Starting phenix.real_space_refine on Fri Dec 8 06:10:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1b_9566/12_2023/5h1b_9566_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1b_9566/12_2023/5h1b_9566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1b_9566/12_2023/5h1b_9566.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1b_9566/12_2023/5h1b_9566.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1b_9566/12_2023/5h1b_9566_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1b_9566/12_2023/5h1b_9566_updated.pdb" } resolution = 4.4 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 3 5.21 5 S 39 5.16 5 C 4557 2.51 5 N 1287 2.21 5 O 1455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 170": "NH1" <-> "NH2" Residue "B ARG 170": "NH1" <-> "NH2" Residue "C ARG 170": "NH1" <-> "NH2" 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: 7359 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2361 Classifications: {'peptide': 308} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 296} Chain breaks: 1 Chain: "B" Number of atoms: 2361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2361 Classifications: {'peptide': 308} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 296} Chain breaks: 1 Chain: "C" Number of atoms: 2361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2361 Classifications: {'peptide': 308} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 296} Chain breaks: 1 Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.54, per 1000 atoms: 0.62 Number of scatterers: 7359 At special positions: 0 Unit cell: (107.092, 69.218, 116.234, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 39 16.00 P 18 15.00 Mg 3 11.99 O 1455 8.00 N 1287 7.00 C 4557 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.45 Conformation dependent library (CDL) restraints added in 1.4 seconds 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1686 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 6 sheets defined 44.5% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 35 through 44 removed outlier: 3.606A pdb=" N GLU A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 68 through 81 Processing helix chain 'A' and resid 89 through 98 Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 133 through 145 removed outlier: 4.713A pdb=" N GLN A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 168 through 178 Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 197 through 213 removed outlier: 3.768A pdb=" N THR A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 removed outlier: 4.100A pdb=" N ASP A 231 " --> pdb=" O TYR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 259 removed outlier: 3.602A pdb=" N ARG A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.698A pdb=" N ALA A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 27 No H-bonds generated for 'chain 'B' and resid 25 through 27' Processing helix chain 'B' and resid 35 through 44 removed outlier: 3.606A pdb=" N GLU B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 68 through 81 Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 133 through 145 removed outlier: 4.713A pdb=" N GLN B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 168 through 178 Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 197 through 213 removed outlier: 3.768A pdb=" N THR B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 removed outlier: 4.101A pdb=" N ASP B 231 " --> pdb=" O TYR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 259 removed outlier: 3.602A pdb=" N ARG B 247 " --> pdb=" O MET B 243 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET B 251 " --> pdb=" O ARG B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.698A pdb=" N ALA B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 27 No H-bonds generated for 'chain 'C' and resid 25 through 27' Processing helix chain 'C' and resid 35 through 44 removed outlier: 3.606A pdb=" N GLU C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 68 through 81 Processing helix chain 'C' and resid 89 through 98 Processing helix chain 'C' and resid 107 through 112 Processing helix chain 'C' and resid 133 through 145 removed outlier: 4.712A pdb=" N GLN C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 168 through 178 Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 197 through 213 removed outlier: 3.768A pdb=" N THR C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 231 removed outlier: 4.100A pdb=" N ASP C 231 " --> pdb=" O TYR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 259 removed outlier: 3.602A pdb=" N ARG C 247 " --> pdb=" O MET C 243 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET C 251 " --> pdb=" O ARG C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.698A pdb=" N ALA C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 122 through 127 removed outlier: 7.224A pdb=" N VAL A 263 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N MET A 125 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE A 265 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N GLY A 127 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN A 267 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LYS A 156 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU A 219 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N MET A 158 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL A 221 " --> pdb=" O MET A 158 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE A 160 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ALA A 190 " --> pdb=" O TYR A 159 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASP A 161 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA A 192 " --> pdb=" O ASP A 161 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 299 through 304 Processing sheet with id= C, first strand: chain 'B' and resid 122 