Starting phenix.real_space_refine on Tue Feb 11 10:54:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x4s_22042/02_2025/6x4s_22042.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x4s_22042/02_2025/6x4s_22042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x4s_22042/02_2025/6x4s_22042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x4s_22042/02_2025/6x4s_22042.map" model { file = "/net/cci-nas-00/data/ceres_data/6x4s_22042/02_2025/6x4s_22042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x4s_22042/02_2025/6x4s_22042.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 15 5.16 5 C 3521 2.51 5 N 890 2.21 5 O 946 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5373 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1158 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 2, 'TRANS': 149} Chain breaks: 1 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 7, 'ASN:plan1': 2, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 79 Chain: "B" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1170 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "C" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1155 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 2, 'TRANS': 149} Chain breaks: 1 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 7, 'ASN:plan1': 2, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 79 Chain: "D" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1165 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "E" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 181 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 23} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 181 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 23} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 181 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 23} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 181 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 23} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.23, per 1000 atoms: 0.79 Number of scatterers: 5373 At special positions: 0 Unit cell: (68.544, 69.632, 120.768, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 15 16.00 O 946 8.00 N 890 7.00 C 3521 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 675.0 milliseconds 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1356 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 91.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 178 through 190 removed outlier: 3.776A pdb=" N LEU A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 254 removed outlier: 3.773A pdb=" N GLN A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) Proline residue: A 216 - end of helix removed outlier: 3.946A pdb=" N ARG A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 286 removed outlier: 3.604A pdb=" N THR A 267 " --> pdb=" O MET A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 313 through 336 Processing helix chain 'B' and resid 176 through 191 Processing helix chain 'B' and resid 194 through 256 removed outlier: 3.521A pdb=" N LYS B 199 " --> pdb=" O HIS B 195 " (cutoff:3.500A) Proline residue: B 216 - end of helix removed outlier: 4.295A pdb=" N ARG B 231 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 300 Processing helix chain 'B' and resid 313 through 336 Processing helix chain 'C' and resid 179 through 190 Processing helix chain 'C' and resid 194 through 256 removed outlier: 3.683A pdb=" N GLN C 198 " --> pdb=" O GLU C 194 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU C 208 " --> pdb=" O THR C 204 " (cutoff:3.500A) Proline residue: C 216 - end of helix removed outlier: 3.706A pdb=" N ARG C 231 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 285 removed outlier: 4.545A pdb=" N VAL C 266 " --> pdb=" O ILE C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 308 Processing helix chain 'C' and resid 313 through 336 Processing helix chain 'D' and resid 176 through 192 Processing helix chain 'D' and resid 197 through 256 Proline residue: D 216 - end of helix removed outlier: 3.987A pdb=" N ARG D 231 " --> pdb=" O VAL D 227 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 300 removed outlier: 3.872A pdb=" N THR D 267 " --> pdb=" O MET D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 336 removed outlier: 3.522A pdb=" N TYR D 317 " --> pdb=" O ASP D 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 92 Proline residue: E 76 - end of helix Processing helix chain 'F' and resid 69 through 92 Proline residue: F 76 - end of helix Processing helix chain 'G' and resid 69 through 92 Proline residue: G 76 - end of helix Processing helix chain 'H' and resid 69 through 92 Proline residue: H 76 - end of helix 519 hydrogen bonds defined for protein. 