Starting phenix.real_space_refine on Mon Sep 23 21:05:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x4s_22042/09_2024/6x4s_22042.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x4s_22042/09_2024/6x4s_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x4s_22042/09_2024/6x4s_22042.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x4s_22042/09_2024/6x4s_22042.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x4s_22042/09_2024/6x4s_22042.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x4s_22042/09_2024/6x4s_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-5461/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: 4.29, per 1000 atoms: 0.80 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: 1.62 Conformation dependent library (CDL) restraints added in 760.3 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: 0.32 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: 1.19 Time building geometry restraints manager: 1.70 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: 1.740 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.530 Find NCS groups from input model: 0.290 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.660 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 5 poor density : 262 time to evaluate : 0.624 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: 0.2139 time to fit residues: 68.4782 Evaluate side-chains 207 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 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 fitting. rotamer outliers: 19 poor density : 228 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 GLU cc_start: 0.9135 (tp30) cc_final: 0.8910 (tp30) REVERT: A 220 LYS cc_start: 0.8920 (mmmt) cc_final: 0.8510 (mtmt) REVERT: A 272 TYR cc_start: 0.8524 (t80) cc_final: 0.8227 (t80) REVERT: A 328 GLU cc_start: 0.8513 (tt0) cc_final: 0.8251 (tt0) REVERT: B 211 GLN cc_start: 0.8856 (mt0) cc_final: 0.8569 (mm-40) REVERT: B 219 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8067 (pt0) REVERT: B 243 MET cc_start: 0.7400 (mtp) cc_final: 0.6934 (mmt) REVERT: B 253 LEU cc_start: 0.8783 (mt) cc_final: 0.8476 (mp) REVERT: B 263 MET cc_start: 0.8167 (mmm) cc_final: 0.7945 (ttm) REVERT: B 316 GLN cc_start: 0.7778 (pt0) cc_final: 0.7548 (tt0) REVERT: B 321 LYS cc_start: 0.9039 (mmmm) cc_final: 0.8621 (mmmm) REVERT: C 221 LYS cc_start: 0.9003 (ttmt) cc_final: 0.8762 (ttpt) REVERT: C 235 MET cc_start: 0.8041 (tpp) cc_final: 0.7622 (tmm) REVERT: C 247 PHE cc_start: 0.9269 (t80) cc_final: 0.8924 (t80) REVERT: D 213 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8656 (tm-30) REVERT: F 70 LEU cc_start: 0.8904 (tt) cc_final: 0.8439 (mp) REVERT: H 70 LEU cc_start: 0.8944 (tt) cc_final: 0.8543 (mp) outliers start: 19 outliers final: 12 residues processed: 237 average time/residue: 0.2000 time to fit residues: 58.1255 Evaluate side-chains 221 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 209 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 34 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 55 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 GLN B 226 GLN C 229 ASN C 315 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5466 Z= 0.233 Angle : 0.611 7.627 7460 Z= 0.310 Chirality : 0.036 0.154 920 Planarity : 0.003 0.025 910 Dihedral : 3.520 15.563 748 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 5.63 % Allowed : 29.13 % Favored : 65.24 % 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: 3.09 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.71 (0.79), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 260 HIS 0.004 0.001 HIS C 195 PHE 0.021 0.001 PHE B 247 TYR 0.017 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 242 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 213 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 GLU cc_start: 0.9097 (tp30) cc_final: 0.8874 (tp30) REVERT: A 220 LYS cc_start: 0.8947 (mmmt) cc_final: 0.8619 (mtmt) REVERT: A 243 MET cc_start: 0.8491 (ttm) cc_final: 0.8155 (ttm) REVERT: B 219 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8081 (pt0) REVERT: B 243 MET cc_start: 0.7408 (mtp) cc_final: 0.7046 (mmt) REVERT: B 253 LEU cc_start: 0.8800 (mt) cc_final: 0.8535 (mp) REVERT: B 260 TRP cc_start: 0.7977 (t-100) cc_final: 0.7402 (t-100) REVERT: B 263 MET cc_start: 0.8248 (mmm) cc_final: 0.7972 (ttm) REVERT: B 316 GLN cc_start: 0.7906 (pt0) cc_final: 0.7552 (tt0) REVERT: C 221 LYS cc_start: 0.8994 (ttmt) cc_final: 0.8720 (ttmt) REVERT: C 226 GLN cc_start: 0.8906 (tt0) cc_final: 0.8653 (tt0) REVERT: C 235 MET cc_start: 0.8061 (tpp) cc_final: 0.7588 (tmm) REVERT: C 246 GLN cc_start: 0.9139 (tt0) cc_final: 0.8890 (tt0) REVERT: D 213 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8588 (tm-30) REVERT: F 70 LEU cc_start: 0.8982 (tt) cc_final: 0.8530 (mp) REVERT: H 70 LEU cc_start: 0.8998 (tt) cc_final: 0.8628 (mp) outliers start: 29 outliers final: 20 residues processed: 225 average time/residue: 0.2028 time to fit residues: 55.9812 Evaluate side-chains 225 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 205 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 274 THR 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 62 optimal weight: 0.0770 chunk 65 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4514 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= 0.229 Angle : 0.624 8.675 7460 Z= 0.313 Chirality : 0.035 0.139 920 Planarity : 0.003 0.023 910 Dihedral : 3.442 15.508 748 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 5.63 % Allowed : 32.62 % Favored : 61.75 % 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: 4.33 (0.32), residues: 682 helix: 3.14 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -2.46 (0.90), residues: 44 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 0.020 0.001 PHE B 247 TYR 0.019 0.002 TYR A 317 ARG 0.006 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 238 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 209 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8922 (mmmt) cc_final: 0.8657 (ttmt) REVERT: A 243 MET cc_start: 0.8523 (ttm) cc_final: 0.8188 (ttm) REVERT: B 219 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8140 (pt0) REVERT: B 226 GLN cc_start: 0.8138 (pp30) cc_final: 0.7712 (pp30) REVERT: B 234 TRP cc_start: 0.8040 (t60) cc_final: 0.7752 (t60) REVERT: B 243 MET cc_start: 0.7528 (mtp) cc_final: 0.7024 (mmt) REVERT: B 253 LEU cc_start: 0.8826 (mt) cc_final: 0.8528 (mp) REVERT: B 260 TRP cc_start: 0.8097 (t-100) cc_final: 0.7770 (t-100) REVERT: B 263 MET cc_start: 0.8148 (mmm) cc_final: 0.7936 (ttm) REVERT: B 316 GLN cc_start: 0.7961 (pt0) cc_final: 0.7635 (tt0) REVERT: B 318 ASN cc_start: 0.8700 (m-40) cc_final: 0.8394 (m110) REVERT: B 321 LYS cc_start: 0.9077 (mmmm) cc_final: 0.8778 (mmtp) REVERT: C 235 MET cc_start: 0.8128 (tpp) cc_final: 0.7502 (tmm) REVERT: C 263 MET cc_start: 0.8050 (tpp) cc_final: 0.7846 (tpp) REVERT: D 213 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8673 (tm-30) REVERT: D 326 LYS cc_start: 0.8810 (tppt) cc_final: 0.8408 (tppt) REVERT: D 329 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8355 (tt) REVERT: F 70 LEU cc_start: 0.9056 (tt) cc_final: 0.8561 (mp) REVERT: H 70 LEU cc_start: 0.8976 (tt) cc_final: 0.8602 (mp) outliers start: 29 outliers final: 20 residues processed: 220 average time/residue: 0.1970 time to fit residues: 53.0892 Evaluate side-chains 218 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 197 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 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 C residue 322 ASP 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 58 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 226 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5466 Z= 0.231 Angle : 0.606 7.785 7460 Z= 0.302 Chirality : 0.035 0.139 920 Planarity : 0.003 0.021 910 Dihedral : 3.380 14.796 748 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 6.02 % Allowed : 31.84 % 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: 3.21 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -2.87 (0.81), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 260 HIS 0.001 0.000 HIS A 304 PHE 0.017 