Starting phenix.real_space_refine on Sat Apr 6 01:13:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2m_35950/04_2024/8j2m_35950_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2m_35950/04_2024/8j2m_35950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2m_35950/04_2024/8j2m_35950.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2m_35950/04_2024/8j2m_35950.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2m_35950/04_2024/8j2m_35950_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2m_35950/04_2024/8j2m_35950_updated.pdb" } resolution = 3.4 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= 0.019 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 P 2 5.49 5 S 22 5.16 5 C 4376 2.51 5 N 1038 2.21 5 O 1136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 157": "OE1" <-> "OE2" Residue "A PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 363": "OE1" <-> "OE2" Residue "A ARG 373": "NH1" <-> "NH2" Residue "A PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 157": "OE1" <-> "OE2" Residue "B PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "B PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 363": "OE1" <-> "OE2" Residue "B ARG 373": "NH1" <-> "NH2" Residue "B PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6574 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3244 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 9, 'TRANS': 414} Chain: "B" Number of atoms: 3244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3244 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 9, 'TRANS': 414} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'46E': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'46E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.96, per 1000 atoms: 0.60 Number of scatterers: 6574 At special positions: 0 Unit cell: (104.94, 72.08, 69.96, 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) S 22 16.00 P 2 15.00 O 1136 8.00 N 1038 7.00 C 4376 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 Amino 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: 2.61 Conformation dependent library (CDL) restraints added in 1.3 seconds 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1536 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 0 sheets defined 79.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 8 through 27 removed outlier: 4.115A pdb=" N VAL A 12 " --> pdb=" O PRO A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 52 Processing helix chain 'A' and resid 61 through 69 Processing helix chain 'A' and resid 73 through 83 removed outlier: 3.932A pdb=" N PHE A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Proline residue: A 82 - end of helix Processing helix chain 'A' and resid 85 through 91 Processing helix chain 'A' and resid 94 through 108 removed outlier: 4.528A pdb=" N LYS A 99 " --> pdb=" O HIS A 95 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ALA A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLN A 103 " --> pdb=" O LYS A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 126 Processing helix chain 'A' and resid 133 through 144 Processing helix chain 'A' and resid 149 through 157 Processing helix chain 'A' and resid 162 through 191 removed outlier: 3.723A pdb=" N SER A 172 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 228 removed outlier: 3.685A pdb=" N SER A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA A 211 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 252 removed outlier: 3.564A pdb=" N PHE A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE A 249 " --> pdb=" O TYR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 272 Processing helix chain 'A' and resid 274 through 277 No H-bonds generated for 'chain 'A' and resid 274 through 277' Processing helix chain 'A' and resid 280 through 314 removed outlier: 3.604A pdb=" N SER A 285 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE A 289 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE A 296 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A 300 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 301 " --> pdb=" O ASN A 298 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE A 302 " --> pdb=" O THR A 299 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 303 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 304 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 354 Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 361 through 368 Processing helix chain 'A' and resid 375 through 389 removed outlier: 3.657A pdb=" N LEU A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 427 removed outlier: 3.501A pdb=" N PHE A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER A 420 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN A 423 " --> pdb=" O GLY A 419 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 27 removed outlier: 4.115A pdb=" N VAL B 12 " --> pdb=" O PRO B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 52 Processing helix chain 'B' and resid 61 through 69 Processing helix chain 'B' and resid 73 through 83 removed outlier: 3.932A pdb=" N PHE B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) Proline residue: B 82 - end of helix Processing helix chain 'B' and resid 85 through 91 Processing helix chain 'B' and resid 94 through 108 removed outlier: 4.528A pdb=" N LYS B 99 " --> pdb=" O