Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 14:23:47 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x4s_22042/12_2021/6x4s_22042.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x4s_22042/12_2021/6x4s_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_22042/12_2021/6x4s_22042.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x4s_22042/12_2021/6x4s_22042.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x4s_22042/12_2021/6x4s_22042.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x4s_22042/12_2021/6x4s_22042.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/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: 3.17, per 1000 atoms: 0.59 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 - 3.50 Amimo acid : False - 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: 2.27 Conformation dependent library (CDL) restraints added in 840.3 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: 0.14 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: 1.58 Time building geometry restraints manager: 2.44 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: 97.60 - 104.90: 56 104.90 - 112.19: 2915 112.19 - 119.49: 1683 119.49 - 126.78: 2729 126.78 - 134.08: 77 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 2.440 nonbonded pdb=" O VAL B 201 " pdb=" OG1 THR B 204 " model vdw 2.247 2.440 nonbonded pdb=" OE1 GLN D 246 " pdb=" OG1 THR D 274 " model vdw 2.289 2.440 ... (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 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 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. 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 Write .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.830 Check model and map are aligned: 0.080 Convert atoms to be neutral: 0.040 Process input model: 18.270 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.210 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 27.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 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 % 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 *********************** 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 : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 266 average time/residue: 0.2129 time to fit residues: 68.6386 Evaluate side-chains 203 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 0.656 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8802 ------------------------------------------------------------------------------- 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: 0.0980 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 0.2980 chunk 61 optimal weight: 5.9990 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 229 ASN ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN ** C 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN D 246 GLN D 315 ASN D 323 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 5466 Z= 0.224 Angle : 0.673 7.969 7460 Z= 0.338 Chirality : 0.037 0.177 920 Planarity : 0.004 0.028 910 Dihedral : 3.669 16.113 748 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer Outliers : 4.66 % 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: 3.82 (0.32), residues: 682 helix: 2.96 (0.20), residues: 624 sheet: None (None), residues: 0 loop : -3.07 (0.66), residues: 58 *********************** 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 246 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 222 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 232 average time/residue: 0.1951 time to fit residues: 55.7399 Evaluate side-chains 217 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 203 time to evaluate : 0.651 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0528 time to fit residues: 2.1570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** D 315 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4240 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= 0.257 Angle : 0.623 7.690 7460 Z= 0.318 Chirality : 0.036 0.167 920 Planarity : 0.003 0.029 910 Dihedral : 3.606 18.289 748 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer Outliers : 2.91 % 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: 4.10 (0.32), residues: 682 helix: 3.01 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -2.73 (0.82), residues: 44 *********************** 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 227 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 212 time to evaluate : 0.599 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 218 average time/residue: 0.1980 time to fit residues: 53.0358 Evaluate side-chains 205 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 199 time to evaluate : 0.657 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0671 time to fit residues: 1.5064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 GLN ** C 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 5466 Z= 0.242 Angle : 0.623 7.622 7460 Z= 0.315 Chirality : 0.035 0.151 920 Planarity : 0.003 0.022 910 Dihedral : 3.530 18.191 748 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer Outliers : 4.27 % 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: 636 sheet: None (None), residues: 0 loop : -3.02 (0.78), residues: 46 *********************** 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 230 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 208 time to evaluate : 0.677 Fit side-chains outliers start: 22 outliers final: 8 residues processed: 217 average time/residue: 0.1966 time to fit residues: 52.4374 Evaluate side-chains 202 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 194 time to evaluate : 0.661 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0524 time to fit residues: 1.6168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 chunk 56 optimal weight: 0.0770 chunk 45 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 GLN C 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4932 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= 0.196 Angle : 0.610 8.183 7460 Z= 0.302 Chirality : 0.034 0.152 920 Planarity : 0.003 0.023 910 Dihedral : 3.540 18.928 748 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer Outliers : 3.50 % 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: 3.14 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -2.79 (0.82), residues: 44 *********************** 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 219 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 201 time to evaluate : 0.574 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 210 average time/residue: 0.1877 time to fit residues: 48.7859 Evaluate side-chains 202 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 191 time to evaluate : 0.692 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0553 time to fit residues: 1.9617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 