Starting phenix.real_space_refine on Sat Dec 9 02:39:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9s_6272/12_2023/3j9s_6272_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9s_6272/12_2023/3j9s_6272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9s_6272/12_2023/3j9s_6272.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9s_6272/12_2023/3j9s_6272.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9s_6272/12_2023/3j9s_6272_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9s_6272/12_2023/3j9s_6272_updated.pdb" } resolution = 2.6 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.007 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: 7 Type Number sf(0) Gaussians Ca 6 9.91 5 Zn 3 6.06 5 S 45 5.16 5 Cl 3 4.86 5 C 6012 2.51 5 N 1638 2.21 5 O 2106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 134": "OE1" <-> "OE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "C GLU 134": "OE1" <-> "OE2" Residue "C GLU 209": "OE1" <-> "OE2" Residue "C GLU 230": "OE1" <-> "OE2" 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: 9813 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3271 Unusual residues: {' CA': 2, ' CL': 1, ' ZN': 1, 'ACE': 1} Inner-chain residues flagged as termini: ['pdbres="LYS A 397 "'] Classifications: {'peptide': 397, 'undetermined': 5, 'water': 105} Modifications used: {'COO': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 376, None: 109} Not linked: pdbres="LYS A 397 " pdbres=" ZN A 501 " Not linked: pdbres=" ZN A 501 " pdbres=" CL A 502 " Not linked: pdbres=" CL A 502 " pdbres=" CA A 503 " Not linked: pdbres=" CA A 503 " pdbres=" CA A 504 " Not linked: pdbres=" CA A 504 " pdbres="HOH A 601 " ... (remaining 104 not shown) Chain: "B" Number of atoms: 3271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3271 Unusual residues: {' CA': 2, ' CL': 1, ' ZN': 1, 'ACE': 1} Inner-chain residues flagged as termini: ['pdbres="LYS B 397 "'] Classifications: {'peptide': 397, 'undetermined': 5, 'water': 105} Modifications used: {'COO': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 376, None: 109} Not linked: pdbres="LYS B 397 " pdbres=" ZN B 501 " Not linked: pdbres=" ZN B 501 " pdbres=" CL B 502 " Not linked: pdbres=" CL B 502 " pdbres=" CA B 503 " Not linked: pdbres=" CA B 503 " pdbres=" CA B 504 " Not linked: pdbres=" CA B 504 " pdbres="HOH B 601 " ... (remaining 104 not shown) Chain: "C" Number of atoms: 3271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3271 Unusual residues: {' CA': 2, ' CL': 1, ' ZN': 1, 'ACE': 1} Inner-chain residues flagged as termini: ['pdbres="LYS C 397 "'] Classifications: {'peptide': 397, 'undetermined': 5, 'water': 105} Modifications used: {'COO': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 376, None: 109} Not linked: pdbres="LYS C 397 " pdbres=" ZN C 501 " Not linked: pdbres=" ZN C 501 " pdbres=" CL C 502 " Not linked: pdbres=" CL C 502 " pdbres=" CA C 503 " Not linked: pdbres=" CA C 503 " pdbres=" CA C 504 " Not linked: pdbres=" CA C 504 " pdbres="HOH C 601 " ... (remaining 104 not shown) Time building chain proxies: 5.75, per 1000 atoms: 0.59 Number of scatterers: 9813 At special positions: 0 Unit cell: (87.978, 84.909, 106.392, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 Ca 6 19.99 Cl 3 17.00 S 45 16.00 O 2106 8.00 N 1638 7.00 C 6012 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: 4.41 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS A 153 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS B 153 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 153 " 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 15 sheets defined 32.7% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 2 through 17 Processing helix chain 'A' and resid 24 through 41 removed outlier: 5.012A pdb=" N ASP A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N LEU A 30 " --> pdb=" O ASN A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 100 removed outlier: 3.735A pdb=" N THR A 84 " --> pdb=" O THR A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 119 Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.867A pdb=" N ARG A 126 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 143 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 302 through 307 removed outlier: 3.636A pdb=" N LEU A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 352 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'A' and resid 376 through 395 removed outlier: 3.994A pdb=" N LEU A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 17 Processing helix chain 'B' and resid 24 through 41 removed outlier: 5.012A pdb=" N ASP B 29 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU B 30 " --> pdb=" O ASN B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 100 removed outlier: 3.736A pdb=" N THR B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.867A