through 127 removed outlier: 7.224A pdb=" N VAL B 263 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N MET B 125 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE B 265 " --> pdb=" O MET B 125 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N GLY B 127 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN B 267 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LYS B 156 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU B 219 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N MET B 158 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL B 221 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE B 160 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ALA B 190 " --> pdb=" O TYR B 159 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASP B 161 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA B 192 " --> pdb=" O ASP B 161 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 299 through 304 Processing sheet with id= E, first strand: chain 'C' and resid 122 through 127 removed outlier: 7.225A pdb=" N VAL C 263 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N MET C 125 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE C 265 " --> pdb=" O MET C 125 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N GLY C 127 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN C 267 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LYS C 156 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU C 219 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N MET C 158 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL C 221 " --> pdb=" O MET C 158 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE C 160 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ALA C 190 " --> pdb=" O TYR C 159 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASP C 161 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA C 192 " --> pdb=" O ASP C 161 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 299 through 304 258 hydrogen bonds defined for protein. 729 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: 2.07 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2372 1.33 - 1.45: 1159 1.45 - 1.57: 3854 1.57 - 1.69: 33 1.69 - 1.81: 63 Bond restraints: 7481 Sorted by residual: bond pdb=" O3A ANP A 600 " pdb=" PB ANP A 600 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" O3A ANP B 600 " pdb=" PB ANP B 600 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" O3A ANP C 600 " pdb=" PB ANP C 600 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" N3B ANP C 600 " pdb=" PG ANP C 600 " ideal model delta sigma weight residual 1.795 1.689 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" N3B ANP A 600 " pdb=" PG ANP A 600 " ideal model delta sigma weight residual 1.795 1.689 0.106 2.00e-02 2.50e+03 2.80e+01 ... (remaining 7476 not shown) Histogram of bond angle deviations from ideal: 98.50 - 105.27: 173 105.27 - 112.04: 3660 112.04 - 118.81: 2356 118.81 - 125.58: 3893 125.58 - 132.35: 63 Bond angle restraints: 10145 Sorted by residual: angle pdb=" PB ANP C 600 " pdb=" N3B ANP C 600 " pdb=" PG ANP C 600 " ideal model delta sigma weight residual 126.95 108.18 18.77 3.00e+00 1.11e-01 3.91e+01 angle pdb=" PB ANP B 600 " pdb=" N3B ANP B 600 " pdb=" PG ANP B 600 " ideal model delta sigma weight residual 126.95 108.18 18.77 3.00e+00 1.11e-01 3.91e+01 angle pdb=" PB ANP A 600 " pdb=" N3B ANP A 600 " pdb=" PG ANP A 600 " ideal model delta sigma weight residual 126.95 108.20 18.75 3.00e+00 1.11e-01 3.91e+01 angle pdb=" N THR A 197 " pdb=" CA THR A 197 " pdb=" C THR A 197 " ideal model delta sigma weight residual 111.71 105.46 6.25 1.15e+00 7.56e-01 2.95e+01 angle pdb=" N THR B 197 " pdb=" CA THR B 197 " pdb=" C THR B 197 " ideal model delta sigma weight residual 111.71 105.47 6.24 1.15e+00 7.56e-01 2.94e+01 ... (remaining 10140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.74: 4322 23.74 - 47.48: 162 47.48 - 71.22: 46 71.22 - 94.96: 27 94.96 - 118.70: 3 Dihedral angle restraints: 4560 sinusoidal: 1926 harmonic: 2634 Sorted by residual: dihedral pdb=" CA CYS C 319 " pdb=" C CYS C 319 " pdb=" N LEU C 320 " pdb=" CA LEU C 320 " ideal model delta harmonic sigma weight residual 180.00 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA CYS B 319 " pdb=" C CYS B 319 " pdb=" N LEU B 320 " pdb=" CA LEU B 320 " ideal model delta harmonic sigma weight residual -180.00 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA CYS A 319 " pdb=" C CYS A 319 " pdb=" N LEU A 320 " pdb=" CA LEU A 320 " ideal model delta harmonic sigma weight residual 180.00 -156.99 -23.01 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 4557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 888 0.064 - 0.129: 244 0.129 - 0.193: 23 0.193 - 0.257: 0 0.257 - 0.321: 3 Chirality restraints: 1158 Sorted by residual: chirality pdb=" C3' ANP C 600 " pdb=" C2' ANP C 600 " pdb=" C4' ANP C 600 " pdb=" O3' ANP C 600 " both_signs ideal model delta sigma weight residual False -2.36 -2.68 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" C3' ANP B 600 " pdb=" C2' ANP B 600 " pdb=" C4' ANP B 600 " pdb=" O3' ANP B 600 " both_signs ideal model delta sigma weight residual False -2.36 -2.68 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C3' ANP A 600 " pdb=" C2' ANP A 600 " pdb=" C4' ANP A 600 " pdb=" O3' ANP A 600 " both_signs ideal model delta sigma weight residual False -2.36 -2.67 0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 1155 not shown) Planarity restraints: 1272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 246 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" C ALA A 246 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA A 246 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG A 247 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 246 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" C