Starting phenix.real_space_refine on Sun Apr 27 23:33:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k7s_36940/04_2025/8k7s_36940.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k7s_36940/04_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_36940/04_2025/8k7s_36940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k7s_36940/04_2025/8k7s_36940.map" model { file = "/net/cci-nas-00/data/ceres_data/8k7s_36940/04_2025/8k7s_36940.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k7s_36940/04_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-5669/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: 6.51, per 1000 atoms: 0.98 Number of scatterers: 6645 At special positions: 0 Unit cell: (78.02, 101.26, 126.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 1333 8.00 N 1083 7.00 C 4202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS F 108 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 121 " - pdb=" SG CYS F 180 " distance=2.03 Simple disulfide: pdb=" SG CYS F 196 " - pdb=" SG CYS E 108 " distance=2.03 Simple disulfide: pdb=" SG CYS F 226 " - pdb=" SG CYS F 285 " distance=2.03 Simple disulfide: pdb=" SG CYS F 330 " - pdb=" SG CYS F 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 93 " distance=2.03 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 176 " distance=2.03 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 180 " distance=2.03 Simple disulfide: pdb=" SG CYS E 226 " - pdb=" SG CYS E 285 " distance=2.03 Simple disulfide: pdb=" SG CYS E 330 " - pdb=" SG CYS E 392 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA x 3 " - " MAN x 4 " " BMA z 3 " - " MAN z 4 " ALPHA1-6 " BMA x 3 " - " MAN x 5 " " BMA z 3 " - " MAN z 5 " BETA1-4 " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " NAG-ASN " NAG A 301 " - " ASN A 160 " " NAG A 302 " - " ASN A 46 " " NAG A 303 " - " ASN A 191 " " NAG E 501 " - " ASN E 238 " " NAG F 501 " - " ASN F 238 " " NAG x 1 " - " ASN F 261 " " NAG y 1 " - " ASN A 67 " " NAG z 1 " - " ASN E 261 " Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 1.7 seconds 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1532 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 17 sheets defined 7.5% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'F' and resid 168 through 173 Processing helix chain 'F' and resid 212 through 218 Processing helix chain 'F' and resid 273 through 280 removed outlier: 3.733A pdb=" N TRP F 277 " --> pdb=" O VAL F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 386 removed outlier: 3.542A pdb=" N GLN F 386 " --> pdb=" O THR F 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'E' and resid 169 through 173 Processing helix chain 'E' and resid 273 through 279 Processing helix chain 'E' and resid 352 through 356 Processing sheet with id=AA1, first strand: chain 'F' and resid 150 through 154 removed outlier: 6.746A pdb=" N SER F 160 " --> pdb=" O ILE F 152 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER F 163 " --> pdb=" O CYS F 121 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLN F 118 " --> pdb=" O SER F 106 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER F 106 " --> pdb=" O GLN F 118 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR F 124 " --> pdb=" O THR F 100 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N HIS F 105 " --> pdb=" O HIS E 105 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N HIS E 105 " --> pdb=" O HIS F 105 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N CYS E 162 " --> pdb=" O LEU E 151 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU E 151 " --> pdb=" O CYS E 162 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LYS E 164 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N THR E 149 " --> pdb=" O LYS E 164 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ASN E 166 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ALA E 147 " --> pdb=" O ASN E 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 132 through 136 Processing sheet with id=AA3, first strand: chain 'F' and resid 205 through 209 removed outlier: 3.976A pdb=" N ASP F 230 " --> pdb=" O THR F 264 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR F 264 " --> pdb=" O ASP F 230 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 238 through 242 Processing