pdb=" N ARG B 126 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 143 Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 302 through 307 removed outlier: 3.637A pdb=" N LEU B 307 " --> pdb=" O ALA B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 352 Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'B' and resid 376 through 395 removed outlier: 3.994A pdb=" N LEU B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 17 Processing helix chain 'C' and resid 24 through 41 removed outlier: 5.012A pdb=" N ASP C 29 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU C 30 " --> pdb=" O ASN C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 100 removed outlier: 3.735A pdb=" N THR C 84 " --> pdb=" O THR C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 119 Processing helix chain 'C' and resid 123 through 127 removed outlier: 3.866A pdb=" N ARG C 126 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 143 Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 302 through 307 removed outlier: 3.637A pdb=" N LEU C 307 " --> pdb=" O ALA C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 352 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'C' and resid 376 through 395 removed outlier: 3.994A pdb=" N LEU C 395 " --> pdb=" O ILE C 391 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 45 through 48 Processing sheet with id= B, first strand: chain 'A' and resid 150 through 153 removed outlier: 6.526A pdb=" N THR A 222 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 251 through 253 removed outlier: 5.867A pdb=" N HIS A 317 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET A 177 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N THR A 179 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU A 166 " --> pdb=" O THR A 179 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TRP A 181 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N PHE A 164 " --> pdb=" O TRP A 181 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ASN A 183 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ALA A 162 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 205 through 213 removed outlier: 6.227A pdb=" N LEU A 265 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ILE A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 236 through 239 Processing sheet with id= F, first strand: chain 'B' and resid 45 through 48 Processing sheet with id= G, first strand: chain 'B' and resid 150 through 153 removed outlier: 6.527A pdb=" N THR B 222 " --> pdb=" O GLU B 327 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 251 through 253 removed outlier: 5.867A pdb=" N HIS B 317 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET B 177 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR B 179 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TRP B 181 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N PHE B 164 " --> pdb=" O TRP B 181 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ASN B 183 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ALA B 162 " --> pdb=" O ASN B 183 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 205 through 213 removed outlier: 6.227A pdb=" N LEU B 265 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ILE B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 236 through 239 Processing sheet with id= K, first strand: chain 'C' and resid 45 through 48 Processing sheet with id= L, first strand: chain 'C' and resid 150 through 153 removed outlier: 6.526A pdb=" N THR C 222 " --> pdb=" O GLU C 327 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 251 through 253 removed outlier: 5.867A pdb=" N HIS C 317 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET C 177 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N THR C 179 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU C 166 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TRP C 181 " --> pdb=" O PHE C 164 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N PHE C 164 " --> pdb=" O TRP C 181 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ASN C 183 " --> pdb=" O ALA C 162 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ALA C 162 " --> pdb=" O ASN C 183 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 205 through 213 removed outlier: 6.228A pdb=" N LEU C 265 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ILE C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 236 through 239 411 hydrogen bonds defined for protein. 