Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 16:25:18 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1b_9566/12_2021/5h1b_9566_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1b_9566/12_2021/5h1b_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_2021/5h1b_9566.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1b_9566/12_2021/5h1b_9566.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1b_9566/12_2021/5h1b_9566_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1b_9566/12_2021/5h1b_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 Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral 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-1.20rc4-4434/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: {'PTRANS': 9, 'CIS': 2, '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: {'PTRANS': 9, 'CIS': 2, '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: {'PTRANS': 9, 'CIS': 2, '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: 4.51, per 1000 atoms: 0.61 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 Amimo 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: 3.74 Conformation dependent library (CDL) restraints added in 1.1 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: 0.75 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: 2.03 Time building geometry restraints manager: 3.58 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=" O3G ANP A 600 " pdb=" PG ANP A 600 " ideal model delta sigma weight residual 1.582 1.494 0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" O3G ANP B 600 " pdb=" PG ANP B 600 " ideal model delta sigma weight residual 1.582 1.495 0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" O3G ANP C 600 " pdb=" PG ANP C 600 " ideal model delta sigma weight residual 1.582 1.495 0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" O1G ANP C 600 " pdb=" PG ANP C 600 " ideal model delta sigma weight residual 1.496 1.578 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" O1G ANP A 600 " pdb=" PG ANP A 600 " ideal model delta sigma weight residual 1.496 1.577 -0.081 2.00e-02 2.50e+03 1.66e+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=" 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 angle pdb=" N THR C 197 " pdb=" CA THR C 197 " pdb=" C THR C 197 " ideal model delta sigma weight residual 111.71 105.48 6.23 1.15e+00 7.56e-01 2.94e+01 angle pdb=" N GLY C 234 " pdb=" CA GLY C 234 " pdb=" C GLY C 234 " ideal model delta sigma weight residual 111.93 117.94 -6.01 1.15e+00 7.56e-01 2.73e+01 angle pdb=" N GLY B 234 " pdb=" CA GLY B 234 " pdb=" C GLY B 234 " ideal model delta sigma weight residual 111.93 117.92 -5.99 1.15e+00 7.56e-01 2.71e+01 ... (remaining 10140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.94: 4384 34.94 - 69.89: 98 69.89 - 104.83: 9 104.83 - 139.77: 0 139.77 - 174.71: 3 Dihedral angle restraints: 4494 sinusoidal: 1860 harmonic: 2634 Sorted by residual: dihedral pdb=" O1B ANP A 600 " pdb=" N3B ANP A 600 " pdb=" PB ANP A 600 " pdb=" PG ANP A 600 " ideal model delta sinusoidal sigma weight residual 328.52 153.81 174.71 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1B ANP B 600 " pdb=" N3B ANP B 600 " pdb=" PB ANP B 600 " pdb=" PG ANP B 600 " ideal model delta sinusoidal sigma weight residual 328.52 153.84 174.68 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1B ANP C 600 " pdb=" N3B ANP C 600 " pdb=" PB ANP C 600 " pdb=" PG ANP C 600 " ideal model delta sinusoidal sigma weight residual 328.52 153.85 174.67 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 4491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 631 0.040 - 0.080: 372 0.080 - 0.119: 128 0.119 - 0.159: 26 0.159 - 0.199: 7 Chirality restraints: 1164 Sorted by residual: chirality pdb=" PA ANP C 600 " pdb=" O2A ANP C 600 " pdb=" O3A ANP C 600 " pdb=" O5' ANP C 600 " both_signs ideal model delta sigma weight residual True 3.18 2.98 0.20 2.00e-01 2.50e+01 9.87e-01 chirality pdb=" PA ANP A 600 " pdb=" O2A ANP A 600 " pdb=" O3A ANP A 600 " pdb=" O5' ANP A 600 " both_signs ideal model delta sigma weight residual True 3.18 2.99 0.20 2.00e-01 2.50e+01 9.64e-01 chirality pdb=" PA ANP B 600 " pdb=" O2A ANP B 600 " pdb=" O3A ANP B 600 " pdb=" O5' ANP B 600 " both_signs ideal model delta sigma weight residual True 3.18 2.99 0.20 2.00e-01 2.50e+01 9.57e-01 ... (remaining 1161 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 Write .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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.010 Check model and map are aligned: 0.110 Convert atoms to be neutral: 0.060 Process input model: 22.760 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 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:2.110 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 30.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 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 0.088 7481 Z= 0.616 Angle : 1.309 8.184 10145 Z= 0.899 Chirality : 0.055 0.199 1164 Planarity : 0.005 0.034 1272 Dihedral : 14.243 174.713 2808 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 : 0.876 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: 0.2803 time to fit residues: 46.1029 Evaluate side-chains 66 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 0.931 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.1158 time to fit residues: 3.4468 ------------------------------------------------------------------------------- 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: 0.0970 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- 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** ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 7481 Z= 0.262 Angle : 0.787 12.360 10145 Z= 0.409 Chirality : 0.042 0.163 1164 Planarity : 0.005 0.085 1272 