Starting phenix.real_space_refine (version: dev) on Sat Feb 18 05:19:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1b_9566/02_2023/5h1b_9566_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1b_9566/02_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_9566/02_2023/5h1b_9566.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1b_9566/02_2023/5h1b_9566.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1b_9566/02_2023/5h1b_9566_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1b_9566/02_2023/5h1b_9566_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 4.63, per 1000 atoms: 0.63 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: 3.17 Conformation dependent library (CDL) restraints added in 1.0 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: 0.77 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: 2.16 Time building geometry restraints manager: 3.38 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: 4298 23.74 - 47.48: 138 47.48 - 71.22: 28 71.22 - 94.96: 9 94.96 - 118.70: 3 Dihedral angle restraints: 4476 sinusoidal: 1842 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 4473 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 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. 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.370 Check model and map are aligned: 0.120 Process input model: 22.480 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.060 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 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 : 1.409 18.767 10145 Z= 0.915 Chirality : 0.056 0.321 1158 Planarity : 0.005 0.034 1272 Dihedral : 13.445 118.695 2790 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 % 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 *********************** 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 : 0.886 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: 0.2955 time to fit residues: 48.0189 Evaluate side-chains 66 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 0.884 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.1160 time to fit residues: 3.4399 ------------------------------------------------------------------------------- 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: 0.7084 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 7481 Z= 0.242 Angle : 0.706 12.330 10145 Z= 0.372 Chirality : 0.041 0.153 1158 Planarity : 0.004 0.048 1272 Dihedral : 12.445 116.545 1107 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 1.32 % Allowed : 4.06 % Favored : 94.63 % Rotamer Outliers : 0.40 % 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: -0.41 (0.23), residues: 411 sheet: -0.38 (0.40), residues: 162 loop : 0.76 (0.37), residues: 339 *********************** 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 74 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 0.897 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 74 average time/residue: 0.2510 time to fit residues: 24.4630 Evaluate side-chains 42 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.869 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3133 ------------------------------------------------------------------------------- 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: 1.9990 chunk 68 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 80 optimal weight: 0.0370 overall best weight: 1.8066 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 7481 Z= 0.194 Angle : 0.631 12.252 10145 Z= 0.324 Chirality : 0.038 0.136 1158 Planarity : 0.003 0.039 1272 Dihedral : 11.927 112.804 1107 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 1.32 % Allowed : 4.71 % Favored : 93.97 % Rotamer Outliers : 0.40 % 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: 0.40 (0.28), residues: 912 helix: 0.50 (0.24), residues: 414 sheet: -0.46 (0.39), residues: 165 loop : 0.67 (0.37), residues: 333 *********************** 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 58 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.924 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 58 average time/residue: 0.1803 time to fit residues: 15.3301 Evaluate side-chains 37 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.866 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1509 ------------------------------------------------------------------------------- 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: 6.9990 chunk 42 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.054 7481 Z= 0.433 Angle : 0.778 12.762 10145 Z= 0.405 Chirality : 0.042 0.181 1158 Planarity : 0.005 0.055 1272 Dihedral : 12.297 115.393 1107 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 1.21 % Allowed : 5.15 % Favored : 93.64 % Rotamer Outliers : 0.27 % 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: 0.06 (0.27), residues: 912 helix: 0.68 (0.25), residues: 402 sheet: -0.66 (0.41), residues: 144 loop : -0.21 (0.33), residues: 366 *********************** 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 47 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.901 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 47 average time/residue: 0.1683 time to fit residues: 12.0376 Evaluate side-chains 33 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.858 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1294 ------------------------------------------------------------------------------- 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: 5.9990 chunk 64 optimal weight: 0.0020 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- 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 267 ASN C 135 GLN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS C 242 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.5642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 7481 Z= 0.209 Angle : 0.628 12.260 10145 Z= 0.319 Chirality : 0.038 0.173 1158 Planarity : 0.003 0.054 1272 Dihedral : 11.942 116.114 1107 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 1.21 % Allowed : 4.39 % Favored : 94.41 % Rotamer Outliers : 0.13 % 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: 0.48 (0.28), residues: 912 helix: 1.16 (0.26), residues: 408 sheet: -0.74 (0.41), residues: 144 loop : -0.04 (0.34), residues: 360 *********************** 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 56 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 56 average time/residue: 0.1823 time to fit residues: 15.1280 Evaluate side-chains 41 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.895 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2152 ------------------------------------------------------------------------------- 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: 0.1980 chunk 21 optimal weight: 0.1980 chunk 87 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 0.0040 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 49 optimal weight: 0.0020 overall best weight: 0.8802 ------------------------------------------------------------------------------- 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** B 47 HIS ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN C 47 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: 0.7120 moved from start: 0.6055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 7481 Z= 0.153 Angle : 0.593 12.300 10145 Z= 0.296 Chirality : 0.038 0.145 1158 Planarity : 0.003 0.044 1272 Dihedral : 11.688 112.809 1107 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 1.21 % Allowed : 