sheet with id=AA5, first strand: chain 'F' and resid 311 through 315 removed outlier: 3.837A pdb=" N THR F 329 " --> pdb=" O PHE F 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 349 through 350 Processing sheet with id=AA7, first strand: chain 'A' and resid 31 through 34 Processing sheet with id=AA8, first strand: chain 'A' and resid 69 through 70 Processing sheet with id=AA9, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AB1, first strand: chain 'A' and resid 121 through 122 removed outlier: 3.657A pdb=" N VAL A 122 " --> pdb=" O THR A 193 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 150 through 157 removed outlier: 6.617A pdb=" N TYR A 145 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR A 154 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL A 143 " --> pdb=" O TYR A 154 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TYR A 156 " --> pdb=" O TYR A 141 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TYR A 141 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL A 143 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR A 177 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TYR A 145 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR A 175 " --> pdb=" O TYR A 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 133 through 137 Processing sheet with id=AB4, first strand: chain 'E' and resid 205 through 209 removed outlier: 3.626A pdb=" N THR E 225 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP E 230 " --> pdb=" O THR E 264 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N THR E 264 " --> pdb=" O ASP E 230 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 238 through 244 removed outlier: 4.132A pdb=" N GLY E 282 " --> pdb=" O GLU E 244 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 311 through 315 removed outlier: 4.005A pdb=" N THR E 329 " --> pdb=" O PHE E 315 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N PHE E 371 " --> pdb=" O ASN E 334 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 311 through 315 removed outlier: 4.005A pdb=" N THR E 329 " --> pdb=" O PHE E 315 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N PHE E 371 " --> pdb=" O ASN E 334 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU E 362 " --> pdb=" O PHE E 372 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 340 through 344 236 hydrogen bonds defined for protein. 561 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.12 Time building geometry restraints manager: 2.55 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: 11.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 25.420 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:4.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.330 ------------------------------------------------------------------------------- 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 : 1.264 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: 0.3202 time to fit residues: 95.9586 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 : 1.091 ------------------------------------------------------------------------------- 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 = 0.176401 restraints weight = 8652.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.175388 restraints weight = 6583.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.176971 restraints weight = 6668.045| |-----------------------------------------------------------------------------| 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 0.00496 ( 8) link_NAG-ASN : angle 2.63624 ( 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 1.48490 ( 18) link_ALPHA1-3 : bond 0.00468 ( 2) link_ALPHA1-3 : angle 1.53352 ( 6) hydrogen bonds : bond 0.02802 ( 222) hydrogen bonds : angle 4.95483 ( 561) SS BOND : bond 0.00287 ( 10) SS BOND : angle 2.43914 ( 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 : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6351 (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: 0.6689 (OUTLIER) cc_final: 0.6452 (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: 0.7253 (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: 0.7704 (mt) cc_final: 0.7312 (mt) REVERT: E 376 ARG cc_start: 0.8451 (ttp80) cc_final: 0.7804 (ttt-90) outliers start: 25 outliers final: 15 residues processed: 149 average time/residue: 0.2347 time to fit residues: 48.5649 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 : 1.242 ------------------------------------------------------------------------------- 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: 0.1980 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: 0.3980 chunk 2 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 HIS E 289 HIS E 353 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.186831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.155274 restraints weight = 8573.