Dihedral : 14.946 179.381 1125 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 22.68 Ramachandran Plot: Outliers : 1.32 % Allowed : 5.48 % Favored : 93.20 % 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: -0.91 (0.27), residues: 912 helix: -1.10 (0.22), residues: 411 sheet: -0.87 (0.38), residues: 165 loop : 0.65 (0.38), residues: 336 *********************** 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 70 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 70 average time/residue: 0.2513 time to fit residues: 23.5662 Evaluate side-chains 42 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.876 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2034 ------------------------------------------------------------------------------- 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: 8.9990 chunk 25 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 ASN ** 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: 0.7181 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 7481 Z= 0.317 Angle : 0.751 12.256 10145 Z= 0.390 Chirality : 0.041 0.173 1164 Planarity : 0.005 0.064 1272 Dihedral : 14.594 178.805 1125 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 20.43 Ramachandran Plot: Outliers : 1.21 % Allowed : 5.37 % Favored : 93.42 % 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: -0.37 (0.27), residues: 912 helix: -0.02 (0.24), residues: 411 sheet: -0.64 (0.41), residues: 156 loop : -0.04 (0.35), residues: 345 *********************** 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 60 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.887 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 60 average time/residue: 0.1920 time to fit residues: 16.4556 Evaluate side-chains 35 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.880 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1751 ------------------------------------------------------------------------------- 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: 0.0050 chunk 42 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.7800 ------------------------------------------------------------------------------- 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: 0.7124 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 7481 Z= 0.201 Angle : 0.650 12.298 10145 Z= 0.336 Chirality : 0.038 0.140 1164 Planarity : 0.004 0.065 1272 Dihedral : 14.311 179.518 1125 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 1.21 % Allowed : 4.39 % Favored : 94.41 % 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: -0.13 (0.27), residues: 912 helix: 0.40 (0.24), residues: 432 sheet: -0.65 (0.41), residues: 147 loop : -0.23 (0.35), residues: 333 *********************** 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 58 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1667 time to fit residues: 14.5493 Evaluate side-chains 37 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.900 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1494 ------------------------------------------------------------------------------- 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: 1.9990 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 17 optimal weight: 0.2980 overall best weight: 3.2588 ------------------------------------------------------------------------------- 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: 0.7177 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 7481 Z= 0.246 Angle : 0.657 12.305 10145 Z= 0.337 Chirality : 0.038 0.137 1164 Planarity : 0.004 0.062 1272 Dihedral : 14.298 179.772 1125 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 1.21 % Allowed : 4.61 % Favored : 94.19 % 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: 0.16 (0.28), residues: 912 helix: 0.78 (0.25), residues: 429 sheet: -0.66 (0.40), residues: 147 loop : -0.21 (0.35), residues: 336 *********************** 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 51 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.898 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1703 time to fit residues: 12.8577 Evaluate side-chains 36 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.861 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1000 ------------------------------------------------------------------------------- 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: 9.9990 chunk 21 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- 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 135 GLN ** 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: 0.7246 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 7481 Z= 0.346 Angle : 0.736 12.345 10145 Z= 0.373 Chirality : 0.040 0.173 1164 Planarity : 0.004 0.060 1272 Dihedral : 14.350 179.980 1125 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 1.21 % Allowed : 4.93 % 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: -0.14 (0.27), residues: 912 helix: 0.70 (0.25), residues: 426 sheet: -0.87 (0.41), residues: 144 loop : -0.60 (0.34), residues: 342 *********************** 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 47 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.860 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1761 time to fit residues: 12.5153 Evaluate side-chains 34 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.862 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1354 ------------------------------------------------------------------------------- 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: 1.9990 chunk 49 optimal weight: 5.9990 chunk 73 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 86 optimal weight: 0.3980 chunk 54 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 34 optimal weight: 0.1980 chunk 51 optimal weight: 6.