1557 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.40 Time building geometry restraints manager: 1.75 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: 1689 1.34 - 1.46: 894 1.46 - 1.57: 2851 1.57 - 1.69: 2 1.69 - 1.81: 30 Bond restraints: 5466 Sorted by residual: bond pdb=" CA VAL A 294 " pdb=" C VAL A 294 " ideal model delta sigma weight residual 1.525 1.468 0.057 2.10e-02 2.27e+03 7.33e+00 bond pdb=" N LYS C 308 " pdb=" CA LYS C 308 " ideal model delta sigma weight residual 1.462 1.497 -0.035 1.46e-02 4.69e+03 5.75e+00 bond pdb=" N LYS A 308 " pdb=" CA LYS A 308 " ideal model delta sigma weight residual 1.461 1.498 -0.036 1.52e-02 4.33e+03 5.75e+00 bond pdb=" CB VAL A 294 " pdb=" CG1 VAL A 294 " ideal model delta sigma weight residual 1.521 1.593 -0.072 3.30e-02 9.18e+02 4.71e+00 bond pdb=" CG GLU B 257 " pdb=" CD GLU B 257 " ideal model delta sigma weight residual 1.516 1.474 0.042 2.50e-02 1.60e+03 2.78e+00 ... (remaining 5461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 7161 1.68 - 3.37: 237 3.37 - 5.05: 42 5.05 - 6.73: 16 6.73 - 8.42: 4 Bond angle restraints: 7460 Sorted by residual: angle pdb=" CD1 LEU D 291 " pdb=" CG LEU D 291 " pdb=" CD2 LEU D 291 " ideal model delta sigma weight residual 110.80 103.62 7.18 2.20e+00 2.07e-01 1.07e+01 angle pdb=" C ASP D 330 " pdb=" CA ASP D 330 " pdb=" CB ASP D 330 " ideal model delta sigma weight residual 110.85 116.27 -5.42 1.70e+00 3.46e-01 1.02e+01 angle pdb=" C MET A 263 " pdb=" N GLU A 264 " pdb=" CA GLU A 264 " ideal model delta sigma weight residual 121.80 115.69 6.11 2.44e+00 1.68e-01 6.28e+00 angle pdb=" CA LEU C 253 " pdb=" CB LEU C 253 " pdb=" CG LEU C 253 " ideal model delta sigma weight residual 116.30 124.72 -8.42 3.50e+00 8.16e-02 5.78e+00 angle pdb=" CA ARG D 252 " pdb=" CB ARG D 252 " pdb=" CG ARG D 252 " ideal model delta sigma weight residual 114.10 109.37 4.73 2.00e+00 2.50e-01 5.60e+00 ... (remaining 7455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.84: 2759 15.84 - 31.69: 323 31.69 - 47.53: 104 47.53 - 63.38: 17 63.38 - 79.22: 5 Dihedral angle restraints: 3208 sinusoidal: 1128 harmonic: 2080 Sorted by residual: dihedral pdb=" CA ALA A 307 " pdb=" C ALA A 307 " pdb=" N LYS A 308 " pdb=" CA LYS A 308 " ideal model delta harmonic sigma weight residual -180.00 -155.11 -24.89 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA ARG A 193 " pdb=" C ARG A 193 " pdb=" N GLU A 194 " pdb=" CA GLU A 194 " ideal model delta harmonic sigma weight residual 180.00 161.41 18.59 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ALA C 307 " pdb=" C ALA C 307 " pdb=" N LYS C 308 " pdb=" CA LYS C 308 " ideal model delta harmonic sigma weight residual 180.00 164.50 15.50 0 5.00e+00 4.00e-02 9.61e+00 ... (remaining 3205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 895 0.115 - 0.229: 22 0.229 - 0.344: 2 0.344 - 0.459: 0 0.459 - 0.574: 1 Chirality restraints: 920 Sorted by residual: chirality pdb=" CG LEU D 291 " pdb=" CB LEU D 291 " pdb=" CD1 LEU D 291 " pdb=" CD2 LEU D 291 " both_signs ideal model delta sigma weight residual False -2.59 -3.16 0.57 2.00e-01 2.50e+01 8.23e+00 chirality pdb=" CB VAL A 294 " pdb=" CA VAL A 294 " pdb=" CG1 VAL A 294 " pdb=" CG2 VAL A 294 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA LEU D 291 " pdb=" N LEU D 291 " pdb=" C LEU D 291 " pdb=" CB LEU D 291 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 917 not shown) Planarity restraints: 910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP D 330 " -0.024 2.00e-02 2.50e+03 4.82e-02 2.33e+01 pdb=" CG ASP D 330 " 0.083 2.00e-02 2.50e+03 pdb=" OD1 ASP D 330 " -0.031 2.00e-02 2.50e+03 pdb=" OD2 ASP D 330 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 307 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.45e+00 pdb=" C ALA A 307 " -0.047 2.00e-02 2.50e+03 pdb=" O ALA A 307 " 0.018 2.00e-02 2.50e+03 pdb=" N LYS A 308 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 307 " 0.014 2.00e-02 2.50e+03 2.70e-02 7.31e+00 pdb=" C ALA C 307 " -0.047 2.00e-02 2.50e+03 pdb=" O ALA C 307 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS C 308 " 0.016 2.00e-02 2.50e+03 ... (remaining 907 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 39 2.64 - 3.21: 5207 3.21 - 3.77: 8739 3.77 - 4.34: 10111 4.34 - 4.90: 16782 Nonbonded interactions: 40878 Sorted by model distance: nonbonded pdb=" OE2 GLU D 264 " pdb="CA CA A 501 " model vdw 2.077 2.510 nonbonded pdb=" OE2 GLU C 264 " pdb="CA CA A 501 " model vdw 2.213 2.510 