1152 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: 3.02 Time building geometry restraints manager: 4.49 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: 1596 1.29 - 1.42: 2547 1.42 - 1.55: 5459 1.55 - 1.68: 13 1.68 - 1.81: 81 Bond restraints: 9696 Sorted by residual: bond pdb=" C ALA C 110 " pdb=" N PRO C 111 " ideal model delta sigma weight residual 1.333 1.408 -0.076 1.17e-02 7.31e+03 4.20e+01 bond pdb=" C ALA A 110 " pdb=" N PRO A 111 " ideal model delta sigma weight residual 1.333 1.408 -0.076 1.17e-02 7.31e+03 4.18e+01 bond pdb=" C ALA B 110 " pdb=" N PRO B 111 " ideal model delta sigma weight residual 1.333 1.408 -0.076 1.17e-02 7.31e+03 4.17e+01 bond pdb=" C PHE B 361 " pdb=" N PRO B 362 " ideal model delta sigma weight residual 1.335 1.406 -0.071 1.15e-02 7.56e+03 3.82e+01 bond pdb=" C PHE A 361 " pdb=" N PRO A 362 " ideal model delta sigma weight residual 1.335 1.406 -0.071 1.15e-02 7.56e+03 3.82e+01 ... (remaining 9691 not shown) Histogram of bond angle deviations from ideal: 96.81 - 105.83: 358 105.83 - 114.84: 5449 114.84 - 123.86: 7069 123.86 - 132.88: 282 132.88 - 141.89: 42 Bond angle restraints: 13200 Sorted by residual: angle pdb=" C PHE C 361 " pdb=" N PRO C 362 " pdb=" CA PRO C 362 " ideal model delta sigma weight residual 119.66 113.23 6.43 7.20e-01 1.93e+00 7.98e+01 angle pdb=" C PHE A 361 " pdb=" N PRO A 362 " pdb=" CA PRO A 362 " ideal model delta sigma weight residual 119.66 113.23 6.43 7.20e-01 1.93e+00 7.98e+01 angle pdb=" C PHE B 361 " pdb=" N PRO B 362 " pdb=" CA PRO B 362 " ideal model delta sigma weight residual 119.66 113.29 6.37 7.20e-01 1.93e+00 7.82e+01 angle pdb=" N SER C 339 " pdb=" CA SER C 339 " pdb=" C SER C 339 " ideal model delta sigma weight residual 111.36 120.50 -9.14 1.09e+00 8.42e-01 7.03e+01 angle pdb=" N SER B 339 " pdb=" CA SER B 339 " pdb=" C SER B 339 " ideal model delta sigma weight residual 111.36 120.49 -9.13 1.09e+00 8.42e-01 7.02e+01 ... (remaining 13195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4970 17.94 - 35.87: 583 35.87 - 53.81: 198 53.81 - 71.75: 42 71.75 - 89.68: 21 Dihedral angle restraints: 5814 sinusoidal: 2325 harmonic: 3489 Sorted by residual: dihedral pdb=" CH3 ACE B 0 " pdb=" C ACE B 0 " pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sinusoidal sigma weight residual -180.00 -160.61 -19.39 1 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CH3 ACE C 0 " pdb=" C ACE C 0 " pdb=" N MET C 1 " pdb=" CA MET C 1 " ideal model delta sinusoidal sigma weight residual -180.00 -160.66 -19.34 1 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CH3 ACE A 0 " pdb=" C ACE A 0 " pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sinusoidal sigma weight residual -180.00 -160.68 -19.32 1 5.00e+00 4.00e-02 2.16e+01 ... (remaining 5811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 965 0.089 - 0.179: 349 0.179 - 0.268: 113 0.268 - 0.357: 37 0.357 - 0.447: 27 Chirality restraints: 1491 Sorted by residual: chirality pdb=" CA LYS B 17 " pdb=" N LYS B 17 " pdb=" C LYS B 17 " pdb=" CB LYS B 17 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.99e+00 chirality pdb=" CA LYS C 17 " pdb=" N LYS C 17 " pdb=" C LYS C 17 " pdb=" CB LYS C 17 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.93e+00 chirality pdb=" CA LYS A 17 " pdb=" N LYS A 17 " pdb=" C LYS A 17 " pdb=" CB LYS A 17 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.93e+00 ... (remaining 1488 not shown) Planarity restraints: 1740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ACE B 0 " -0.031 2.00e-02 2.50e+03 1.01e-01 1.28e+02 pdb=" O ACE B 0 " -0.024 2.00e-02 2.50e+03 pdb=" CH3 ACE B 0 " 0.092 2.00e-02 2.50e+03 pdb=" N MET B 1 " -0.161 2.00e-02 2.50e+03 pdb=" CA MET B 1 " 0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE C 0 " -0.030 2.00e-02 2.50e+03 1.01e-01 1.28e+02 pdb=" O ACE C 0 " -0.024 2.00e-02 2.50e+03 pdb=" CH3 ACE C 0 " 0.091 2.00e-02 2.50e+03 pdb=" N MET C 1 " -0.161 2.00e-02 2.50e+03 pdb=" CA MET C 1 " 0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE A 0 " -0.030 2.00e-02 2.50e+03 1.01e-01 1.28e+02 pdb=" O ACE A 0 " -0.024 2.00e-02 2.50e+03 pdb=" CH3 ACE A 0 " 0.091 2.00e-02 2.50e+03 pdb=" N MET A 1 " -0.161 2.00e-02 2.50e+03 pdb=" CA MET A 1 " 0.124 2.00e-02 2.50e+03 ... (remaining 1737 not shown) Histogram of nonbonded interaction distances: 0.22 - 1.15: 9 1.15 - 2.09: 8 2.09 - 3.03: 6279 3.03 - 3.96: 26780 3.96 - 4.90: 54775 Warning: very small nonbonded interaction distances. Nonbonded interactions: 87851 Sorted by model distance: nonbonded pdb="CA CA A 503 " pdb="CA CA C 503 " model vdw 0.216 1.980 nonbonded pdb="CA CA B 503 " pdb="CA CA C 503 " model vdw 0.216 1.980 nonbonded pdb="CA CA A 503 " pdb="CA CA B 503 " model vdw 0.217 1.980 nonbonded pdb="CL CL B 502 " pdb="CL CL C 502 " model vdw 0.273 3.340 nonbonded pdb="CL CL A 502 " pdb="CL CL B 502 " model vdw 0.273 3.340 ... (remaining 87846 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' selection = chain 'C' } 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: 0.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.850 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 32.360 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 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:12.