3.95 % Favored : 94.85 % Rotamer Outliers : 0.00 % 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: 0.62 (0.28), residues: 912 helix: 1.27 (0.25), residues: 429 sheet: -0.56 (0.40), residues: 147 loop : -0.10 (0.35), residues: 336 *********************** 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 61 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1913 time to fit residues: 16.7092 Evaluate side-chains 38 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.871 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1775 ------------------------------------------------------------------------------- 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: 0.5980 chunk 49 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 40 optimal weight: 0.0870 chunk 53 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.9362 ------------------------------------------------------------------------------- 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 206 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.6303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 7481 Z= 0.153 Angle : 0.585 12.421 10145 Z= 0.291 Chirality : 0.038 0.144 1158 Planarity : 0.003 0.036 1272 Dihedral : 11.690 124.256 1107 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 1.21 % Allowed : 4.17 % Favored : 94.63 % Rotamer Outliers : 0.00 % 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: 0.77 (0.28), residues: 912 helix: 1.41 (0.25), residues: 417 sheet: -0.51 (0.43), residues: 138 loop : -0.01 (0.34), residues: 357 *********************** 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 53 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2043 time to fit residues: 15.6544 Evaluate side-chains 37 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.915 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1834 ------------------------------------------------------------------------------- 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: 0.0040 chunk 17 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 overall best weight: 2.3596 ------------------------------------------------------------------------------- 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 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN ** B 145 GLN ** 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: 0.7161 moved from start: 0.6386 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= 0.194 Angle : 0.602 12.614 10145 Z= 0.299 Chirality : 0.038 0.144 1158 Planarity : 0.003 0.039 1272 Dihedral : 11.762 126.821 1107 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.88 % Allowed : 4.17 % Favored : 94.96 % Rotamer Outliers : 0.13 % 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: 0.92 (0.29), residues: 912 helix: 1.62 (0.26), residues: 396 sheet: -0.44 (0.43), residues: 138 loop : 0.06 (0.34), residues: 378 *********************** 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 52 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.794 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 0.1658 time to fit residues: 12.8246 Evaluate side-chains 39 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.794 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0631 ------------------------------------------------------------------------------- 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: 1.9990 chunk 83 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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** ** A 206 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.6359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 7481 Z= 0.330 Angle : 0.707 13.088 10145 Z= 0.353 Chirality : 0.040 0.141 1158 Planarity : 0.004 0.042 1272 Dihedral : 12.131 132.909 1107 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.88 % Allowed : 5.26 % Favored : 93.86 % Rotamer Outliers : 0.00 % 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: 0.33 (0.28), residues: 912 helix: 0.96 (0.25), residues: 411 sheet: -0.47 (0.41), residues: 147 loop : -0.20 (0.35), residues: 354 *********************** 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 44 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.943 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1783 time to fit residues: 11.9373 Evaluate side-chains 36 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.058 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1154 ------------------------------------------------------------------------------- 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: 0.9980 chunk 59 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 55 optimal weight: 0.0570 chunk 43 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 76 optimal weight: 0.0170 chunk 21 optimal weight: 6.9990 overall best weight: 1.8140 ------------------------------------------------------------------------------- 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 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** 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: 0.7179 moved from start: 0.6560 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= 0.185 Angle : 0.632 12.660 10145 Z= 0.310 Chirality : 0.038 0.171 1158 Planarity : 0.003 0.044 1272 Dihedral : 11.714 127.152 1107 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.88 % Allowed : 4.06 % Favored : 95.07 % Rotamer Outliers : 0.00 % 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: 0.66 (0.29), residues: 912 helix: 1.29 (0.26), residues: 411 sheet: -0.35 (0.43), residues: 147 loop : -0.08 (0.36), residues: 354 ********************** 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 49 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.033 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1788 time to fit residues: 13.3125 Evaluate side-chains 40 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.845 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2626 ------------------------------------------------------------------------------- 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: 5.9990 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 29 optimal weight: 0.1980 chunk 73 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 51 optimal weight: 0.1980 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** 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 = 0.2881 r_free = 0.2881 target = 0.039641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.034508 restraints weight = 52450.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.035630 restraints weight = 28879.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.036389 restraints weight = 18129.449| |-----------------------------------------------------------------------------| r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.6639 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= 0.195 Angle : 0.626 12.897 10145 Z= 0.306 Chirality : 0.038 0.137 1158 Planarity : 0.003 0.041 1272 Dihedral : 11.613 128.181 1107 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.88 % Allowed : 4.50 % Favored : 94.63 % Rotamer Outliers : 0.00 % 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: 0.68 (0.29), residues: 912 helix: 1.28 (0.25), residues: 411 sheet: -0.27 (0.44), residues: 147 loop : -0.08 (0.36), residues: 354 =============================================================================== Job complete usr+sys time: 1345.22 seconds wall clock time: 25 minutes 51.85 seconds (1551.85 seconds total)