Starting phenix.real_space_refine on Fri Dec 8 02:05:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2m_35950/12_2023/8j2m_35950_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2m_35950/12_2023/8j2m_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_35950/12_2023/8j2m_35950.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2m_35950/12_2023/8j2m_35950.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2m_35950/12_2023/8j2m_35950_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2m_35950/12_2023/8j2m_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-1.21rc1-5172/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: 4.15, per 1000 atoms: 0.63 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: 2.73 Conformation dependent library (CDL) restraints added in 1.1 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: 1.25 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: 1.72 Time building geometry restraints manager: 2.96 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: 1.770 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: 4.270 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 21.740 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.130 ------------------------------------------------------------------------------- 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 : 0.645 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 outliers start: 20 outliers final: 5 residues processed: 299 average time/residue: 0.1803 time to fit residues: 70.7185 Evaluate side-chains 198 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 193 time to evaluate : 0.727 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0630 time to fit residues: 1.5365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 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: 0.6980 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.7656 moved from start: 0.3104 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= 0.210 Angle : 0.613 6.599 9114 Z= 0.323 Chirality : 0.038 0.127 1100 Planarity : 0.005 0.065 1098 Dihedral : 15.518 179.701 970 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 5.09 % Allowed : 20.06 % Favored : 74.85 % 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 (0.26), residues: 844 helix: 0.08 (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 369 HIS 0.007 0.001 HIS A 427 PHE 0.033 0.002 PHE B 405 TYR 0.022 0.002 TYR A 334 ARG 0.006 0.001 ARG A 193 *********************** 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: 35 poor density : 211 time to evaluate : 0.734 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 outliers start: 35 outliers final: 20 residues processed: 230 average time/residue: 0.1374 time to fit residues: 44.8642 Evaluate side-chains 194 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 174 time to evaluate : 0.665 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0763 time to fit residues: 3.4599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 75 optimal weight: 0.0040 chunk 26 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 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: 0.7647 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6718 Z= 0.207 Angle : 0.596 7.680 9114 Z= 0.308 Chirality : 0.037 0.145 1100 Planarity : 0.005 0.069 1098 Dihedral : 13.839 155.217 970 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.78 % Allowed : 24.85 % Favored : 71.37 % 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: 0.28 (0.28), residues: 844 helix: 0.72 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -1.72 (0.41), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 290 HIS 0.011 0.001 HIS B 427 PHE 0.013 0.001 PHE B 278 TYR 0.023 0.002 TYR A 36 ARG 0.002 0.000 ARG A 193 *********************** 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 219 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 193 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 201 average time/residue: 0.1386 time to fit residues: 40.0740 Evaluate side-chains 183 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 171 time to evaluate : 0.671 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0679 time to fit residues: 2.4563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 8 optimal weight: 0.0030 chunk 36 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 76 optimal weight: 0.0980 chunk 81 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- 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 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN ** B 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6718 Z= 0.175 Angle : 0.578 7.716 9114 Z= 0.297 Chirality : 0.037 0.143 1100 Planarity : 0.005 0.070 1098 Dihedral : 12.450 127.568 970 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.78 % Allowed : 25.87 % Favored : 70.35 % 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: 0.45 (0.28), residues: 844 helix: 0.82 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.67 (0.42), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 68 HIS 0.007 0.001 HIS B 427 PHE 0.011 0.001 PHE B 278 TYR 0.019 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 218 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 192 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 13 residues processed: 206 average time/residue: 0.1359 time to fit residues: 40.2693 Evaluate side-chains 179 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 166 time to evaluate : 0.723 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0652 time to fit residues: 2.4961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 1 optimal weight: 3.9990 chunk 60 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 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 103 GLN A 392 GLN B 103 GLN B 316 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6718 Z= 0.202 Angle : 0.618 8.235 9114 Z= 0.311 Chirality : 0.038 0.189 1100 Planarity : 0.005 0.067 1098 Dihedral : 11.471 115.052 970 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.62 % Allowed : 29.80 % Favored : 67.59 % 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: 0.46 (0.28), residues: 844 helix: 0.83 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -1.64 (0.41), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 369 HIS 0.011 0.001 HIS A 427 PHE 0.017 0.001 PHE A 336 TYR 0.030 0.002 TYR A 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 203 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 185 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 193 average time/residue: 0.1460 time to fit residues: 40.0446 Evaluate side-chains 164 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 156 time to evaluate : 0.750 