HIS B 95 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ALA B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLN B 103 " --> pdb=" O LYS B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 126 Processing helix chain 'B' and resid 133 through 144 Processing helix chain 'B' and resid 149 through 157 Processing helix chain 'B' and resid 162 through 191 removed outlier: 3.723A pdb=" N SER B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 228 removed outlier: 3.685A pdb=" N SER B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA B 211 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY B 215 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU B 216 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 252 removed outlier: 3.564A pdb=" N PHE B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE B 249 " --> pdb=" O TYR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 272 Processing helix chain 'B' and resid 274 through 277 No H-bonds generated for 'chain 'B' and resid 274 through 277' Processing helix chain 'B' and resid 280 through 314 removed outlier: 3.603A pdb=" N SER B 285 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE B 289 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE B 296 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU B 300 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE B 301 " --> pdb=" O ASN B 298 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE B 302 " --> pdb=" O THR B 299 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 303 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 304 " --> pdb=" O ILE B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 354 Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 361 through 368 Processing helix chain 'B' and resid 375 through 389 removed outlier: 3.656A pdb=" N LEU B 380 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 427 removed outlier: 3.500A pdb=" N PHE B 405 " --> pdb=" O THR B 401 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER B 420 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN B 423 " --> pdb=" O GLY B 419 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1230 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: 1.76 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 998 1.29 - 1.42: 1752 1.42 - 1.55: 3920 1.55 - 1.68: 6 1.68 - 1.81: 42 Bond restraints: 6718 Sorted by residual: bond pdb=" C MET B 174 " pdb=" O MET B 174 " ideal model delta sigma weight residual 1.236 1.163 0.072 1.29e-02 6.01e+03 3.14e+01 bond pdb=" C MET A 174 " pdb=" O MET A 174 " ideal model delta sigma weight residual 1.236 1.163 0.072 1.29e-02 6.01e+03 3.14e+01 bond pdb=" N PRO A 148 " pdb=" CD PRO A 148 " ideal model delta sigma weight residual 1.473 1.415 0.058 1.40e-02 5.10e+03 1.70e+01 bond pdb=" N PRO B 148 " pdb=" CD PRO B 148 " ideal model delta sigma weight residual 1.473 1.415 0.058 1.40e-02 5.10e+03 1.70e+01 bond pdb=" N HIS B 323 " pdb=" CA HIS B 323 " ideal model delta sigma weight residual 1.456 1.504 -0.048 1.22e-02 6.72e+03 1.55e+01 ... (remaining 6713 not shown) Histogram of bond angle deviations from ideal: 97.95 - 105.21: 104 105.21 - 112.48: 3370 112.48 - 119.74: 2661 119.74 - 127.00: 2913 127.00 - 134.27: 66 Bond angle restraints: 9114 Sorted by residual: angle pdb=" N THR B 422 " pdb=" CA THR B 422 " pdb=" C THR B 422 " ideal model delta sigma weight residual 111.71 102.71 9.00 1.15e+00 7.56e-01 6.13e+01 angle pdb=" N THR A 422 " pdb=" CA THR A 422 " pdb=" C THR A 422 " ideal model delta sigma weight residual 111.71 102.72 8.99 1.15e+00 7.56e-01 6.12e+01 angle pdb=" N ILE B 339 " pdb=" CA ILE B 339 " pdb=" C ILE B 339 " ideal model delta sigma weight residual 110.42 103.75 6.67 9.60e-01 1.09e+00 4.83e+01 angle pdb=" N ILE A 339 " pdb=" CA ILE A 339 " pdb=" C ILE A 339 " ideal model delta sigma weight residual 110.42 103.77 6.65 9.60e-01 1.09e+00 4.80e+01 angle pdb=" N MET B 402 " pdb=" CA MET B 402 " pdb=" C MET B 402 " ideal model delta sigma weight residual 111.11 118.91 -7.80 1.20e+00 6.94e-01 4.23e+01 ... (remaining 9109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.80: 3736 33.80 - 67.59: 116 67.59 - 101.39: 20 101.39 - 135.18: 2 135.18 - 168.98: 6 Dihedral angle restraints: 3880 sinusoidal: 1478 harmonic: 2402 Sorted by residual: dihedral pdb=" C PHE A 302 " pdb=" N PHE A 302 " pdb=" CA PHE A 302 " pdb=" CB PHE A 302 " ideal model delta harmonic sigma weight residual -122.60 -135.99 13.39 0 2.50e+00 1.60e-01 2.87e+01 dihedral pdb=" C PHE B 302 " pdb=" N PHE B 302 " pdb=" CA PHE B 302 " pdb=" CB PHE B 302 " ideal model delta harmonic sigma weight residual -122.60 -135.99 13.39 0 2.50e+00 1.60e-01 2.87e+01 dihedral pdb=" N HIS A 427 " pdb=" C HIS A 427 " pdb=" CA HIS A 427 " pdb=" CB HIS A 427 " ideal model delta harmonic sigma weight residual 122.80 134.31 -11.51 0 2.50e+00 1.60e-01 2.12e+01 ... (remaining 3877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 855 0.083 - 0.165: 189 0.165 - 0.248: 42 0.248 - 0.330: 8 0.330 - 0.413: 6 Chirality restraints: 1100 Sorted by residual: chirality pdb=" CA PHE A 302 " pdb=" N PHE A 302 " pdb=" C PHE A 302 " pdb=" CB PHE A 302 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CA PHE B 302 " pdb=" N PHE B 302 " pdb=" C PHE B 302 " pdb=" CB PHE B 302 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CA HIS A 