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.153895 restraints weight = 6788.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.155117 restraints weight = 6284.116| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.132 6839 Z= 0.228 Angle : 0.762 9.211 9357 Z= 0.373 Chirality : 0.049 0.298 1097 Planarity : 0.006 0.110 1157 Dihedral : 6.374 53.401 1215 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.44 % Favored : 91.06 % Rotamer: Outliers : 5.95 % Allowed : 13.40 % Favored : 80.65 % 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: -0.26 (0.31), residues: 794 helix: -1.46 (0.76), residues: 42 sheet: 0.84 (0.28), residues: 364 loop : -1.04 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 254 HIS 0.012 0.002 HIS E 289 PHE 0.040 0.004 PHE F 113 TYR 0.021 0.003 TYR F 313 ARG 0.007 0.001 ARG A 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 8) link_NAG-ASN : angle 2.51849 ( 24) link_ALPHA1-6 : bond 0.00480 ( 2) link_ALPHA1-6 : angle 1.74728 ( 6) link_BETA1-4 : bond 0.00171 ( 6) link_BETA1-4 : angle 1.90995 ( 18) link_ALPHA1-3 : bond 0.00323 ( 2) link_ALPHA1-3 : angle 1.67957 ( 6) hydrogen bonds : bond 0.03420 ( 222) hydrogen bonds : angle 5.51071 ( 561) SS BOND : bond 0.00573 ( 10) SS BOND : angle 1.72329 ( 20) covalent geometry : bond 0.00553 ( 6811) covalent geometry : angle 0.74306 ( 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 142 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 98 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6489 (m) cc_final: 0.6219 (p) REVERT: F 298 ARG cc_start: 0.6892 (ttm-80) cc_final: 0.6471 (ttm170) REVERT: F 365 ASN cc_start: 0.7010 (m-40) cc_final: 0.6538 (t0) REVERT: A 50 THR cc_start: 0.8074 (m) cc_final: 0.7779 (m) REVERT: A 52 ASN cc_start: 0.7816 (OUTLIER) cc_final: 0.6189 (p0) REVERT: A 63 LYS cc_start: 0.7626 (pttt) cc_final: 0.7280 (pttm) REVERT: A 115 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6920 (pt) REVERT: E 205 ILE cc_start: 0.7755 (mt) cc_final: 0.7395 (mt) REVERT: E 327 THR cc_start: 0.7295 (OUTLIER) cc_final: 0.7064 (t) REVERT: E 376 ARG cc_start: 0.8571 (ttp80) cc_final: 0.7823 (ttt-90) outliers start: 44 outliers final: 30 residues processed: 136 average time/residue: 0.2607 time to fit residues: 50.3550 Evaluate side-chains 118 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 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 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 382 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 327 THR Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain E residue 385 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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** E 218 GLN E 284 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.188834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.156984 restraints weight = 8778.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.156212 restraints weight = 6640.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.157045 restraints weight = 6171.582| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 6839 Z= 0.160 Angle : 0.695 11.517 9357 Z= 0.337 Chirality : 0.047 0.236 1097 Planarity : 0.006 0.119 1157 Dihedral : 5.896 53.483 1214 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.19 % Favored : 91.31 % Rotamer: Outliers : 5.14 % Allowed : 16.24 % 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: -0.32 (0.31), residues: 794 helix: -1.46 (0.74), residues: 41 sheet: 0.74 (0.28), residues: 368 loop : -1.04 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 254 HIS 0.009 0.002 HIS E 289 PHE 0.042 0.003 PHE F 113 TYR 0.013 0.002 TYR E 283 ARG 0.002 0.000 ARG A 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 