nonbonded pdb=" O ASP B 178 " pdb=" OG1 THR B 181 " model vdw 2.219 3.040 nonbonded pdb=" O VAL B 201 " pdb=" OG1 THR B 204 " model vdw 2.247 3.040 nonbonded pdb=" OE1 GLN D 246 " pdb=" OG1 THR D 274 " model vdw 2.289 3.040 ... (remaining 40873 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 'A' and (resid 178 through 191 or (resid 192 through 196 and (name N or n \ ame CA or name C or name O or name CB )) or resid 197 through 199 or (resid 200 \ and (name N or name CA or name C or name O or name CB )) or resid 201 through 21 \ 9 or (resid 220 and (name N or name CA or name C or name O or name CB or name CG \ or name CD )) or resid 221 through 241 or (resid 242 through 243 and (name N or \ name CA or name C or name O or name CB )) or resid 244 through 286 or resid 302 \ or resid 312 through 327 or (resid 328 and (name N or name CA or name C or name \ O or name CB )) or resid 329 through 336)) selection = (chain 'B' and (resid 178 through 179 or (resid 180 and (name N or name CA or na \ me C or name O or name CB )) or resid 181 through 183 or (resid 184 through 185 \ and (name N or name CA or name C or name O or name CB )) or resid 186 through 18 \ 7 or (resid 188 through 189 and (name N or name CA or name C or name O or name C \ B )) or resid 190 or (resid 191 through 196 and (name N or name CA or name C or \ name O or name CB )) or resid 197 or (resid 198 through 200 and (name N or name \ CA or name C or name O or name CB )) or resid 201 through 224 or (resid 225 and \ (name N or name CA or name C or name O or name CB )) or resid 226 through 241 or \ (resid 242 through 243 and (name N or name CA or name C or name O or name CB )) \ or resid 244 through 286 or (resid 291 and (name N or name CA or name C or name \ O or name CB )) or resid 312 through 336)) selection = (chain 'C' and (resid 178 through 191 or (resid 192 through 196 and (name N or n \ ame CA or name C or name O or name CB )) or resid 197 through 199 or (resid 200 \ and (name N or name CA or name C or name O or name CB )) or resid 201 through 21 \ 9 or (resid 220 and (name N or name CA or name C or name O or name CB or name CG \ or name CD )) or resid 221 through 242 or (resid 243 and (name N or name CA or \ name C or name O or name CB )) or resid 244 through 286 or resid 302 or resid 31 \ 2 through 327 or (resid 328 and (name N or name CA or name C or name O or name C \ B )) or resid 329 through 336)) selection = (chain 'D' and (resid 178 through 179 or (resid 180 and (name N or name CA or na \ me C or name O or name CB )) or resid 181 through 183 or (resid 184 through 185 \ and (name N or name CA or name C or name O or name CB )) or resid 186 through 18 \ 7 or (resid 188 through 189 and (name N or name CA or name C or name O or name C \ B )) or resid 190 or (resid 191 through 196 and (name N or name CA or name C or \ name O or name CB )) or resid 197 or (resid 198 through 200 and (name N or name \ CA or name C or name O or name CB )) or resid 201 through 224 or (resid 225 and \ (name N or name CA or name C or name O or name CB )) or resid 226 through 241 or \ (resid 242 through 243 and (name N or name CA or name C or name O or name CB )) \ or resid 244 through 286 or (resid 291 and (name N or name CA or name C or name \ O or name CB )) or resid 312 through 336)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.040 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 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 : 0.007 0.072 5466 Z= 0.427 Angle : 0.768 8.418 7460 Z= 0.404 Chirality : 0.050 0.574 920 Planarity : 0.004 0.048 910 Dihedral : 15.586 79.222 1852 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.97 % Allowed : 21.94 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.34 (0.30), residues: 682 helix: 1.29 (0.19), residues: 636 sheet: None (None), residues: 0 loop : -4.42 (0.58), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 260 HIS 0.006 0.002 HIS C 195 PHE 0.011 0.002 PHE D 247 TYR 0.013 0.002 TYR C 258 ARG 0.002 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 262 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 TYR cc_start: 0.9238 (t80) cc_final: 0.8677 (t80) REVERT: A 321 LYS cc_start: 0.8763 (mttt) cc_final: 0.8372 (ttmm) REVERT: A 328 GLU cc_start: 0.8547 (tt0) cc_final: 0.8301 (tm-30) REVERT: B 211 GLN cc_start: 0.8862 (mt0) cc_final: 0.8606 (mm-40) REVERT: B 230 ARG cc_start: 0.8068 (ptp-170) cc_final: 0.7337 (ptm160) REVERT: B 243 MET cc_start: 0.7462 (mtp) cc_final: 0.7033 (mtt) REVERT: B 253 LEU cc_start: 0.8766 (mt) cc_final: 0.8526 (mp) REVERT: B 263 MET cc_start: 0.8190 (mmm) cc_final: 0.7862 (ttm) REVERT: B 313 ASP cc_start: 0.8041 (t0) cc_final: 0.7809 (t0) REVERT: B 316 GLN cc_start: 0.7632 (pt0) cc_final: 0.7311 (tt0) REVERT: B 318 ASN cc_start: 0.8886 (t0) cc_final: 0.8643 (m-40) REVERT: C 226 GLN cc_start: 0.8819 (tt0) cc_final: 0.8270 (tt0) REVERT: C 229 ASN cc_start: 0.8826 (m-40) cc_final: 0.8593 (t0) REVERT: C 235 MET cc_start: 0.8076 (tpp) cc_final: 0.7624 (tmm) REVERT: C 246 GLN cc_start: 0.9072 (tt0) cc_final: 0.8859 (tt0) REVERT: C 247 PHE cc_start: 0.9312 (t80) cc_final: 0.8958 (t80) REVERT: C 263 MET cc_start: 0.8537 (mmm) cc_final: 0.8172 (tpp) REVERT: C 276 MET cc_start: 0.7603 (mtp) cc_final: 0.7226 (mmp) REVERT: C 317 TYR cc_start: 0.9096 (t80) cc_final: 0.8693 (t80) REVERT: C 328 GLU cc_start: 0.8459 (tt0) cc_final: 0.7985 (pt0) REVERT: D 256 TRP cc_start: 0.8287 (m-90) cc_final: 0.7796 (m-90) REVERT: D 260 TRP cc_start: 0.8026 (t-100) cc_final: 0.7807 (t-100) REVERT: D 262 ILE cc_start: 0.8261 (tt) cc_final: 0.8002 (tt) REVERT: E 90 ASN cc_start: 0.6849 (m-40) cc_final: 0.6368 (m110) REVERT: F 70 LEU cc_start: 0.9020 (tt) cc_final: 0.8566 (mp) REVERT: F 73 THR cc_start: 0.8314 (p) cc_final: 0.8104 (p) outliers start: 5 outliers final: 0 residues processed: 266 average time/residue: 0.2212 time to fit residues: 70.7117 Evaluate side-chains 207 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 28 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 61 optimal weight: 6.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN D 315 ASN D 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.127570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.103741 restraints weight = 13237.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.107280 restraints weight = 7025.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.109603 restraints weight = 4850.965| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5466 Z= 0.231 Angle : 0.664 8.158 7460 Z= 0.334 Chirality : 0.037 0.177 920 Planarity : 0.004 0.029 910 Dihedral : 3.636 17.114 748 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.69 % Allowed : 28.35 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.86 (0.32), residues: 682 helix: 2.98 (0.20), residues: 624 sheet: None (None), residues: 0 loop : -3.00 (0.65), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 260 HIS 0.003 0.001 HIS C 195 PHE 0.010 0.001 PHE C 247 TYR 0.013 0.002 TYR B 279 ARG 0.007 0.001 ARG D 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 228 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8930 (mmmt) cc_final: 0.8567 (mtmt) REVERT: A 272 TYR cc_start: 0.8515 (t80) cc_final: 0.8185 (t80) REVERT: B 211 GLN cc_start: 0.8804 (mt0) cc_final: 0.8550 (mm-40) REVERT: B 243 MET cc_start: 0.7272 (mtp) cc_final: 0.6945 (mmt) REVERT: B 246 GLN cc_start: 0.9016 (tt0) cc_final: 0.8801 (tt0) REVERT: B 253 LEU cc_start: 0.8662 (mt) cc_final: 0.8438 (mp) REVERT: B 316 GLN cc_start: 0.7743 (pt0) cc_final: 0.7529 (tt0) REVERT: B 321 LYS cc_start: 0.9038 (mmmm) cc_final: 0.8610 (mmmm) REVERT: C 221 LYS cc_start: 0.9100 (ttmt) cc_final: 0.8860 (ttpt) REVERT: C 235 MET cc_start: 0.8011 (tpp) cc_final: 0.7733 (tmm) REVERT: C 247 PHE cc_start: 0.9296 (t80) cc_final: 0.9016 (t80) REVERT: D 213 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8571 (tm-30) REVERT: D 226 GLN cc_start: 0.8521 (pp30) cc_final: 0.8319 (pp30) REVERT: F 70 LEU cc_start: 0.8922 (tt) cc_final: 0.8426 (mp) REVERT: H 70 LEU cc_start: 0.8958 (tt) cc_final: 0.8544 (mp) outliers start: 19 outliers final: 12 residues processed: 237 average time/residue: 0.2006 time to fit residues: 58.2954 Evaluate side-chains 222 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 210 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 237 TRP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain D residue 198 GLN Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 70 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 44 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN B 246 GLN ** C 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.126085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.103027 restraints weight = 13192.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.106579 restraints weight = 6689.