0.001 PHE B 247 TYR 0.018 0.002 TYR A 317 ARG 0.004 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 237 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 206 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8913 (mmmt) cc_final: 0.8648 (ttmt) REVERT: B 226 GLN cc_start: 0.8223 (pp30) cc_final: 0.7769 (pp30) REVERT: B 234 TRP cc_start: 0.8074 (t60) cc_final: 0.7823 (t60) REVERT: B 243 MET cc_start: 0.7556 (mtp) cc_final: 0.7030 (mmt) REVERT: B 253 LEU cc_start: 0.8851 (mt) cc_final: 0.8512 (mp) REVERT: B 263 MET cc_start: 0.8229 (mmm) cc_final: 0.7913 (ttm) REVERT: B 316 GLN cc_start: 0.8021 (pt0) cc_final: 0.7668 (tt0) REVERT: B 318 ASN cc_start: 0.8736 (m-40) cc_final: 0.8463 (m110) REVERT: B 321 LYS cc_start: 0.9103 (mmmm) cc_final: 0.8902 (mmtm) REVERT: C 218 GLU cc_start: 0.8946 (tp30) cc_final: 0.8714 (tp30) REVERT: C 220 LYS cc_start: 0.8911 (mmmt) cc_final: 0.8590 (ttmt) REVERT: C 235 MET cc_start: 0.8178 (tpp) cc_final: 0.7581 (tmm) REVERT: D 213 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8655 (tm-30) REVERT: D 329 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8381 (tt) REVERT: F 70 LEU cc_start: 0.9019 (tt) cc_final: 0.8545 (mp) REVERT: H 70 LEU cc_start: 0.8965 (tt) cc_final: 0.8635 (mp) outliers start: 31 outliers final: 24 residues processed: 218 average time/residue: 0.1822 time to fit residues: 49.1741 Evaluate side-chains 225 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 200 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 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 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 263 MET 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5466 Z= 0.252 Angle : 0.635 7.753 7460 Z= 0.315 Chirality : 0.036 0.147 920 Planarity : 0.003 0.022 910 Dihedral : 3.369 15.455 748 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 5.24 % Allowed : 32.04 % Favored : 62.72 % 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: 4.31 (0.32), residues: 682 helix: 3.18 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -2.80 (0.83), 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 0.022 0.001 PHE B 247 TYR 0.017 0.002 TYR A 317 ARG 0.003 0.000 ARG F 69 *********************** 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 fitting. rotamer outliers: 27 poor density : 204 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8916 (mmmt) cc_final: 0.8607 (ttmt) REVERT: A 243 MET cc_start: 0.8628 (ttm) cc_final: 0.8208 (ttm) REVERT: A 257 GLU cc_start: 0.8073 (tt0) cc_final: 0.7776 (tt0) REVERT: B 226 GLN cc_start: 0.8217 (pp30) cc_final: 0.7736 (pp30) REVERT: B 243 MET cc_start: 0.7606 (mtp) cc_final: 0.7064 (mmt) REVERT: B 253 LEU cc_start: 0.8870 (mt) cc_final: 0.8520 (mp) REVERT: B 263 MET cc_start: 0.8235 (mmm) cc_final: 0.7914 (ttm) REVERT: B 313 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7378 (m-30) REVERT: B 316 GLN cc_start: 0.8053 (pt0) cc_final: 0.7696 (tt0) REVERT: B 318 ASN cc_start: 0.8740 (m-40) cc_final: 0.8445 (m110) REVERT: C 220 LYS cc_start: 0.8911 (mmmt) cc_final: 0.8620 (ttmt) REVERT: C 235 MET cc_start: 0.8192 (tpp) cc_final: 0.7583 (tmm) REVERT: C 246 GLN cc_start: 0.9137 (tt0) cc_final: 0.8854 (tt0) REVERT: D 213 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8637 (tm-30) REVERT: D 257 GLU cc_start: 0.8276 (mp0) cc_final: 0.8029 (mp0) REVERT: D 329 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8400 (tt) REVERT: F 70 LEU cc_start: 0.9037 (tt) cc_final: 0.8578 (mp) REVERT: H 70 LEU cc_start: 0.8970 (tt) cc_final: 0.8641 (mp) outliers start: 27 outliers final: 24 residues processed: 213 average time/residue: 0.1946 time to fit residues: 51.0850 Evaluate side-chains 224 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 198 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 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 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 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 H residue 69 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** G 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5466 