8) link_NAG-ASN : angle 1.99255 ( 24) link_ALPHA1-6 : bond 0.00662 ( 2) link_ALPHA1-6 : angle 1.57248 ( 6) link_BETA1-4 : bond 0.00261 ( 6) link_BETA1-4 : angle 1.84977 ( 18) link_ALPHA1-3 : bond 0.00516 ( 2) link_ALPHA1-3 : angle 1.48419 ( 6) hydrogen bonds : bond 0.02943 ( 222) hydrogen bonds : angle 5.30933 ( 561) SS BOND : bond 0.00214 ( 10) SS BOND : angle 1.68565 ( 20) covalent geometry : bond 0.00390 ( 6811) covalent geometry : angle 0.67907 ( 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 127 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 89 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6334 (m) cc_final: 0.6037 (p) REVERT: F 298 ARG cc_start: 0.6572 (ttm-80) cc_final: 0.6177 (ttm170) REVERT: F 321 GLU cc_start: 0.5933 (OUTLIER) cc_final: 0.5310 (pm20) REVERT: F 327 THR cc_start: 0.8779 (p) cc_final: 0.8398 (t) REVERT: F 355 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7299 (mp10) REVERT: A 63 LYS cc_start: 0.7810 (pttt) cc_final: 0.7379 (pttm) REVERT: E 205 ILE cc_start: 0.7869 (mt) cc_final: 0.7579 (mt) REVERT: E 296 ILE cc_start: 0.6020 (OUTLIER) cc_final: 0.5415 (tp) REVERT: E 331 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8045 (tt) REVERT: E 376 ARG cc_start: 0.8506 (ttp80) cc_final: 0.7789 (ttt-90) outliers start: 38 outliers final: 22 residues processed: 123 average time/residue: 0.2074 time to fit residues: 34.6073 Evaluate side-chains 101 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 273 VAL 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 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 287 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain E residue 385 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 96 GLN ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 HIS ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.188331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.155811 restraints weight = 8790.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.155077 restraints weight = 6963.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.156119 restraints weight = 6329.399| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 6839 Z= 0.156 Angle : 0.696 11.025 9357 Z= 0.336 Chirality : 0.047 0.243 1097 Planarity : 0.006 0.118 1157 Dihedral : 5.767 53.793 1213 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.93 % Favored : 91.56 % Rotamer: Outliers : 5.01 % Allowed : 18.54 % 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: -0.40 (0.31), residues: 794 helix: -1.32 (0.74), residues: 41 sheet: 0.68 (0.28), residues: 377 loop : -1.14 (0.32), residues: 376 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 0.031 0.003 PHE F 113 TYR 0.019 0.002 TYR F 255 ARG 0.003 0.000 ARG E 195 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 8) link_NAG-ASN : angle 1.80182 ( 24) link_ALPHA1-6 : bond 0.00622 ( 2) link_ALPHA1-6 : angle 1.56550 ( 6) link_BETA1-4 : bond 0.00233 ( 6) link_BETA1-4 : angle 1.89666 ( 18) link_ALPHA1-3 : bond 0.00423 ( 2) link_ALPHA1-3 : angle 1.40218 ( 6) hydrogen bonds : bond 0.02933 ( 222) hydrogen bonds : angle 5.22212 ( 561) SS BOND : bond 0.00241 ( 10) SS BOND : angle 1.82019 ( 20) covalent geometry : bond 0.00382 ( 6811) covalent geometry : angle 0.68009 ( 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 119 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 82 time to evaluate : 0.788 Fit side-chains revert: symmetry clash REVERT: F 100 THR cc_start: 0.6356 (m) cc_final: 0.6081 (p) REVERT: F 298 ARG cc_start: 0.6706 (ttm-80) cc_final: 0.6331 (ttm170) REVERT: F 321 GLU cc_start: 0.5691 (OUTLIER) cc_final: 0.5238 (pm20) REVERT: F 327 THR cc_start: 0.8804 (p) cc_final: 0.8390 (t) REVERT: F 355 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7302 (mp10) REVERT: A 52 ASN cc_start: 0.7750 (m110) cc_final: 0.6235 (p0) REVERT: A 63 LYS cc_start: 0.7693 (pttt) cc_final: 0.7250 (pttm) REVERT: A 67 ASN cc_start: 0.7021 (m-40) cc_final: 0.6520 (m-40) REVERT: E 137 MET cc_start: 0.5297 (ttp) cc_final: 0.5037 (ttp) REVERT: E 205 ILE cc_start: 0.7852 (mt) cc_final: 0.7553 (mt) REVERT: E 296 ILE cc_start: 0.6586 (OUTLIER) cc_final: 0.5812 (tp) REVERT: E 331 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7854 (tt) REVERT: E 376 ARG cc_start: 0.8469 (ttp80) cc_final: 0.7823 (ttt-90) outliers