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.108778 restraints weight = 4547.919| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5466 Z= 0.221 Angle : 0.605 7.517 7460 Z= 0.306 Chirality : 0.035 0.153 920 Planarity : 0.003 0.029 910 Dihedral : 3.515 15.477 748 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 5.05 % Allowed : 29.51 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.25 (0.32), residues: 682 helix: 3.12 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.72 (0.79), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 260 HIS 0.003 0.001 HIS C 195 PHE 0.021 0.001 PHE B 247 TYR 0.016 0.002 TYR A 317 ARG 0.005 0.001 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 218 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8939 (mmmt) cc_final: 0.8664 (mtmt) REVERT: A 272 TYR cc_start: 0.8521 (t80) cc_final: 0.8156 (t80) REVERT: B 243 MET cc_start: 0.7343 (mtp) cc_final: 0.7029 (mmt) REVERT: B 316 GLN cc_start: 0.7866 (pt0) cc_final: 0.7540 (tt0) REVERT: C 221 LYS cc_start: 0.9112 (ttmt) cc_final: 0.8783 (ttmt) REVERT: C 235 MET cc_start: 0.8002 (tpp) cc_final: 0.7708 (tmm) REVERT: C 246 GLN cc_start: 0.9127 (tt0) cc_final: 0.8893 (tt0) REVERT: D 213 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8495 (tm-30) REVERT: D 226 GLN cc_start: 0.8573 (pp30) cc_final: 0.8346 (pp30) REVERT: F 70 LEU cc_start: 0.8971 (tt) cc_final: 0.8498 (mp) REVERT: H 70 LEU cc_start: 0.8993 (tt) cc_final: 0.8621 (mp) outliers start: 26 outliers final: 18 residues processed: 228 average time/residue: 0.2037 time to fit residues: 56.9496 Evaluate side-chains 228 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 237 TRP Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 237 TRP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 70 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 63 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 0.3980 chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 2 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 229 ASN B 318 ASN C 226 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.128213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.105052 restraints weight = 12384.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.108299 restraints weight = 6478.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.110468 restraints weight = 4466.289| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5466 Z= 0.223 Angle : 0.609 7.563 7460 Z= 0.307 Chirality : 0.035 0.145 920 Planarity : 0.003 0.026 910 Dihedral : 3.485 16.843 748 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 5.83 % Allowed : 32.04 % Favored : 62.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.35 (0.32), residues: 682 helix: 3.24 (0.20), residues: 632 sheet: None (None), residues: 0 loop : -3.00 (0.75), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 260 HIS 0.001 0.000 HIS A 304 PHE 0.020 0.001 PHE B 247 TYR 0.019 0.002 TYR A 317 ARG 0.007 0.001 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 226 GLN cc_start: 0.8227 (pp30) cc_final: 0.7814 (pp30) REVERT: B 234 TRP cc_start: 0.8178 (t60) cc_final: 0.7822 (t60) REVERT: B 316 GLN cc_start: 0.7858 (pt0) cc_final: 0.7618 (tt0) REVERT: C 226 GLN cc_start: 0.8777 (tt0) cc_final: 0.8565 (tt0) REVERT: C 235 MET cc_start: 0.7989 (tpp) cc_final: 0.7777 (tmm) REVERT: C 246 GLN cc_start: 0.9093 (tt0) cc_final: 0.8856 (tt0) REVERT: C 263 MET cc_start: 0.7889 (tpp) cc_final: 0.7668 (tpp) REVERT: D 226 GLN cc_start: 0.8645 (pp30) cc_final: 0.8413 (pp30) REVERT: D 329 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8682 (tt) REVERT: F 70 LEU cc_start: 0.9021 (tt) cc_final: 0.8464 (mp) REVERT: H 70 LEU cc_start: 0.8972 (tt) cc_final: 0.8567 (mp) outliers start: 30 outliers final: 17 residues processed: 222 average time/residue: 0.2156 time to fit residues: 58.8332 Evaluate side-chains 214 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 196 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 TRP Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 237 TRP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain D residue 198 GLN Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 70 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 51 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 318 ASN ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN E 87 ASN G 90 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.126202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.102941 restraints weight = 12440.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.106251 restraints weight = 6419.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.108346 restraints weight = 4419.205| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5466 Z= 0.243 Angle : 0.619 9.576 7460 Z= 0.310 Chirality : 0.035 0.140 920 Planarity : 0.003 0.025 910 Dihedral : 3.407 16.611 748 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 7.57 % Allowed : 30.29 % Favored : 62.