427 " pdb=" N HIS A 427 " pdb=" C HIS A 427 " pdb=" CB HIS A 427 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 ... (remaining 1097 not shown) Planarity restraints: 1098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 316 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.52e+00 pdb=" C ASN A 316 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN A 316 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN A 317 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 316 " -0.012 2.00e-02 2.50e+03 2.53e-02 6.38e+00 pdb=" C ASN B 316 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN B 316 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN B 317 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 297 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.76e+00 pdb=" C ALA A 297 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA A 297 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN A 298 " 0.015 2.00e-02 2.50e+03 ... (remaining 1095 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 118 2.68 - 3.23: 6793 3.23 - 3.79: 10306 3.79 - 4.34: 13953 4.34 - 4.90: 22505 Nonbonded interactions: 53675 Sorted by model distance: nonbonded pdb=" O THR B 146 " pdb=" OD1 ASP B 147 " model vdw 2.121 3.040 nonbonded pdb=" O THR A 146 " pdb=" OD1 ASP A 147 " model vdw 2.122 3.040 nonbonded pdb=" O GLY B 140 " pdb=" OG SER B 144 " model vdw 2.267 2.440 nonbonded pdb=" O GLY A 140 " pdb=" OG SER A 144 " model vdw 2.267 2.440 nonbonded pdb=" O PHE A 118 " pdb=" OG SER A 121 " model vdw 2.317 2.440 ... (remaining 53670 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' selection = chain 'B' } 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 individual isotropic 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.700 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.140 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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 : 0.009 0.072 6718 Z= 0.616 Angle : 1.363 9.961 9114 Z= 1.008 Chirality : 0.079 0.413 1100 Planarity : 0.006 0.057 1098 Dihedral : 18.826 168.976 2344 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.91 % Allowed : 9.45 % Favored : 87.65 % Cbeta Deviations : 1.30 % 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: -2.01 (0.26), residues: 844 helix: -1.02 (0.18), residues: 678 sheet: None (None), residues: 0 loop : -1.90 (0.37), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 68 HIS 0.005 0.001 HIS B 95 PHE 0.015 0.002 PHE A 405 TYR 0.014 0.002 TYR B 183 ARG 0.002 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 288 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.8126 (mp) cc_final: 0.7900 (mp) REVERT: A 234 ILE cc_start: 0.8150 (mm) cc_final: 0.7774 (mm) REVERT: B 40 LEU cc_start: 0.8452 (mt) cc_final: 0.8240 (mt) REVERT: B 124 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8058 (tptp) REVERT: B 275 LYS cc_start: 0.7133 (mmmt) cc_final: 0.6843 (mmmt) outliers start: 20 outliers final: 5 residues processed: 299 average time/residue: 0.1858 time to fit residues: 72.6730 Evaluate side-chains 197 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 191 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 337 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 175 ASN A 338 GLN B 56 HIS B 175 ASN B 418 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6718 Z= 0.209 Angle : 0.606 6.393 9114 Z= 0.321 Chirality : 0.038 0.126 1100 Planarity : 0.005 0.066 1098 Dihedral : 15.576 179.437 981 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 5.23 % Allowed : 20.06 % Favored : 74.71 % 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: -0.57 (0.26), residues: 844 helix: 0.06 (0.18), residues: 686 sheet: None (None), residues: 0 loop : -1.85 (0.41), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 68 HIS 0.007 0.001 HIS A 427 PHE 0.034 0.002 PHE B 405 TYR 0.023 0.002 TYR A 334 ARG 0.004 0.001 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 210 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 ASP cc_start: 0.7565 (t0) cc_final: 0.6971 (t0) REVERT: A 360 ASP cc_start: 0.7608 (m-30) cc_final: 0.7348 (m-30) REVERT: B 72 ASN cc_start: 0.7359 (m-40) cc_final: 0.6744 (m-40) outliers start: 36 outliers final: 22 residues processed: 230 average time/residue: 0.1441 time to fit residues: 46.7458 Evaluate side-chains 197 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 175 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 56 HIS Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 428 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 103 GLN B 27 HIS B 103 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6718 Z= 0.205 Angle : 0.599 7.314 9114 Z= 0.309 Chirality : 0.037 0.152 1100 Planarity : 0.005 0.068 1098 Dihedral : 14.078 158.755 972 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 5.52 % Allowed : 25.15 % Favored : 69.33 % 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: 0.13 (0.28), residues: 844 helix: 0.60 (0.19), residues: 676 sheet: None (None), residues: 0 loop : -1.76 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 68 HIS 0.008 0.001 HIS A 427 PHE 0.013 0.001 PHE B 278 TYR 0.023 0.002 TYR A 36 ARG 0.004 0.000 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 191 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8118 (tp) cc_final: 0.7902 (tp) REVERT: A 