start: 37 outliers final: 27 residues processed: 113 average time/residue: 0.1783 time to fit residues: 27.2769 Evaluate side-chains 101 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 273 VAL Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 339 ASP Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 355 GLN Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 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 278 ILE Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 327 THR Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain E residue 385 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 54 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 39 optimal weight: 0.0970 chunk 13 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 253 GLN ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.188612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.156015 restraints weight = 8574.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.157234 restraints weight = 6455.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.158054 restraints weight = 5365.461| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 6839 Z= 0.125 Angle : 0.644 10.152 9357 Z= 0.312 Chirality : 0.045 0.210 1097 Planarity : 0.005 0.114 1157 Dihedral : 5.550 54.195 1213 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.30 % Favored : 92.07 % Rotamer: Outliers : 3.92 % Allowed : 19.76 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.31), residues: 794 helix: -1.22 (0.75), residues: 42 sheet: 0.63 (0.28), residues: 380 loop : -1.10 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 254 HIS 0.006 0.001 HIS F 105 PHE 0.031 0.002 PHE E 372 TYR 0.017 0.001 TYR F 255 ARG 0.002 0.000 ARG E 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00223 ( 8) link_NAG-ASN : angle 1.60538 ( 24) link_ALPHA1-6 : bond 0.00738 ( 2) link_ALPHA1-6 : angle 1.50202 ( 6) link_BETA1-4 : bond 0.00318 ( 6) link_BETA1-4 : angle 1.76118 ( 18) link_ALPHA1-3 : bond 0.00517 ( 2) link_ALPHA1-3 : angle 1.34417 ( 6) hydrogen bonds : bond 0.02725 ( 222) hydrogen bonds : angle 5.11258 ( 561) SS BOND : bond 0.00265 ( 10) SS BOND : angle 1.25969 ( 20) covalent geometry : bond 0.00305 ( 6811) covalent geometry : angle 0.63220 ( 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 114 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: F 100 THR cc_start: 0.6383 (m) cc_final: 0.6105 (p) REVERT: F 298 ARG cc_start: 0.6628 (ttm-80) cc_final: 0.6216 (ttm170) REVERT: F 321 GLU cc_start: 0.5941 (OUTLIER) cc_final: 0.5251 (pm20) REVERT: F 327 THR cc_start: 0.8784 (p) cc_final: 0.8424 (t) REVERT: F 355 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7217 (mp10) REVERT: F 363 LYS cc_start: 0.8610 (tppp) cc_final: 0.8291 (tppt) REVERT: A 63 LYS cc_start: 0.7377 (pttt) cc_final: 0.6973 (pttm) REVERT: A 67 ASN cc_start: 0.6850 (m-40) cc_final: 0.6460 (m-40) REVERT: E 205 ILE cc_start: 0.7741 (mt) cc_final: 0.7442 (mt) REVERT: E 296 ILE cc_start: 0.6478 (OUTLIER) cc_final: 0.5819 (tp) REVERT: E 376 ARG cc_start: 0.8444 (ttp80) cc_final: 0.7807 (ttt-90) outliers start: 29 outliers final: 22 residues processed: 112 average time/residue: 0.1723 time to fit residues: 26.3543 Evaluate side-chains 96 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 273 VAL Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 355 GLN Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain 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 296 ILE Chi-restraints excluded: chain E residue 327 THR Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain E residue 385 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 6 optimal weight: 9.9990 chunk 71 optimal weight: 0.1980 chunk 38 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 55 optimal weight: 0.1980 chunk 28 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 218 GLN E 289 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.189386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.156795 restraints weight = 8656.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.158211 restraints weight = 6353.