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 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: 0.7141 moved from start: 0.5309 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= 0.167 Angle : 0.655 11.975 10145 Z= 0.325 Chirality : 0.039 0.187 1164 Planarity : 0.003 0.049 1272 Dihedral : 14.088 177.182 1125 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 1.21 % Allowed : 4.61 % Favored : 94.19 % 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: 0.17 (0.28), residues: 912 helix: 0.91 (0.25), residues: 435 sheet: -0.78 (0.43), residues: 135 loop : -0.39 (0.35), residues: 342 *********************** 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 56 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.867 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1707 time to fit residues: 14.2831 Evaluate side-chains 41 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.843 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1556 ------------------------------------------------------------------------------- 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: 9.9990 chunk 17 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 55 optimal weight: 0.0870 chunk 59 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 overall best weight: 5.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 7481 Z= 0.345 Angle : 0.729 12.371 10145 Z= 0.366 Chirality : 0.040 0.146 1164 Planarity : 0.004 0.055 1272 Dihedral : 14.230 177.089 1125 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 1.10 % Allowed : 5.37 % Favored : 93.53 % 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: -0.03 (0.28), residues: 912 helix: 0.90 (0.25), residues: 423 sheet: -0.88 (0.40), residues: 144 loop : -0.65 (0.34), residues: 345 *********************** 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 46 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.659 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1769 time to fit residues: 12.2284 Evaluate side-chains 34 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.915 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2308 ------------------------------------------------------------------------------- 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: 0.9990 chunk 83 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 85 optimal weight: 0.4980 chunk 52 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7206 moved from start: 0.5604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 7481 Z= 0.217 Angle : 0.653 12.175 10145 Z= 0.325 Chirality : 0.039 0.169 1164 Planarity : 0.003 0.049 1272 Dihedral : 14.082 177.528 1125 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.88 % Allowed : 4.61 % Favored : 94.52 % 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: 0.08 (0.28), residues: 912 helix: 1.10 (0.25), residues: 429 sheet: -0.81 (0.43), residues: 135 loop : -0.82 (0.34), residues: 348 *********************** 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 50 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.923 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1717 time to fit residues: 13.2101 Evaluate side-chains 35 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.889 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1006 ------------------------------------------------------------------------------- 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: 4.9990 chunk 59 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 0.0070 chunk 21 optimal weight: 8.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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: 0.7190 moved from start: 0.5769 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= 0.196 Angle : 0.659 12.224 10145 Z= 0.325 Chirality : 0.038 0.152 1164 Planarity : 0.004 0.079 1272 Dihedral : 14.042 178.655 1125 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.88 % Allowed : 4.71 % Favored : 94.41 % 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: 0.15 (0.28), residues: 912 helix: 1.11 (0.25), residues: 429 sheet: -0.69 (0.44), residues: 135 loop : -0.77 (0.34), residues: 348 ********************** 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 54 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.854 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1609 time to fit residues: 13.1842 Evaluate side-chains 39 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.892 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1795 ------------------------------------------------------------------------------- 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: 7.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 = 0.2878 r_free = 0.2878 target = 0.039331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.034423 restraints weight = 55987.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.035459 restraints weight = 31219.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.036195 restraints weight = 19872.790| |-----------------------------------------------------------------------------| r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.5861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 7481 Z= 0.232 Angle : 0.659 12.301 10145 Z= 0.327 Chirality : 0.038 0.143 1164 Planarity : 0.004 0.044 1272 Dihedral : 14.053 179.100 1125 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.88 % Allowed : 4.82 % Favored : 94.30 % 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: 0.18 (0.28), residues: 912 helix: 1.03 (0.25), residues: 429 sheet: -0.71 (0.42), residues: 147 loop : -0.55 (0.35), residues: 336 =============================================================================== Job complete usr+sys time: 1259.41 seconds wall clock time: 24 minutes 5.23 seconds (1445.23 seconds total)