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.29 (0.32), residues: 682 helix: 3.20 (0.20), residues: 632 sheet: None (None), residues: 0 loop : -3.00 (0.76), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 260 HIS 0.001 0.000 HIS A 304 PHE 0.022 0.001 PHE B 247 TYR 0.019 0.002 TYR A 317 ARG 0.006 0.001 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 203 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 243 MET cc_start: 0.8575 (ttm) cc_final: 0.8309 (ttp) REVERT: B 226 GLN cc_start: 0.8328 (pp30) cc_final: 0.7875 (pp30) REVERT: B 234 TRP cc_start: 0.8172 (t60) cc_final: 0.7921 (t60) REVERT: B 316 GLN cc_start: 0.7955 (pt0) cc_final: 0.7700 (tt0) REVERT: B 321 LYS cc_start: 0.9122 (mmmm) cc_final: 0.8846 (mmtp) REVERT: C 235 MET cc_start: 0.8083 (tpp) cc_final: 0.7637 (tmm) REVERT: C 246 GLN cc_start: 0.9135 (tt0) cc_final: 0.8901 (tt0) REVERT: D 329 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8626 (tt) REVERT: F 70 LEU cc_start: 0.9009 (tt) cc_final: 0.8505 (mp) REVERT: H 70 LEU cc_start: 0.9026 (tt) cc_final: 0.8584 (mp) outliers start: 39 outliers final: 28 residues processed: 220 average time/residue: 0.1943 time to fit residues: 52.8050 Evaluate side-chains 224 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 237 TRP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 237 TRP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 198 GLN Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain H residue 69 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 24 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 60 optimal weight: 0.0970 chunk 64 optimal weight: 0.0970 chunk 53 optimal weight: 0.0020 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 overall best weight: 0.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.126539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.103375 restraints weight = 12892.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.106748 restraints weight = 6840.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.108948 restraints weight = 4762.943| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5466 Z= 0.184 Angle : 0.623 8.991 7460 Z= 0.307 Chirality : 0.034 0.144 920 Planarity : 0.003 0.023 910 Dihedral : 3.453 15.732 748 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.47 % Allowed : 33.01 % Favored : 62.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.26 (0.32), residues: 682 helix: 3.16 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -2.98 (0.78), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 260 HIS 0.001 0.000 HIS A 304 PHE 0.017 0.001 PHE B 247 TYR 0.017 0.001 TYR A 317 ARG 0.004 0.001 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 243 MET cc_start: 0.8607 (ttm) cc_final: 0.8396 (ttp) REVERT: A 257 GLU cc_start: 0.7617 (tt0) cc_final: 0.7399 (tt0) REVERT: B 226 GLN cc_start: 0.8304 (pp30) cc_final: 0.7840 (pp30) REVERT: B 234 TRP cc_start: 0.8126 (t60) cc_final: 0.7797 (t60) REVERT: B 272 TYR cc_start: 0.8670 (t80) cc_final: 0.8227 (t80) REVERT: B 316 GLN cc_start: 0.7841 (pt0) cc_final: 0.7580 (tt0) REVERT: C 218 GLU cc_start: 0.8695 (tp30) cc_final: 0.8466 (tp30) REVERT: C 235 MET cc_start: 0.8056 (tpp) cc_final: 0.7637 (tmm) REVERT: C 246 GLN cc_start: 0.9087 (tt0) cc_final: 0.8861 (tt0) REVERT: D 329 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8728 (tt) REVERT: F 70 LEU cc_start: 0.8986 (tt) cc_final: 0.8514 (mp) REVERT: H 70 LEU cc_start: 0.8933 (tt) cc_final: 0.8530 (mp) outliers start: 23 outliers final: 19 residues processed: 216 average time/residue: 0.2001 time to fit residues: 53.3207 Evaluate side-chains 217 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 237 TRP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 237 TRP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 263 MET Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 70 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 63 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.125487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.102280 restraints weight = 12932.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.105724 restraints weight = 6772.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.107870 restraints weight = 4686.261| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5466 Z= 0.227 Angle : 0.623 7.761 7460 Z= 0.312 Chirality : 0.036 0.164 920 Planarity : 0.003 0.022 910 Dihedral : 3.444 15.888 748 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.66 % Allowed : 32.82 % Favored : 62.