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.159244 restraints weight = 5331.585| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6839 Z= 0.129 Angle : 0.657 9.444 9357 Z= 0.318 Chirality : 0.046 0.207 1097 Planarity : 0.006 0.119 1157 Dihedral : 5.494 54.493 1213 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.56 % Favored : 91.94 % Rotamer: Outliers : 4.60 % Allowed : 20.16 % Favored : 75.24 % 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: -0.36 (0.31), residues: 794 helix: -1.78 (0.69), residues: 48 sheet: 0.67 (0.28), residues: 369 loop : -0.93 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 254 HIS 0.006 0.001 HIS F 105 PHE 0.029 0.002 PHE E 372 TYR 0.020 0.001 TYR F 255 ARG 0.005 0.000 ARG E 195 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 8) link_NAG-ASN : angle 1.57693 ( 24) link_ALPHA1-6 : bond 0.00698 ( 2) link_ALPHA1-6 : angle 1.53149 ( 6) link_BETA1-4 : bond 0.00298 ( 6) link_BETA1-4 : angle 1.78287 ( 18) link_ALPHA1-3 : bond 0.00495 ( 2) link_ALPHA1-3 : angle 1.36173 ( 6) hydrogen bonds : bond 0.02783 ( 222) hydrogen bonds : angle 5.11208 ( 561) SS BOND : bond 0.00388 ( 10) SS BOND : angle 1.64456 ( 20) covalent geometry : bond 0.00312 ( 6811) covalent geometry : angle 0.64314 ( 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 117 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 83 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: F 100 THR cc_start: 0.6361 (m) cc_final: 0.6077 (p) REVERT: F 298 ARG cc_start: 0.6629 (ttm-80) cc_final: 0.6220 (ttm170) REVERT: F 321 GLU cc_start: 0.5666 (OUTLIER) cc_final: 0.5197 (pm20) REVERT: F 327 THR cc_start: 0.8816 (p) cc_final: 0.8440 (t) REVERT: F 355 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.7217 (mp10) REVERT: F 363 LYS cc_start: 0.8630 (tppp) cc_final: 0.8338 (tppt) REVERT: A 63 LYS cc_start: 0.7297 (pttt) cc_final: 0.6962 (pttm) REVERT: A 67 ASN cc_start: 0.7093 (m-40) cc_final: 0.6706 (m-40) REVERT: E 205 ILE cc_start: 0.7735 (mt) cc_final: 0.7446 (mt) REVERT: E 254 TRP cc_start: 0.4748 (p-90) cc_final: 0.4358 (p-90) REVERT: E 296 ILE cc_start: 0.6495 (OUTLIER) cc_final: 0.5818 (tp) REVERT: E 376 ARG cc_start: 0.8447 (ttp80) cc_final: 0.7786 (ttt180) outliers start: 34 outliers final: 27 residues processed: 112 average time/residue: 0.1624 time to fit residues: 24.9783 Evaluate side-chains 104 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 248 SER Chi-restraints excluded: chain F residue 253 GLN Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 339 ASP Chi-restraints excluded: chain F residue 355 GLN Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 369 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 106 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 2.9990 chunk 52 optimal weight: 0.0170 chunk 25 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 22 optimal weight: 0.0470 chunk 36 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4174 r_free = 0.4174 target = 0.186792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.155406 restraints weight = 8600.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.154849 restraints weight = 6532.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.155072 restraints weight = 5840.908| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6839 Z= 0.127 Angle : 0.661 9.466 9357 Z= 0.320 Chirality : 0.046 0.220 1097 Planarity : 0.005 0.117 1157 Dihedral : 5.512 54.516 1213 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.56 % Favored : 91.94 % Rotamer: Outliers : 4.33 % Allowed : 20.30 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.31), residues: 794 helix: -1.73 (0.70), residues: 48 sheet: 0.69 (0.28), residues: 368 loop : -0.92 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 254 HIS 0.007 0.001 HIS A 95 PHE 0.031 0.002 PHE E 372 TYR 0.018 0.001 TYR F 255 ARG 0.005 0.000 ARG E 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00238 ( 8) link_NAG-ASN : angle 1.52685 ( 24) link_ALPHA1-6 : bond 0.00656 ( 2) link_ALPHA1-6 : angle 1.50768 ( 6) link_BETA1-4 : bond 0.00335 ( 6) link_BETA1-4 : angle 1.74376 ( 18) link_ALPHA1-3 : bond 0.00486 ( 2) link_ALPHA1-3 : angle 1.34571 ( 6) hydrogen bonds : bond 0.02791 ( 222) hydrogen bonds : angle 5.09393 ( 561) SS BOND : bond 0.00369 ( 10) SS BOND : angle 1.92819 ( 20) covalent geometry : bond 0.00309 ( 6811) covalent geometry : angle 0.64617 ( 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 110 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 