ( 6) hydrogen bonds : bond 0.02803 ( 222) hydrogen bonds : angle 5.27160 ( 561) SS BOND : bond 0.00205 ( 10) SS BOND : angle 1.74796 ( 20) covalent geometry : bond 0.00332 ( 6811) covalent geometry : angle 0.68326 ( 9283) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2266.39 seconds wall clock time: 40 minutes 32.19 seconds (2432.19 seconds total)