Z= 0.263 Angle : 0.646 9.251 7460 Z= 0.323 Chirality : 0.037 0.151 920 Planarity : 0.003 0.023 910 Dihedral : 3.382 16.210 748 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 6.21 % Allowed : 32.82 % 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: 4.24 (0.32), residues: 682 helix: 3.13 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -2.77 (0.84), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 234 HIS 0.001 0.000 HIS A 304 PHE 0.021 0.001 PHE B 247 TYR 0.016 0.002 TYR A 317 ARG 0.007 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 232 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 200 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 LEU cc_start: 0.9054 (tp) cc_final: 0.8835 (tt) REVERT: A 220 LYS cc_start: 0.8943 (mmmt) cc_final: 0.8637 (ttmt) REVERT: A 243 MET cc_start: 0.8699 (ttm) cc_final: 0.8225 (ttm) REVERT: A 257 GLU cc_start: 0.7923 (tt0) cc_final: 0.7663 (tt0) REVERT: B 226 GLN cc_start: 0.8265 (pp30) cc_final: 0.8010 (pp30) REVERT: B 243 MET cc_start: 0.7577 (mtp) cc_final: 0.7089 (mmt) REVERT: B 253 LEU cc_start: 0.8898 (mt) cc_final: 0.8606 (mp) REVERT: B 263 MET cc_start: 0.8357 (mmm) cc_final: 0.7997 (ttt) REVERT: B 313 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7356 (m-30) REVERT: B 316 GLN cc_start: 0.8089 (pt0) cc_final: 0.7730 (tt0) REVERT: B 318 ASN cc_start: 0.8754 (m-40) cc_final: 0.8451 (m110) REVERT: C 219 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7926 (mt-10) REVERT: C 220 LYS cc_start: 0.8904 (mmmt) cc_final: 0.8621 (ttmt) REVERT: C 235 MET cc_start: 0.8186 (tpp) cc_final: 0.7498 (tmm) REVERT: C 246 GLN cc_start: 0.9101 (tt0) cc_final: 0.8825 (tt0) REVERT: D 213 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8669 (tm-30) REVERT: D 329 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8507 (tt) REVERT: F 70 LEU cc_start: 0.9067 (tt) cc_final: 0.8686 (mp) REVERT: G 69 ARG cc_start: 0.6138 (ptp-170) cc_final: 0.5536 (ttm170) REVERT: H 70 LEU cc_start: 0.9036 (tt) cc_final: 0.8597 (mp) outliers start: 32 outliers final: 28 residues processed: 215 average time/residue: 0.1831 time to fit residues: 48.9011 Evaluate side-chains 223 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 193 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 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 245 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 322 ASP 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 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 H residue 69 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 0.2980 chunk 41 optimal weight: 0.0470 chunk 44 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 chunk 51 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 62 optimal weight: 0.0370 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 overall best weight: 0.2556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5466 Z= 0.176 Angle : 0.615 8.884 7460 Z= 0.303 Chirality : 0.035 0.182 920 Planarity : 0.003 0.024 910 Dihedral : 3.406 17.583 748 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.88 % Allowed : 35.73 % Favored : 60.39 % 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: 4.33 (0.32), residues: 682 helix: 3.25 (0.20), residues: 626 sheet: None (None), residues: 0 loop : -2.62 (0.76), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 260 HIS 0.000 0.000 HIS A 304 PHE 0.018 0.001 PHE B 247 TYR 0.015 0.001 TYR A 317 ARG 0.006 0.001 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 225 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 205 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8854 (mmmt) cc_final: 0.8564 (ttmt) REVERT: A 243 MET cc_start: 0.8649 (ttm) cc_final: 0.8301 (ttm) REVERT: A 257 GLU cc_start: 0.7863 (tt0) cc_final: 0.7660 (tt0) REVERT: A 321 LYS cc_start: 0.8716 (mmmm) cc_final: 0.8135 (ttmm) REVERT: B 226 GLN cc_start: 0.8187 (pp30) cc_final: 0.7723 (pp30) REVERT: B 243 MET cc_start: 0.7592 (mtp) cc_final: 0.7050 (mmt) REVERT: B 253 LEU cc_start: 0.8876 (mt) cc_final: 0.8617 (mp) REVERT: B 263 MET cc_start: 0.8222 (mmm) cc_final: 