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.21 (0.32), residues: 682 helix: 3.19 (0.20), residues: 626 sheet: None (None), residues: 0 loop : -2.94 (0.70), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 260 HIS 0.001 0.000 HIS A 304 PHE 0.017 0.001 PHE B 247 TYR 0.017 0.002 TYR C 317 ARG 0.005 0.001 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: B 226 GLN cc_start: 0.8381 (pp30) cc_final: 0.7898 (pp30) REVERT: B 234 TRP cc_start: 0.8200 (t60) cc_final: 0.7852 (t60) REVERT: B 313 ASP cc_start: 0.7235 (OUTLIER) cc_final: 0.6932 (m-30) REVERT: B 316 GLN cc_start: 0.7978 (pt0) cc_final: 0.7692 (tt0) REVERT: C 235 MET cc_start: 0.8105 (tpp) cc_final: 0.7707 (tmm) REVERT: C 246 GLN cc_start: 0.9114 (tt0) cc_final: 0.8910 (tt0) REVERT: D 329 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8756 (tt) REVERT: F 70 LEU cc_start: 0.9060 (tt) cc_final: 0.8590 (mp) REVERT: H 70 LEU cc_start: 0.8988 (tt) cc_final: 0.8595 (mp) outliers start: 24 outliers final: 20 residues processed: 207 average time/residue: 0.2058 time to fit residues: 52.4936 Evaluate side-chains 215 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 237 TRP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 237 TRP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 263 MET Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain H residue 69 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 24 optimal weight: 0.6980 chunk 2 optimal weight: 0.0010 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 36 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 315 ASN ** 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 = 0.3978 r_free = 0.3978 target = 0.126256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.103206 restraints weight = 12953.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.106660 restraints weight = 6808.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.108858 restraints weight = 4720.923| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5466 Z= 0.203 Angle : 0.641 7.795 7460 Z= 0.319 Chirality : 0.035 0.180 920 Planarity : 0.003 0.024 910 Dihedral : 3.446 15.424 748 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.66 % Allowed : 33.01 % Favored : 62.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.23 (0.32), residues: 682 helix: 3.21 (0.20), residues: 626 sheet: None (None), residues: 0 loop : -2.94 (0.70), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 260 HIS 0.001 0.000 HIS A 304 PHE 0.024 0.001 PHE B 247 TYR 0.015 0.002 TYR A 317 ARG 0.004 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: B 226 GLN cc_start: 0.8364 (pp30) cc_final: 0.7874 (pp30) REVERT: B 313 ASP cc_start: 0.7294 (OUTLIER) cc_final: 0.6975 (m-30) REVERT: B 316 GLN cc_start: 0.7906 (pt0) cc_final: 0.7584 (tt0) REVERT: B 317 TYR cc_start: 0.9183 (t80) cc_final: 0.8917 (t80) REVERT: B 321 LYS cc_start: 0.9085 (mmtm) cc_final: 0.8813 (mttp) REVERT: C 219 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7881 (mt-10) REVERT: C 235 MET cc_start: 0.8039 (tpp) cc_final: 0.7555 (tmm) REVERT: D 329 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8727 (tt) REVERT: F 70 LEU cc_start: 0.9042 (tt) cc_final: 0.8597 (mp) REVERT: H 70 LEU cc_start: 0.8985 (tt) cc_final: 0.8579 (mp) outliers start: 24 outliers final: 20 residues processed: 201 average time/residue: 0.1954 time to fit residues: 48.7178 Evaluate side-chains 211 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 237 TRP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 237 TRP Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 263 MET Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 70 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 54 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 64 optimal weight: 0.0870 chunk 28 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 ASN ** 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 = 0.3974 r_free = 0.3974 target = 0.126224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.103540 restraints weight = 13000.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.106846 restraints weight = 6887.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.109002 restraints weight = 4774.813| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5466 Z= 0.217 Angle : 0.643 7.218 7460 Z= 0.321 Chirality : 0.037 0.187 920 Planarity : 0.003 0.024 910 Dihedral : 3.407 16.135 748 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 5.63 % Allowed : 33.40 % Favored : 60.