ALA B 246 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA B 246 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG B 247 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 246 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" C ALA C 246 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA C 246 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG C 247 " -0.013 2.00e-02 2.50e+03 ... (remaining 1269 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 46 2.18 - 2.86: 3060 2.86 - 3.54: 11410 3.54 - 4.22: 18728 4.22 - 4.90: 29915 Nonbonded interactions: 63159 Sorted by model distance: nonbonded pdb=" CB ALA A 271 " pdb=" OP2 DT D 4 " model vdw 1.503 3.460 nonbonded pdb=" CA ALA A 271 " pdb=" OP2 DT D 4 " model vdw 1.572 3.470 nonbonded pdb=" N ALA A 271 " pdb=" OP2 DT D 4 " model vdw 1.580 2.520 nonbonded pdb=" OH TYR B 159 " pdb=" OD2 ASP B 222 " model vdw 1.586 2.440 nonbonded pdb=" OH TYR A 159 " pdb=" OD2 ASP A 222 " model vdw 1.586 2.440 ... (remaining 63154 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.780 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.260 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 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 : 0.010 0.150 7481 Z= 0.660 Angle : 1.411 18.767 10145 Z= 0.917 Chirality : 0.056 0.321 1158 Planarity : 0.005 0.034 1272 Dihedral : 16.126 118.695 2874 Min Nonbonded Distance : 1.503 Molprobity Statistics. All-atom Clashscore : 54.25 Ramachandran Plot: Outliers : 2.63 % Allowed : 6.25 % Favored : 91.12 % Rotamer: Outliers : 5.67 % Allowed : 2.43 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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 (0.27), residues: 912 helix: -2.43 (0.18), residues: 378 sheet: -0.80 (0.40), residues: 159 loop : 0.92 (0.36), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS C 138 PHE 0.018 0.003 PHE C 86 TYR 0.019 0.002 TYR A 315 ARG 0.010 0.002 ARG C 215 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 98 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 13 residues processed: 132 average time/residue: 0.3067 time to fit residues: 49.9072 Evaluate side-chains 66 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 0.861 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.1157 time to fit residues: 3.4408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 36 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 HIS ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 HIS C 138 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7481 Z= 0.239 Angle : 0.711 7.513 10145 Z= 0.380 Chirality : 0.042 0.167 1158 Planarity : 0.004 0.037 1272 Dihedral : 13.099 114.007 1191 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 1.32 % Allowed : 4.06 % Favored : 94.63 % Rotamer: Outliers : 0.40 % Allowed : 0.94 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: -0.22 (0.28), residues: 912 helix: -0.44 (0.23), residues: 411 sheet: -0.39 (0.40), residues: 162 loop : 0.74 (0.37), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 294 PHE 0.020 0.002 PHE B 126 TYR 0.016 0.002 TYR B 315 ARG 0.007 0.001 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 0.931 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 75 average time/residue: 0.2419 time to fit residues: 24.0215 Evaluate side-chains 41 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 7481 Z= 0.368 Angle : 0.737 9.003 10145 Z= 0.391 Chirality : 0.041 0.179 1158 Planarity : 0.004 0.042 1272 Dihedral : 12.239 108.927 1191 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 19.95 Ramachandran Plot: Outliers : 1.32 % Allowed : 5.70 % Favored : 92.98 % Rotamer: Outliers : 0.40 % Allowed : 2.29 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: -0.02 (0.27), residues: 912 helix: 0.37 (0.24), residues: 408 sheet: -0.90 (0.38), residues: 165 loop : 0.27 (0.36), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 294 PHE 0.026 0.003 PHE B 86 TYR 0.011 0.001 TYR B 216 ARG 0.007 0.001 ARG B 130 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.803 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 51 average time/residue: 0.1566 time to fit residues: 12.2527 Evaluate side-chains 33 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.941 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS C 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.5466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7481 Z= 0.359 Angle : 0.709 7.782 10145 Z= 0.376 Chirality : 0.041 0.184 1158 Planarity : 0.004 0.050 1272 Dihedral : 12.351 110.667 1191 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 1.21 % Allowed : 5.04 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: -0.07 (0.27), residues: 912 helix: 0.66 (0.25), residues: 402 sheet: -0.80 (0.41), residues: 144 loop : -0.37 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 294 PHE 0.020 0.003 PHE C 195 TYR 0.021 0.002 TYR B 315 ARG 0.006 0.001 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.900 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1632 time to fit residues: 10.9418 Evaluate side-chains 34 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.933 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 74 optimal weight: 0.0050 chunk 60 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.5810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7481 Z= 0.218 Angle : 0.607 7.725 10145 Z= 0.320 Chirality : 0.038 0.166 1158 Planarity : 0.003 0.054 1272 Dihedral : 12.090 109.827 1191 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 1.21 % Allowed : 5.15 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 0.15 (0.28), residues: 912 helix: 0.94 (0.25), residues: 429 sheet: -0.75 (0.41), residues: 144 loop : -0.45 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 294 PHE 0.011 0.002 PHE B 126 TYR 0.009 0.001 TYR C 315 ARG 0.004 0.000 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1660 time to fit residues: 13.6357 Evaluate side-chains 39 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.954 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.4980 chunk 21 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 overall best weight: 4.