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 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 : 0.020 0.084 9696 Z= 1.334 Angle : 1.797 17.372 13200 Z= 1.164 Chirality : 0.119 0.447 1491 Planarity : 0.009 0.101 1740 Dihedral : 18.550 89.683 3546 Min Nonbonded Distance : 0.216 Molprobity Statistics. All-atom Clashscore : 25.10 Ramachandran Plot: Outliers : 0.76 % Allowed : 1.27 % Favored : 97.97 % Rotamer: Outliers : 6.86 % Allowed : 17.71 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.24), residues: 1185 helix: 2.81 (0.23), residues: 387 sheet: 1.93 (0.30), residues: 315 loop : -0.44 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 247 HIS 0.012 0.004 HIS A 316 PHE 0.043 0.004 PHE A 129 TYR 0.022 0.005 TYR C 135 ARG 0.006 0.001 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 245 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 15 residues processed: 286 average time/residue: 1.5407 time to fit residues: 465.5739 Evaluate side-chains 144 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 1.173 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 3 average time/residue: 1.6543 time to fit residues: 6.7618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 63 optimal weight: 0.1980 chunk 38 optimal weight: 5.9990 chunk 76 optimal weight: 0.0570 chunk 60 optimal weight: 9.9990 chunk 117 optimal weight: 20.0000 chunk 45 optimal weight: 50.0000 chunk 71 optimal weight: 20.0000 chunk 87 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 overall best weight: 1.6504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.167 9696 Z= 0.847 Angle : 1.625 29.505 13200 Z= 0.869 Chirality : 0.096 2.027 1491 Planarity : 0.019 0.388 1740 Dihedral : 6.883 35.294 1302 Min Nonbonded Distance : 0.841 Molprobity Statistics. All-atom Clashscore : 23.66 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.28 % Favored : 97.38 % Rotamer: Outliers : 6.29 % Allowed : 22.76 % Favored : 70.95 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.16 (0.23), residues: 1185 helix: 0.47 (0.23), residues: 393 sheet: 1.13 (0.27), residues: 369 loop : -1.13 (0.26), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.009 TRP C 181 HIS 0.036 0.005 HIS C 316 PHE 0.110 0.008 PHE C 193 TYR 0.161 0.011 TYR C 195 ARG 0.186 0.006 ARG C 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 132 time to evaluate : 1.123 Fit side-chains outliers start: 66 outliers final: 20 residues processed: 179 average time/residue: 1.4731 time to fit residues: 280.5830 Evaluate side-chains 143 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 1.158 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 3 average time/residue: 0.7344 time to fit residues: 3.9617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 50.0000 chunk 113 optimal weight: 7.9990 chunk 92 optimal weight: 50.0000 chunk 37 optimal weight: 6.9990 chunk 136 optimal weight: 0.0060 chunk 147 optimal weight: 50.0000 chunk 121 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 chunk 46 optimal weight: 50.0000 chunk 109 optimal weight: 5.9990 overall best weight: 6.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 175 ASN C 345 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9696 Z= 0.273 Angle : 0.614 12.527 13200 Z= 0.322 Chirality : 0.041 0.160 1491 Planarity : 0.005 0.044 1740 Dihedral : 5.129 19.880 1302 Min Nonbonded Distance : 1.144 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.33 % Allowed : 22.00 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.24), residues: 1185 helix: 1.78 (0.24), residues: 393 sheet: 1.40 (0.30), residues: 318 loop : -0.51 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 139 HIS 0.004 0.001 HIS A 317 PHE 0.024 0.002 PHE C 129 TYR 0.012 0.002 TYR B 160 ARG 0.009 0.001 ARG C 144 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 177 time to evaluate : 1.176 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 13 residues processed: 201 average time/residue: 1.4145 time to fit residues: 302.2729 Evaluate side-chains 148 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 135 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 1.5245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 15 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 91 optimal weight: 50.0000 chunk 136 optimal weight: 8.9990 chunk 144 optimal weight: 50.0000 chunk 71 optimal weight: 5.9990 chunk 129 optimal weight: 30.0000 chunk 39 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN B 83 ASN B 175 ASN ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9696 Z= 0.306 Angle : 0.546 5.279 13200 Z= 0.289 Chirality : 0.040 0.156 1491 Planarity : 0.004 0.033 1740 Dihedral : 4.646 20.305 1302 Min Nonbonded Distance : 0.996 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.86 % Allowed : 22.86 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.24), residues: 1185 helix: 2.21 (0.25), residues: 393 sheet: 1.20 (0.29), residues: 333 loop : -0.19 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 59 HIS 0.004 0.001 HIS B 317 PHE 0.020 0.001 PHE C 129 TYR 0.017 0.002 TYR B 135 ARG 0.007 0.001 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 146 time to evaluate : 1.156 Fit side-chains outliers start: 30 outliers final: 14 residues processed: 163 average time/residue: 1.4578 time to fit residues: 252.8023 Evaluate side-chains 144 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 130 time to evaluate : 1.075 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.1370 time to fit residues: 2.1169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 107 optimal weight: 0.1980 chunk 59 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 74 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9696 Z= 0.190 Angle : 0.519 5.223 13200 Z= 0.270 Chirality : 0.039 0.150 1491 Planarity : 0.003 0.030 1740 Dihedral : 4.405 19.331 1302 Min Nonbonded Distance : 1.164 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.67 % Allowed : 22.95 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.24), residues: 1185 helix: 2.28 (0.25), residues: 393 sheet: 1.05 (0.29), residues: 336 loop : -0.13 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 139 HIS 0.003 0.001 HIS B 317 PHE 0.015 0.001 PHE A 292 TYR 0.021 0.002 TYR B 135 ARG 0.006 0.001 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 156 time to evaluate : 1.285 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 9 residues processed: 173 average time/residue: 1.3565 time to fit residues: 250.4357 Evaluate side-chains 149 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 140 time to evaluate : 1.141 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 1.5081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 50.0000 chunk 130 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 35 optimal weight: 0.0470 chunk 145 optimal weight: 50.0000 chunk 120 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 76 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 overall best weight: 3.4684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 345 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9696 Z= 0.177 Angle : 0.513 5.864 13200 Z= 0.265 Chirality : 0.038 0.151 1491 Planarity : 0.003 0.027 1740 Dihedral : 4.267 18.678 1302 Min Nonbonded Distance : 1.152 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.38 % Allowed : 23.43 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.25), residues: 1185 helix: 2.20 (0.25), residues: 396 sheet: 0.97 (0.30), residues: 336 loop : -0.08 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 139 HIS 0.003 0.001 HIS B 317 PHE 0.016 0.001 PHE C 129 TYR 0.023 0.002 TYR B 135 ARG 0.008 0.001 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 167 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 10 residues processed: 184 average time/residue: 1.3528 time to fit residues: 265.6941 Evaluate side-chains 159 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 1.070 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.2545 time to fit residues: 1.8717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 6.9990 chunk 82 optimal weight: 30.0000 chunk 105 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 144 optimal weight: 50.0000 chunk 90 optimal weight: 50.0000 chunk 88 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9696 Z= 0.242 Angle : 0.526 5.780 13200 Z= 0.272 Chirality : 0.039 0.151 1491 Planarity : 0.003 0.029 1740 Dihedral : 4.269 19.325 1302 Min Nonbonded Distance : 1.094 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.38 % Allowed : 23.62 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.25), residues: 1185 helix: 2.25 (0.25), residues: 393 sheet: 1.04 (0.30), residues: 327 loop : -0.08 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 139 HIS 0.003 0.001 HIS B 317 PHE 0.013 0.001 PHE A 292 TYR 0.016 0.002 TYR A 353 ARG 0.007 0.001 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 1.056 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 159 average time/residue: 1.4097 time to fit residues: 238.9863 Evaluate side-chains 154 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 1.205 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.9699 time to fit residues: 3.6439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.0070 chunk 43 optimal weight: 50.0000 chunk 28 optimal weight: 8.9990 chunk 91 optimal weight: 50.0000 chunk 98 optimal weight: 50.0000 chunk 71 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 overall best weight: 4.