0.7866 (ttt) REVERT: B 313 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7297 (m-30) REVERT: B 316 GLN cc_start: 0.7901 (pt0) cc_final: 0.7552 (tt0) REVERT: B 318 ASN cc_start: 0.8743 (m-40) cc_final: 0.8456 (m110) REVERT: C 213 GLU cc_start: 0.9043 (tp30) cc_final: 0.8793 (tp30) REVERT: C 219 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7933 (mt-10) REVERT: C 220 LYS cc_start: 0.8898 (mmmt) cc_final: 0.8627 (ttmt) REVERT: C 235 MET cc_start: 0.8092 (tpp) cc_final: 0.7390 (tmm) REVERT: C 246 GLN cc_start: 0.9091 (tt0) cc_final: 0.8786 (tt0) REVERT: D 213 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8539 (tm-30) REVERT: D 317 TYR cc_start: 0.9097 (t80) cc_final: 0.8873 (t80) REVERT: D 329 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8493 (tt) REVERT: F 70 LEU cc_start: 0.9055 (tt) cc_final: 0.8683 (mp) REVERT: H 70 LEU cc_start: 0.9028 (tt) cc_final: 0.8629 (mp) outliers start: 20 outliers final: 17 residues processed: 210 average time/residue: 0.1951 time to fit residues: 50.6249 Evaluate side-chains 215 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 196 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 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 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 245 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain D residue 253 LEU 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 26 optimal weight: 0.0770 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 57 optimal weight: 0.0970 chunk 60 optimal weight: 0.3980 chunk 40 optimal weight: 0.0670 chunk 64 optimal weight: 0.0030 chunk 39 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.5554 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= 0.183 Angle : 0.653 8.414 7460 Z= 0.321 Chirality : 0.035 0.174 920 Planarity : 0.003 0.038 910 Dihedral : 3.419 16.295 748 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 4.27 % Allowed : 35.53 % Favored : 60.19 % 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: 4.33 (0.32), residues: 682 helix: 3.25 (0.20), residues: 626 sheet: None (None), residues: 0 loop : -2.60 (0.78), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 260 HIS 0.000 0.000 HIS A 304 PHE 0.017 0.001 PHE B 247 TYR 0.015 0.001 TYR A 317 ARG 0.010 0.001 ARG A 286 *********************** 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 220 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 198 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8779 (mmmt) cc_final: 0.8492 (ttmt) REVERT: A 243 MET cc_start: 0.8699 (ttm) cc_final: 0.8349 (ttm) REVERT: A 321 LYS cc_start: 0.8694 (mmmm) cc_final: 0.8113 (ttmm) REVERT: B 226 GLN cc_start: 0.8163 (pp30) cc_final: 0.7687 (pp30) REVERT: B 253 LEU cc_start: 0.8887 (mt) cc_final: 0.8632 (mp) REVERT: B 263 MET cc_start: 0.8115 (mmm) cc_final: 0.7764 (ttt) REVERT: B 313 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7316 (m-30) REVERT: B 316 GLN cc_start: 0.7841 (pt0) cc_final: 0.7596 (tt0) REVERT: B 318 ASN cc_start: 0.8745 (m-40) cc_final: 0.8477 (m110) REVERT: C 219 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7910 (mt-10) REVERT: C 220 LYS cc_start: 0.8883 (mmmt) cc_final: 0.8624 (ttmt) REVERT: C 235 MET cc_start: 0.8039 (tpp) cc_final: 0.7264 (tmm) REVERT: C 246 GLN cc_start: 0.9032 (tt0) cc_final: 0.8738 (tt0) REVERT: D 213 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8493 (tm-30) REVERT: D 329 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8492 (tt) REVERT: E 79 LEU cc_start: 0.8050 (tt) cc_final: 0.7812 (mt) REVERT: F 70 LEU cc_start: 0.9050 (tt) cc_final: 0.8681 (mp) REVERT: H 70 LEU cc_start: 0.9001 (tt) cc_final: 0.8600 (mp) outliers start: 22 outliers final: 18 residues processed: 206 average time/residue: 0.2131 time to fit residues: 54.6408 Evaluate side-chains 217 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 197 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 294 VAL Chi-restraints excluded: chain A residue 323 GLN 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 B residue 313 ASP Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain D residue 253 LEU 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 67 optimal weight: 0.9980 chunk 62 optimal weight: 0.0270 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 33 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 chunk 49 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 overall best weight: 0.3238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5466 Z= 0.197 Angle : 0.651 8.506 7460 Z= 0.320 Chirality : 0.037 0.242 920 Planarity : 0.003 0.044 910 Dihedral : 3.408 15.876 748 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.27 % Allowed : 36.12 % Favored : 59.61 % 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: 3.21 (0.20), residues: 626 sheet: None (None), residues: 0 loop : -2.54 (0.80), 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 A 317 ARG 0.011 0.001 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 220 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 198 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8787 (mmmt) cc_final: 0.8487 (ttmt) REVERT: A 243 MET cc_start: 0.8680 (ttm) cc_final: 0.8324 (ttm) REVERT: B 226 GLN cc_start: 0.8176 (pp30) cc_final: 0.7681 (pp30) REVERT: B 253 LEU cc_start: 0.8899 (mt) cc_final: 0.8650 (mp) REVERT: B 257 GLU cc_start: 0.7980 (mp0) cc_final: 0.7664 (mp0) REVERT: B 263 MET cc_start: 0.8158 (mmm) cc_final: 0.7794 (ttt) REVERT: B 313 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7330 (m-30) REVERT: B 316 GLN cc_start: 0.7924 (pt0) cc_final: 0.7611 (tt0) REVERT: B 318 ASN cc_start: 0.8751 (m-40) cc_final: 0.8470 (m110) REVERT: C 219 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7919 (mt-10) REVERT: C 220 LYS cc_start: 0.8807 (mmmt) cc_final: 0.8566 (ttmt) REVERT: C 235 MET cc_start: 0.8091 (tpp) cc_final: 0.7334 (tmm) REVERT: C 246 GLN cc_start: 0.9028 (tt0) cc_final: 0.8780 (tt0) REVERT: D 213 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8493 (tm-30) REVERT: D 258 TYR cc_start: 0.8776 (m-80) cc_final: 0.8372 (m-10) REVERT: D 281 TYR cc_start: 0.7478 (t80) cc_final: 0.7175 (t80) REVERT: D 329 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8508 (tt) REVERT: E 79 LEU cc_start: 0.8065 (tt) cc_final: 0.7839 (mt) REVERT: F 70 LEU cc_start: 0.9051 (tt) cc_final: 0.8682 (mp) REVERT: H 70 LEU cc_start: 0.8989 (tt) cc_final: 0.8593 (mp) outliers start: 22 outliers final: 18 residues processed: 205 average time/residue: 0.1922 time to fit residues: 48.3528 Evaluate side-chains 211 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 191 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 294 VAL Chi-restraints excluded: chain A residue 323 GLN 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 B residue 313 ASP Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain D residue 253 LEU 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 14 optimal weight: 0.1980 chunk 54 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 6 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 229 ASN A 315 ASN ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.124518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.100402 restraints weight = 12542.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.103895 restraints weight = 6298.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.106245 restraints weight = 4259.276| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.5657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5466 Z= 0.211 Angle : 0.674 8.786 7460 Z= 0.334 Chirality : 0.037 0.189 920 Planarity : 0.003 0.043 910 Dihedral : 3.427 16.141 748 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.27 % Allowed : 36.89 % Favored : 58.83 % 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: 3.17 (0.20), residues: 630 sheet: None (None), residues: 0 loop : -2.32 (0.85), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 234 HIS 0.001 0.000 HIS A 304 PHE 0.027 0.001 PHE C 247 TYR 0.027 0.002 TYR D 317 ARG 0.011 0.001 ARG A 286 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1584.82 seconds wall clock time: 28 minutes 52.39 seconds (1732.39 seconds total)