78 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6401 (m) cc_final: 0.6132 (p) REVERT: F 298 ARG cc_start: 0.6580 (ttm-80) cc_final: 0.6148 (ttm170) REVERT: F 327 THR cc_start: 0.8794 (p) cc_final: 0.8424 (t) REVERT: F 355 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.7265 (mp10) REVERT: F 363 LYS cc_start: 0.8689 (tppp) cc_final: 0.8373 (tppt) REVERT: A 63 LYS cc_start: 0.7120 (pttt) cc_final: 0.6849 (pttm) REVERT: A 67 ASN cc_start: 0.7101 (m-40) cc_final: 0.6705 (m-40) REVERT: E 205 ILE cc_start: 0.7736 (mt) cc_final: 0.7426 (mt) REVERT: E 296 ILE cc_start: 0.6480 (OUTLIER) cc_final: 0.5838 (tp) REVERT: E 376 ARG cc_start: 0.8447 (ttp80) cc_final: 0.7780 (ttt180) outliers start: 32 outliers final: 24 residues processed: 107 average time/residue: 0.1742 time to fit residues: 25.5916 Evaluate side-chains 100 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 248 SER Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 339 ASP Chi-restraints excluded: chain F residue 355 GLN Chi-restraints excluded: chain F residue 358 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 106 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 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 385 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 75 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 68 optimal weight: 0.0970 chunk 6 optimal weight: 4.9990 chunk 42 optimal weight: 0.3980 chunk 28 optimal weight: 0.5980 chunk 53 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.184103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.151690 restraints weight = 8640.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.150871 restraints weight = 6781.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.151180 restraints weight = 6693.051| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6839 Z= 0.185 Angle : 0.707 9.882 9357 Z= 0.346 Chirality : 0.047 0.224 1097 Planarity : 0.006 0.113 1157 Dihedral : 5.785 53.758 1213 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.76 % Allowed : 8.06 % Favored : 91.18 % Rotamer: Outliers : 4.33 % Allowed : 19.89 % Favored : 75.78 % 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: -1.22 (0.73), residues: 42 sheet: 0.65 (0.28), residues: 366 loop : -1.10 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 254 HIS 0.020 0.002 HIS A 95 PHE 0.031 0.003 PHE E 372 TYR 0.016 0.002 TYR E 283 ARG 0.005 0.001 ARG A 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 8) link_NAG-ASN : angle 1.70303 ( 24) link_ALPHA1-6 : bond 0.00539 ( 2) link_ALPHA1-6 : angle 1.62880 ( 6) link_BETA1-4 : bond 0.00229 ( 6) link_BETA1-4 : angle 1.92466 ( 18) link_ALPHA1-3 : bond 0.00321 ( 2) link_ALPHA1-3 : angle 1.43623 ( 6) hydrogen bonds : bond 0.03042 ( 222) hydrogen bonds : angle 5.28358 ( 561) SS BOND : bond 0.00286 ( 10) SS BOND : angle 1.73539 ( 20) covalent geometry : bond 0.00451 ( 6811) covalent geometry : angle 0.69218 ( 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: 32 poor density : 74 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6705 (m) cc_final: 0.6379 (p) REVERT: F 298 ARG cc_start: 0.6638 (ttm-80) cc_final: 0.6421 (ttm170) REVERT: F 327 THR cc_start: 0.8969 (p) cc_final: 0.8648 (t) REVERT: F 355 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7265 (mp10) REVERT: A 63 LYS cc_start: 0.7069 (pttt) cc_final: 0.6804 (pttm) REVERT: A 67 ASN cc_start: 0.7325 (m-40) cc_final: 0.6857 (m-40) REVERT: A 94 GLN cc_start: 0.4759 (tt0) cc_final: 0.4422 (mt0) REVERT: E 205 ILE cc_start: 0.7798 (mt) cc_final: 0.7465 (mt) REVERT: E 254 TRP cc_start: 0.4910 (p-90) cc_final: 0.4691 (p-90) REVERT: E 296 ILE cc_start: 0.6311 (OUTLIER) cc_final: 0.5636 (tp) REVERT: E 376 ARG cc_start: 0.8480 (ttp80) cc_final: 0.7891 (ttt-90) outliers start: 32 outliers final: 27 residues processed: 104 average time/residue: 0.1713 time to fit residues: 24.4086 Evaluate side-chains 100 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 248 SER Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 339 ASP Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 355 GLN Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain 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 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 25 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 0.0000 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.184984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.152364 restraints weight = 8778.