234 ILE cc_start: 0.8618 (mm) cc_final: 0.8339 (mm) REVERT: A 360 ASP cc_start: 0.7683 (m-30) cc_final: 0.7482 (m-30) outliers start: 38 outliers final: 24 residues processed: 210 average time/residue: 0.1486 time to fit residues: 45.0155 Evaluate side-chains 195 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 428 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.0970 chunk 57 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS A 56 HIS A 103 GLN ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6718 Z= 0.193 Angle : 0.589 7.702 9114 Z= 0.305 Chirality : 0.037 0.202 1100 Planarity : 0.005 0.067 1098 Dihedral : 12.993 136.684 970 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 5.23 % Allowed : 27.76 % Favored : 67.01 % 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: 0.27 (0.28), residues: 844 helix: 0.73 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -1.84 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 369 HIS 0.008 0.001 HIS A 427 PHE 0.011 0.001 PHE B 405 TYR 0.020 0.002 TYR A 36 ARG 0.002 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 183 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.7396 (m-80) REVERT: B 19 LEU cc_start: 0.7329 (tt) cc_final: 0.7059 (tp) REVERT: B 336 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7760 (m-80) outliers start: 36 outliers final: 27 residues processed: 203 average time/residue: 0.1403 time to fit residues: 40.5891 Evaluate side-chains 201 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 172 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 336 PHE Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 428 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.6980 chunk 46 optimal weight: 0.2980 chunk 1 optimal weight: 0.9990 chunk 60 optimal weight: 0.0570 chunk 33 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 72 optimal weight: 0.0570 chunk 20 optimal weight: 2.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 103 GLN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6718 Z= 0.174 Angle : 0.603 8.364 9114 Z= 0.304 Chirality : 0.037 0.175 1100 Planarity : 0.005 0.067 1098 Dihedral : 11.563 114.347 970 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 6.69 % Allowed : 27.33 % Favored : 65.99 % 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: 0.36 (0.28), residues: 844 helix: 0.84 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -2.00 (0.41), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 327 HIS 0.009 0.001 HIS A 427 PHE 0.010 0.001 PHE B 278 TYR 0.021 0.002 TYR B 36 ARG 0.002 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 202 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7318 (m-80) REVERT: B 336 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.7719 (m-80) outliers start: 46 outliers final: 25 residues processed: 224 average time/residue: 0.1676 time to fit residues: 53.9191 Evaluate side-chains 194 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 167 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 336 PHE Chi-restraints excluded: chain B residue 428 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6718 Z= 0.207 Angle : 0.647 8.747 9114 Z= 0.323 Chirality : 0.038 0.169 1100 Planarity : 0.005 0.069 1098 Dihedral : 11.048 112.341 970 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 5.23 % Allowed : 29.22 % Favored : 65.55 % 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: 0.43 (0.28), residues: 844 helix: 0.88 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -1.91 (0.42), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 68 HIS 0.012 0.001 HIS A 56 PHE 0.055 0.001 PHE A 320 TYR 0.031 0.002 TYR A 36 ARG 0.002 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 176 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7330 (m-80) REVERT: B 336 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.7672 (m-80) outliers start: 36 outliers final: 27 residues processed: 197 average time/residue: 0.1515 time to fit residues: 41.8797 Evaluate side-chains 191 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 162 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 336 PHE Chi-restraints excluded: chain B residue 428 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 316 ASN B 288 HIS ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6718 Z= 0.207 Angle : 0.674 12.933 9114 Z= 0.333 Chirality : 0.038 0.197 1100 Planarity : 0.005 0.068 1098 Dihedral : 10.658 109.494 970 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 5.96 % Allowed : 30.96 % Favored : 63.08 % 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: 0.47 (0.28), residues: 844 helix: 0.88 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -1.77 (0.42), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 68 HIS 0.008 0.001 HIS A 427 PHE 0.049 0.001 PHE B 320 TYR 0.027 0.002 TYR A 36 ARG 0.002 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 180 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7368 (m-80) REVERT: B 19 LEU cc_start: 0.7217 (tt) cc_final: 0.6942 (tp) REVERT: B 142 LEU cc_start: 0.8452 (mt) cc_final: 0.7739 (mt) REVERT: B 336 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7637 (m-80) outliers start: 41 outliers final: 29 residues processed: 204 average time/residue: 0.1459 time to fit residues: 42.2109 Evaluate side-chains 191 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 336 PHE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 428 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 HIS ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6718 Z= 0.224 Angle : 0.701 12.210 9114 Z= 0.345 Chirality : 0.038 0.155 1100 Planarity : 0.005 0.068 1098 Dihedral : 10.458 107.713 970 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.94 % Allowed : 31.54 % Favored : 63.