GLN C 315 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.5209 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= 0.258 Angle : 0.653 7.458 7460 Z= 0.325 Chirality : 0.036 0.141 920 Planarity : 0.003 0.021 910 Dihedral : 3.509 17.476 748 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer Outliers : 2.14 % 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: 4.11 (0.32), residues: 682 helix: 3.01 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -2.67 (0.85), residues: 44 *********************** 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 206 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 195 time to evaluate : 0.692 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 198 average time/residue: 0.1848 time to fit residues: 45.5298 Evaluate side-chains 197 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 188 time to evaluate : 0.651 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0555 time to fit residues: 1.7184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 41 optimal weight: 0.0060 chunk 39 optimal weight: 0.2980 chunk 30 optimal weight: 0.0980 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.5351 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= 0.187 Angle : 0.619 7.132 7460 Z= 0.307 Chirality : 0.035 0.180 920 Planarity : 0.003 0.040 910 Dihedral : 3.464 17.030 748 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer Outliers : 2.33 % 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: 4.28 (0.32), residues: 682 helix: 3.12 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -2.68 (0.87), residues: 44 *********************** 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 208 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 196 time to evaluate : 0.578 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 199 average time/residue: 0.1845 time to fit residues: 45.6640 Evaluate side-chains 193 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 186 time to evaluate : 0.511 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1088 time to fit residues: 1.8357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 0.8980 chunk 41 optimal weight: 0.0370 chunk 44 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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: 0.7606 moved from start: 0.5528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 5466 Z= 0.207 Angle : 0.644 7.459 7460 Z= 0.318 Chirality : 0.035 0.184 920 Planarity : 0.003 0.034 910 Dihedral : 3.429 16.789 748 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer Outliers : 1.55 % 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: 4.25 (0.32), residues: 682 helix: 3.11 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -2.73 (0.90), residues: 44 *********************** 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 196 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 188 time to evaluate : 0.602 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 190 average time/residue: 0.1873 time to fit residues: 44.3585 Evaluate side-chains 190 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 185 time to evaluate : 0.646 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0629 time to fit residues: 1.3954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 57 optimal weight: 0.3980 chunk 60 optimal weight: 0.0570 chunk 40 optimal weight: 0.4980 chunk 64 optimal weight: 0.0770 chunk 39 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 315 ASN E 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.5617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 5466 Z= 0.195 Angle : 0.654 7.366 7460 Z= 0.320 Chirality : 0.035 0.180 920 Planarity : 0.003 0.031 910 Dihedral : 3.434 17.726 748 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer Outliers : 0.78 % 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: 4.28 (0.32), residues: 682 helix: 3.12 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -2.71 (0.90), residues: 44 *********************** 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 193 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 189 time to evaluate : 0.636 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 191 average time/residue: 0.1908 time to fit residues: 45.3206 Evaluate side-chains 187 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 186 time to evaluate : 0.684 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0525 time to fit residues: 0.9889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 0.7980 chunk 62 optimal weight: 0.0050 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN D 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.5744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 5466 Z= 0.237 Angle : 0.687 8.915 7460 Z= 0.338 Chirality : 0.037 0.204 920 Planarity : 0.003 0.031 910 Dihedral : 3.393 16.494 748 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer Outliers : 1.17 % 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: 4.20 (0.32), residues: 682 helix: 3.07 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -2.79 (0.89), residues: 44 ********************** 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 192 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 186 time to evaluate : 0.655 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 189 average time/residue: 0.1886 time to fit residues: 44.4323 Evaluate side-chains 187 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 185 time to evaluate : 0.657 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0646 time to fit residues: 1.0994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 0.0980 chunk 54 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 chunk 55 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 39 optimal weight: 0.0980 chunk 61 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN E 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.126227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.102244 restraints weight = 13119.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.105733 restraints weight = 6747.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.107997 restraints weight = 4596.146| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.5820 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= 0.200 Angle : 0.682 12.221 7460 Z= 0.333 Chirality : 0.037 0.202 920 Planarity : 0.003 0.032 910 Dihedral : 3.445 16.498 748 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 0.78 % 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: 4.19 (0.32), residues: 682 helix: 3.06 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -2.62 (0.93), residues: 44 =============================================================================== Job complete usr+sys time: 1457.44 seconds wall clock time: 27 minutes 10.18 seconds (1630.18 seconds total)