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1303 time to fit residues: 2.4242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 316 ASN B 316 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6718 Z= 0.204 Angle : 0.638 10.133 9114 Z= 0.320 Chirality : 0.038 0.155 1100 Planarity : 0.005 0.067 1098 Dihedral : 10.873 111.961 970 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.76 % Allowed : 31.25 % 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: 0.52 (0.28), residues: 844 helix: 0.86 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -1.60 (0.40), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 327 HIS 0.008 0.001 HIS B 427 PHE 0.023 0.001 PHE B 405 TYR 0.035 0.002 TYR A 36 ARG 0.003 0.000 ARG B 322 *********************** 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 197 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 178 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 192 average time/residue: 0.1294 time to fit residues: 36.0111 Evaluate side-chains 179 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 167 time to evaluate : 0.762 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0688 time to fit residues: 2.5293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 49 optimal weight: 0.0570 chunk 37 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.5204 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= 0.203 Angle : 0.680 12.733 9114 Z= 0.328 Chirality : 0.038 0.184 1100 Planarity : 0.005 0.066 1098 Dihedral : 10.472 108.274 970 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.33 % Allowed : 33.28 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.28), residues: 844 helix: 0.85 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -1.47 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 225 HIS 0.010 0.001 HIS A 427 PHE 0.056 0.002 PHE B 320 TYR 0.033 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 197 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 181 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 189 average time/residue: 0.1429 time to fit residues: 38.2026 Evaluate side-chains 170 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 164 time to evaluate : 0.757 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0665 time to fit residues: 1.5810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 70 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: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.5347 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= 0.208 Angle : 0.687 11.730 9114 Z= 0.334 Chirality : 0.038 0.170 1100 Planarity : 0.005 0.065 1098 Dihedral : 10.156 105.546 970 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.60 % Allowed : 34.59 % Favored : 63.81 % 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: 0.60 (0.29), residues: 844 helix: 0.90 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -1.43 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 225 HIS 0.010 0.001 HIS A 427 PHE 0.030 0.001 PHE A 320 TYR 0.031 0.002 TYR A 36 ARG 0.002 0.000 ARG A 193 *********************** 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 184 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 173 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 181 average time/residue: 0.1415 time to fit residues: 36.8860 Evaluate side-chains 181 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 172 time to evaluate : 0.740 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0719 time to fit residues: 2.0942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.5470 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 : 0.703 12.174 9114 Z= 0.336 Chirality : 0.039 0.210 1100 Planarity : 0.005 0.064 1098 Dihedral : 9.899 103.741 970 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.87 % Allowed : 34.16 % Favored : 64.97 % 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: 0.58 (0.28), residues: 844 helix: 0.85 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -1.30 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 369 HIS 0.011 0.001 HIS B 427 PHE 0.027 0.001 PHE B 320 TYR 0.029 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 187 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 181 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 184 average time/residue: 0.1412 time to fit residues: 37.1382 Evaluate side-chains 169 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 167 time to evaluate : 0.710 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0640 time to fit residues: 1.1890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.5624 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= 0.218 Angle : 0.724 11.328 9114 Z= 0.350 Chirality : 0.040 0.239 1100 Planarity : 0.005 0.064 1098 Dihedral : 9.628 101.324 970 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.02 % Allowed : 35.03 % Favored : 63.95 % 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: 0.53 (0.29), residues: 844 helix: 0.83 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -1.35 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 369 HIS 0.010 0.001 HIS B 427 PHE 0.029 0.001 PHE A 320 TYR 0.029 0.002 TYR B 36 ARG 0.002 0.000 ARG A 322 ********************** 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 177 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 170 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 173 average time/residue: 0.1351 time to fit residues: 33.7537 Evaluate side-chains 165 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 162 time to evaluate : 0.726 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0732 time to fit residues: 1.3373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 68 optimal weight: 0.0870 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN A 323 HIS ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.111811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.093494 restraints weight = 15838.568| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 4.17 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.5767 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= 0.212 Angle : 0.725 12.315 9114 Z= 0.348 Chirality : 0.041 0.307 1100 Planarity : 0.005 0.064 1098 Dihedral : 9.447 99.499 970 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.02 % Allowed : 35.90 % 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: 0.57 (0.29), residues: 844 helix: 0.84 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.28 (0.45), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 369 HIS 0.009 0.001 HIS B 427 PHE 0.029 0.001 PHE B 320 TYR 0.029 0.002 TYR B 36 ARG 0.001 0.000 ARG A 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1636.65 seconds wall clock time: 30 minutes 49.58 seconds (1849.58 seconds total)