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9696 Z= 0.195 Angle : 0.517 6.014 13200 Z= 0.267 Chirality : 0.039 0.155 1491 Planarity : 0.003 0.027 1740 Dihedral : 4.210 19.655 1302 Min Nonbonded Distance : 1.148 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.38 % Allowed : 23.52 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.25), residues: 1185 helix: 2.22 (0.26), residues: 393 sheet: 0.96 (0.30), residues: 327 loop : -0.08 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 139 HIS 0.003 0.001 HIS B 317 PHE 0.014 0.001 PHE C 129 TYR 0.013 0.002 TYR C 135 ARG 0.006 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 1.126 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 172 average time/residue: 1.4545 time to fit residues: 266.2292 Evaluate side-chains 154 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 1.070 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 1.6949 time to fit residues: 3.3526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 58 optimal weight: 20.0000 chunk 105 optimal weight: 7.9990 chunk 41 optimal weight: 50.0000 chunk 121 optimal weight: 9.9990 chunk 127 optimal weight: 30.0000 chunk 88 optimal weight: 5.9990 chunk 142 optimal weight: 50.0000 chunk 86 optimal weight: 0.0020 overall best weight: 5.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9696 Z= 0.224 Angle : 0.546 10.888 13200 Z= 0.281 Chirality : 0.039 0.155 1491 Planarity : 0.003 0.029 1740 Dihedral : 4.217 18.858 1302 Min Nonbonded Distance : 1.119 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.81 % Allowed : 24.38 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.25), residues: 1185 helix: 2.17 (0.26), residues: 393 sheet: 0.88 (0.30), residues: 312 loop : 0.03 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 139 HIS 0.003 0.001 HIS B 317 PHE 0.016 0.001 PHE C 129 TYR 0.016 0.002 TYR C 353 ARG 0.007 0.001 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 1.214 Fit side-chains outliers start: 19 outliers final: 10 residues processed: 165 average time/residue: 1.3826 time to fit residues: 243.1697 Evaluate side-chains 148 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 138 time to evaluate : 1.181 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 1.1053 time to fit residues: 2.7058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 30.0000 chunk 99 optimal weight: 50.0000 chunk 149 optimal weight: 50.0000 chunk 137 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 91 optimal weight: 50.0000 chunk 72 optimal weight: 0.0020 chunk 94 optimal weight: 50.0000 chunk 126 optimal weight: 0.7980 chunk 36 optimal weight: 0.0670 overall best weight: 2.3730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN B 345 ASN C 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9696 Z= 0.161 Angle : 0.540 10.716 13200 Z= 0.277 Chirality : 0.039 0.154 1491 Planarity : 0.003 0.027 1740 Dihedral : 4.126 17.479 1302 Min Nonbonded Distance : 1.224 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.24 % Allowed : 25.14 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.25), residues: 1185 helix: 2.04 (0.26), residues: 396 sheet: 0.87 (0.30), residues: 327 loop : -0.04 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 139 HIS 0.003 0.001 HIS B 317 PHE 0.019 0.001 PHE A 129 TYR 0.024 0.002 TYR B 135 ARG 0.007 0.001 ARG B 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 154 time to evaluate : 1.160 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 166 average time/residue: 1.4441 time to fit residues: 255.5799 Evaluate side-chains 151 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 143 time to evaluate : 1.156 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 1.6247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 30.0000 chunk 119 optimal weight: 0.9990 chunk 49 optimal weight: 50.0000 chunk 122 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.065814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.054357 restraints weight = 16322.223| |-----------------------------------------------------------------------------| r_work (start): 0.2598 rms_B_bonded: 2.52 r_work: 0.2458 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9696 Z= 0.180 Angle : 0.538 10.580 13200 Z= 0.276 Chirality : 0.039 0.154 1491 Planarity : 0.003 0.030 1740 Dihedral : 4.100 17.433 1302 Min Nonbonded Distance : 1.129 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.33 % Allowed : 24.95 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.25), residues: 1185 helix: 2.13 (0.26), residues: 393 sheet: 0.81 (0.30), residues: 327 loop : -0.01 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 139 HIS 0.003 0.001 HIS B 317 PHE 0.017 0.001 PHE A 129 TYR 0.013 0.002 TYR C 353 ARG 0.007 0.001 ARG B 126 =============================================================================== Job complete usr+sys time: 4192.17 seconds wall clock time: 74 minutes 57.11 seconds (4497.11 seconds total)