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN B 47 HIS ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.6009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7481 Z= 0.310 Angle : 0.670 7.810 10145 Z= 0.349 Chirality : 0.040 0.179 1158 Planarity : 0.004 0.055 1272 Dihedral : 12.213 110.968 1191 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 1.21 % Allowed : 4.71 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 0.17 (0.28), residues: 912 helix: 0.94 (0.25), residues: 405 sheet: -0.58 (0.43), residues: 135 loop : -0.41 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.001 HIS B 294 PHE 0.018 0.002 PHE C 195 TYR 0.022 0.001 TYR C 191 ARG 0.004 0.001 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.862 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1648 time to fit residues: 11.4943 Evaluate side-chains 34 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.997 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.6276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7481 Z= 0.201 Angle : 0.609 7.729 10145 Z= 0.315 Chirality : 0.039 0.167 1158 Planarity : 0.004 0.046 1272 Dihedral : 11.957 110.536 1191 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 1.21 % Allowed : 4.50 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 0.30 (0.28), residues: 912 helix: 1.14 (0.25), residues: 426 sheet: -1.12 (0.38), residues: 174 loop : -0.11 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS B 294 PHE 0.014 0.002 PHE C 259 TYR 0.018 0.001 TYR C 191 ARG 0.006 0.000 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.876 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1851 time to fit residues: 13.9366 Evaluate side-chains 39 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.929 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.6383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7481 Z= 0.350 Angle : 0.717 8.581 10145 Z= 0.368 Chirality : 0.041 0.183 1158 Planarity : 0.005 0.074 1272 Dihedral : 12.258 111.018 1191 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 1.10 % Allowed : 5.15 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 0.03 (0.28), residues: 912 helix: 0.79 (0.25), residues: 405 sheet: -0.58 (0.42), residues: 138 loop : -0.46 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.001 HIS B 294 PHE 0.021 0.002 PHE C 195 TYR 0.014 0.002 TYR C 191 ARG 0.010 0.001 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.885 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1805 time to fit residues: 11.6092 Evaluate side-chains 34 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.809 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.6539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7481 Z= 0.214 Angle : 0.622 7.760 10145 Z= 0.322 Chirality : 0.039 0.176 1158 Planarity : 0.004 0.044 1272 Dihedral : 11.909 111.136 1191 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.88 % Allowed : 4.28 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 0.19 (0.28), residues: 912 helix: 1.03 (0.25), residues: 426 sheet: -0.99 (0.40), residues: 165 loop : -0.30 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS B 294 PHE 0.013 0.002 PHE C 86 TYR 0.015 0.001 TYR C 191 ARG 0.006 0.000 ARG B 167 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.919 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1796 time to fit residues: 12.9335 Evaluate side-chains 37 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 chunk 56 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.6637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7481 Z= 0.253 Angle : 0.636 7.793 10145 Z= 0.330 Chirality : 0.039 0.175 1158 Planarity : 0.004 0.053 1272 Dihedral : 11.859 112.161 1191 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.88 % Allowed : 4.71 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 0.24 (0.28), residues: 912 helix: 0.97 (0.25), residues: 426 sheet: -0.28 (0.44), residues: 138 loop : -0.56 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS B 294 PHE 0.016 0.002 PHE C 86 TYR 0.014 0.001 TYR C 191 ARG 0.008 0.001 ARG B 167 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.877 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1806 time to fit residues: 12.0702 Evaluate side-chains 34 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.874 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.038225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.033035 restraints weight = 54258.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.034107 restraints weight = 30297.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.034859 restraints weight = 19360.586| |-----------------------------------------------------------------------------| r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.6710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7481 Z= 0.266 Angle : 0.644 7.925 10145 Z= 0.334 Chirality : 0.039 0.179 1158 Planarity : 0.004 0.056 1272 Dihedral : 11.873 112.367 1191 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.88 % Allowed : 4.82 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 0.18 (0.28), residues: 912 helix: 0.92 (0.24), residues: 426 sheet: -0.29 (0.44), residues: 138 loop : -0.59 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS B 294 PHE 0.018 0.002 PHE C 86 TYR 0.013 0.001 TYR C 191 ARG 0.009 0.001 ARG B 167 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1311.26 seconds wall clock time: 24 minutes 58.01 seconds (1498.01 seconds total)