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.29), residues: 844 helix: 0.90 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -1.60 (0.44), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 68 HIS 0.019 0.002 HIS A 56 PHE 0.038 0.001 PHE B 320 TYR 0.037 0.002 TYR A 36 ARG 0.004 0.000 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 167 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7388 (m-80) REVERT: B 19 LEU cc_start: 0.7285 (tt) cc_final: 0.6960 (tp) REVERT: B 311 ASP cc_start: 0.7430 (t0) cc_final: 0.6733 (t0) REVERT: B 336 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.7630 (m-80) outliers start: 34 outliers final: 28 residues processed: 186 average time/residue: 0.1705 time to fit residues: 45.0123 Evaluate side-chains 193 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 163 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 336 PHE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 428 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 68 optimal weight: 0.1980 chunk 71 optimal weight: 0.7980 chunk 49 optimal weight: 0.0670 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN ** A 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.5590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6718 Z= 0.202 Angle : 0.700 11.264 9114 Z= 0.341 Chirality : 0.038 0.187 1100 Planarity : 0.005 0.066 1098 Dihedral : 10.043 104.868 970 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.23 % Allowed : 32.56 % Favored : 62.21 % 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: 0.64 (0.29), residues: 844 helix: 0.94 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -1.48 (0.45), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 68 HIS 0.010 0.001 HIS A 427 PHE 0.036 0.001 PHE B 320 TYR 0.028 0.002 TYR B 36 ARG 0.002 0.000 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 175 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7333 (m-80) REVERT: B 19 LEU cc_start: 0.7220 (tt) cc_final: 0.6928 (tp) REVERT: B 336 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7555 (m-80) outliers start: 36 outliers final: 27 residues processed: 195 average time/residue: 0.1371 time to fit residues: 38.2413 Evaluate side-chains 197 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 168 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 336 PHE Chi-restraints excluded: chain B residue 428 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN ** A 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.5639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6718 Z= 0.224 Angle : 0.721 11.987 9114 Z= 0.349 Chirality : 0.039 0.192 1100 Planarity : 0.005 0.070 1098 Dihedral : 9.852 103.796 970 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.94 % Allowed : 33.87 % Favored : 61.19 % 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: 0.54 (0.29), residues: 844 helix: 0.86 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -1.51 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 68 HIS 0.009 0.001 HIS A 427 PHE 0.047 0.001 PHE B 405 TYR 0.029 0.002 TYR B 36 ARG 0.002 0.000 ARG B 193 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 168 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.7399 (m-80) REVERT: B 171 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7394 (tm-30) REVERT: B 336 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.7511 (m-80) outliers start: 34 outliers final: 28 residues processed: 188 average time/residue: 0.1440 time to fit residues: 38.8777 Evaluate side-chains 200 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 170 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 336 PHE Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 428 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.0020 chunk 68 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.0060 chunk 58 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 overall best weight: 0.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.113764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.095767 restraints weight = 15554.602| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 4.24 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.5792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6718 Z= 0.200 Angle : 0.711 11.195 9114 Z= 0.345 Chirality : 0.038 0.187 1100 Planarity : 0.005 0.065 1098 Dihedral : 9.540 101.304 970 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.07 % Allowed : 34.74 % Favored : 61.19 % 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: 0.66 (0.29), residues: 844 helix: 0.97 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -1.53 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 68 HIS 0.010 0.001 HIS A 427 PHE 0.047 0.001 PHE B 405 TYR 0.030 0.002 TYR B 36 ARG 0.001 0.000 ARG B 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1650.18 seconds wall clock time: 31 minutes 4.25 seconds (1864.25 seconds total)