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.22 (0.32), residues: 682 helix: 3.14 (0.20), residues: 630 sheet: None (None), residues: 0 loop : -2.69 (0.77), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 234 HIS 0.001 0.000 HIS A 304 PHE 0.022 0.001 PHE B 247 TYR 0.017 0.002 TYR D 187 ARG 0.004 0.000 ARG F 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: B 226 GLN cc_start: 0.8374 (pp30) cc_final: 0.7885 (pp30) REVERT: B 234 TRP cc_start: 0.8134 (t60) cc_final: 0.7750 (t60) REVERT: B 313 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.6952 (m-30) REVERT: C 219 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7814 (mt-10) REVERT: C 235 MET cc_start: 0.8007 (tpp) cc_final: 0.7571 (tmm) REVERT: C 246 GLN cc_start: 0.9225 (tt0) cc_final: 0.8910 (tt0) REVERT: D 231 ARG cc_start: 0.8158 (ttt90) cc_final: 0.7876 (tmm-80) REVERT: D 329 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8755 (tt) REVERT: F 70 LEU cc_start: 0.9049 (tt) cc_final: 0.8587 (mp) REVERT: H 70 LEU cc_start: 0.8975 (tt) cc_final: 0.8590 (mp) outliers start: 29 outliers final: 23 residues processed: 204 average time/residue: 0.1943 time to fit residues: 48.7884 Evaluate side-chains 210 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 237 TRP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 237 TRP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 263 MET Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 51 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 0.1980 chunk 46 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.122500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.098555 restraints weight = 12836.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.101995 restraints weight = 6408.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.104182 restraints weight = 4310.197| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5466 Z= 0.242 Angle : 0.693 9.046 7460 Z= 0.346 Chirality : 0.038 0.191 920 Planarity : 0.003 0.023 910 Dihedral : 3.501 16.602 748 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 5.24 % Allowed : 33.20 % Favored : 61.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.13 (0.32), residues: 682 helix: 3.09 (0.20), residues: 630 sheet: None (None), residues: 0 loop : -2.71 (0.70), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 234 HIS 0.001 0.000 HIS A 304 PHE 0.022 0.001 PHE B 247 TYR 0.024 0.002 TYR A 258 ARG 0.004 0.000 ARG A 286 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 221 LYS cc_start: 0.9068 (ttpp) cc_final: 0.8856 (ttpp) REVERT: B 226 GLN cc_start: 0.8355 (pp30) cc_final: 0.7851 (pp30) REVERT: B 243 MET cc_start: 0.6935 (mmt) cc_final: 0.6718 (mmt) REVERT: B 313 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.7119 (m-30) REVERT: C 219 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7797 (mt-10) REVERT: C 235 MET cc_start: 0.8075 (tpp) cc_final: 0.7490 (tmm) REVERT: C 246 GLN cc_start: 0.9182 (tt0) cc_final: 0.8868 (tt0) REVERT: D 329 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8636 (tt) REVERT: F 70 LEU cc_start: 0.9022 (tt) cc_final: 0.8609 (mp) REVERT: H 70 LEU cc_start: 0.9019 (tt) cc_final: 0.8638 (mp) outliers start: 27 outliers final: 24 residues processed: 198 average time/residue: 0.2016 time to fit residues: 49.4993 Evaluate side-chains 211 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 237 TRP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 237 TRP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 263 MET Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 58 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 60 optimal weight: 0.0980 chunk 54 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 chunk 49 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 GLN ** 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 = 0.3932 r_free = 0.3932 target = 0.124110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.099942 restraints weight = 12929.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.103415 restraints weight = 6499.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.105733 restraints weight = 4382.720| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5466 Z= 0.205 Angle : 0.665 7.474 7460 Z= 0.330 Chirality : 0.037 0.185 920 Planarity : 0.003 0.022 910 Dihedral : 3.574 20.194 748 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.47 % Allowed : 34.17 % Favored : 61.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.13 (0.32), residues: 682 helix: 3.09 (0.20), residues: 630 sheet: None (None), residues: 0 loop : -2.69 (0.72), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 234 HIS 0.000 0.000 HIS A 304 PHE 0.021 0.001 PHE B 247 TYR 0.029 0.002 TYR A 258 ARG 0.003 0.000 ARG A 286 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2140.08 seconds wall clock time: 38 minutes 57.55 seconds (2337.55 seconds total)