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.151250 restraints weight = 7340.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.153308 restraints weight = 7035.863| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6839 Z= 0.151 Angle : 0.680 9.416 9357 Z= 0.331 Chirality : 0.047 0.223 1097 Planarity : 0.005 0.107 1157 Dihedral : 5.712 53.901 1213 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.68 % Favored : 91.56 % Rotamer: Outliers : 3.92 % Allowed : 20.57 % 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: -0.38 (0.30), residues: 794 helix: -1.12 (0.73), residues: 42 sheet: 0.65 (0.28), residues: 368 loop : -1.06 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 254 HIS 0.007 0.001 HIS A 95 PHE 0.033 0.002 PHE E 372 TYR 0.015 0.002 TYR F 255 ARG 0.006 0.001 ARG A 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00200 ( 8) link_NAG-ASN : angle 1.63718 ( 24) link_ALPHA1-6 : bond 0.00587 ( 2) link_ALPHA1-6 : angle 1.53029 ( 6) link_BETA1-4 : bond 0.00263 ( 6) link_BETA1-4 : angle 1.87626 ( 18) link_ALPHA1-3 : bond 0.00381 ( 2) link_ALPHA1-3 : angle 1.35095 ( 6) hydrogen bonds : bond 0.02885 ( 222) hydrogen bonds : angle 5.23878 ( 561) SS BOND : bond 0.00385 ( 10) SS BOND : angle 1.46649 ( 20) covalent geometry : bond 0.00368 ( 6811) covalent geometry : angle 0.66699 ( 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 107 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6766 (m) cc_final: 0.6387 (p) REVERT: F 298 ARG cc_start: 0.6677 (ttm-80) cc_final: 0.6331 (ttm170) REVERT: F 327 THR cc_start: 0.8995 (p) cc_final: 0.8679 (t) REVERT: F 355 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7274 (mp10) REVERT: A 67 ASN cc_start: 0.7266 (m-40) cc_final: 0.6815 (m-40) REVERT: E 205 ILE cc_start: 0.7782 (mt) cc_final: 0.7254 (mt) REVERT: E 254 TRP cc_start: 0.5610 (p-90) cc_final: 0.5095 (p-90) REVERT: E 296 ILE cc_start: 0.6350 (OUTLIER) cc_final: 0.5684 (tp) REVERT: E 376 ARG cc_start: 0.8480 (ttp80) cc_final: 0.7893 (ttt-90) outliers start: 29 outliers final: 24 residues processed: 102 average time/residue: 0.1798 time to fit residues: 25.2225 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 : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 342 VAL Chi-restraints excluded: chain F residue 355 GLN Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 378 GLU 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 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: 0.9980 chunk 34 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.184210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.151808 restraints weight = 8766.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.151207 restraints weight = 6819.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.151625 restraints weight = 6507.980| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6839 Z= 0.163 Angle : 0.699 10.562 9357 Z= 0.340 Chirality : 0.047 0.232 1097 Planarity : 0.005 0.101 1157 Dihedral : 5.777 53.688 1213 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.68 % Favored : 91.56 % Rotamer: Outliers : 3.79 % Allowed : 20.43 % Favored : 75.78 % 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: -0.41 (0.30), residues: 794 helix: -1.10 (0.74), residues: 42 sheet: 0.69 (0.28), residues: 364 loop : -1.13 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 254 HIS 0.007 0.001 HIS F 105 PHE 0.034 0.002 PHE E 372 TYR 0.015 0.002 TYR E 283 ARG 0.007 0.001 ARG A 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00201 ( 8) link_NAG-ASN : angle 1.70503 ( 24) link_ALPHA1-6 : bond 0.00511 ( 2) link_ALPHA1-6 : angle 1.59541 ( 6) link_BETA1-4 : bond 0.00245 ( 6) link_BETA1-4 : angle 1.91200 ( 18) link_ALPHA1-3 : bond 0.00366 ( 2) link_ALPHA1-3 : angle 1.40488 ( 6) hydrogen bonds : bond 0.02924 ( 222) hydrogen bonds : angle 5.37932 ( 561) SS BOND : bond 0.00420 ( 10) SS BOND : angle 1.59818 ( 20) covalent geometry : bond 0.00403 ( 6811) covalent geometry : angle 0.68523 ( 9283) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2807.80 seconds wall clock time: 51 minutes 24.41 seconds (3084.41 seconds total)