Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 20:08:32 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wj3_21687/12_2021/6wj3_21687_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wj3_21687/12_2021/6wj3_21687.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wj3_21687/12_2021/6wj3_21687_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wj3_21687/12_2021/6wj3_21687_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wj3_21687/12_2021/6wj3_21687_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wj3_21687/12_2021/6wj3_21687.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wj3_21687/12_2021/6wj3_21687.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wj3_21687/12_2021/6wj3_21687_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wj3_21687/12_2021/6wj3_21687_updated.pdb" } resolution = 3.9 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= 0.001 sd= 0.011 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 None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 8912 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 640 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 6, 'TRANS': 89} Chain breaks: 1 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 905 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain breaks: 1 Chain: "C" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "D" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 650 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 47 Chain: "E" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 663 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "F" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2167 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 104 Chain: "G" Number of atoms: 2487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2487 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 300} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 419 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 53} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'U3J': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.30, per 1000 atoms: 0.59 Number of scatterers: 8912 At special positions: 0 Unit cell: (71.631, 101.193, 155.769, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 4 15.00 O 1687 8.00 N 1515 7.00 C 5660 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=0, symmetry=0 Time building additional restraints: 3.58 Conformation dependent library (CDL) restraints added in 1.4 seconds 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2234 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 8 sheets defined 37.1% alpha, 12.9% 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 50 through 64 Processing helix chain 'A' and resid 84 through 96 Processing helix chain 'A' and resid 115 through 118 No H-bonds generated for 'chain 'A' and resid 115 through 118' Processing helix chain 'A' and resid 127 through 143 Processing helix chain 'B' and resid 4 through 14 removed outlier: 4.356A pdb=" N ALA B 14 " --> pdb=" O VAL B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 58 Processing helix chain 'B' and resid 103 through 122 removed outlier: 5.261A pdb=" N GLU B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) Proline residue: B 118 - end of helix Processing helix chain 'C' and resid 7 through 15 Proline residue: C 14 - end of helix Processing helix chain 'C' and resid 42 through 44 No H-bonds generated for 'chain 'C' and resid 42 through 44' Processing helix chain 'C' and resid 47 through 60 Processing helix chain 'C' and resid 100 through 109 Processing helix chain 'C' and resid 111 through 120 Processing helix chain 'D' and resid 4 through 10 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 37 through 51 Processing helix chain 'E' and resid 85 through 93 Processing helix chain 'E' and resid 124 through 137 Processing helix chain 'F' and resid 22 through 28 Processing helix chain 'F' and resid 70 through 78 Processing helix chain 'F' and resid 100 through 115 removed outlier: 4.010A pdb=" N HIS F 104 " --> pdb=" O GLU F 100 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR F 105 " --> pdb=" O LYS F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 151 Processing helix chain 'F' and resid 168 through 180 Processing helix chain 'F' and resid 185 through 197 Processing helix chain 'F' and resid 228 through 245 removed outlier: 3.995A pdb=" N LYS F 244 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LEU F 245 " --> pdb=" O SER F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 300 Processing helix chain 'G' and resid 77 through 81 Processing helix chain 'G' and resid 89 through 92 removed outlier: 3.739A pdb=" N PHE G 92 " --> pdb=" O GLU G 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 89 through 92' Processing helix chain 'G' and resid 131 through 135 Processing helix chain 'G' and resid 151 through 167 Processing helix chain 'G' and resid 185 through 204 Processing helix chain 'G' and resid 224 through 236 removed outlier: 3.983A pdb=" N LEU G 236 " --> pdb=" O VAL G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 254 Processing helix chain 'G' and resid 282 through 299 Processing helix chain 'G' and resid 344 through 346 No H-bonds generated for 'chain 'G' and resid 344 through 346' Processing helix chain 'G' and resid 349 through 368 Processing helix chain 'H' and resid 61 through 73 Processing helix chain 'H' and resid 92 through 94 No H-bonds generated for 'chain 'H' and resid 92 through 94' Processing sheet with id= A, first strand: chain 'B' and resid 72 through 75 removed outlier: 3.784A pdb=" N SER B 21 " --> pdb=" O TYR B 94 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA B 33 " --> pdb=" O LEU B 24 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 21 through 25 removed outlier: 4.602A pdb=" N LEU C 86 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL C 90 " --> pdb=" O ASN C 84 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ASN C 84 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N PHE C 92 " --> pdb=" O GLN C 82 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N GLN C 82 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ALA C 94 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N VAL C 80 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL C 80 " --> pdb=" O CYS C 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 18 through 21 removed outlier: 3.559A pdb=" N SER D 80 " --> pdb=" O ARG D 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 156 through 160 removed outlier: 3.654A pdb=" N THR E 165 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY E 102 " --> pdb=" O HIS E 169 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG E 116 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS E 105 " --> pdb=" O GLY E 114 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY E 114 " --> pdb=" O CYS E 105 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'F' and resid 58 through 61 removed outlier: 7.478A pdb=" N VAL F 10 " --> pdb=" O ASN F 59 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N TRP F 61 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU F 12 " --> pdb=" O TRP F 61 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU F 11 " --> pdb=" O GLU F 86 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU F 88 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N MET F 13 " --> pdb=" O LEU F 88 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TYR F 90 " --> pdb=" O MET F 13 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N PHE F 123 " --> pdb=" O TYR F 90 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N PHE F 92 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU F 125 " --> pdb=" O PHE F 92 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE F 160 " --> pdb=" O CYS F 124 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 202 through 204 removed outlier: 3.896A pdb=" N GLU F 202 " --> pdb=" O VAL F 275 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET F 273 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL F 272 " --> pdb=" O ILE F 265 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ILE F 265 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL F 274 " --> pdb=" O ILE F 263 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ILE F 263 " --> pdb=" O VAL F 274 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 64 through 67 removed outlier: 7.512A pdb=" N ALA G 139 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N MET G 67 " --> pdb=" O ALA G 139 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE G 141 " --> pdb=" O MET G 67 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASN G 172 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N TYR G 142 " --> pdb=" O ASN G 172 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLU G 174 " --> pdb=" O TYR G 142 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE G 144 " --> pdb=" O GLU G 174 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE G 176 " --> pdb=" O ILE G 144 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N SER G 214 " --> pdb=" O VAL G 175 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE G 177 " --> pdb=" O SER G 214 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TYR G 216 " --> pdb=" O ILE G 177 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'G' and resid 258 through 263 removed outlier: 3.741A pdb=" N LYS G 258 " --> pdb=" O ILE G 340 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL G 325 " --> pdb=" O LEU G 341 " (cutoff:3.500A) 345 hydrogen bonds defined for protein. 1017 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: 2.45 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2941 1.34 - 1.46: 1796 1.46 - 1.58: 4250 1.58 - 1.69: 8 1.69 - 1.81: 74 Bond restraints: 9069 Sorted by residual: bond pdb=" C4' U3J G 500 " pdb=" O4' U3J G 500 " ideal model delta sigma weight residual 1.274 1.652 -0.378 2.00e-02 2.50e+03 3.56e+02 bond pdb=" C1' U3J G 500 " pdb=" O4' U3J G 500 " ideal model delta sigma weight residual 1.622 1.304 0.318 2.00e-02 2.50e+03 2.53e+02 bond pdb=" C1' U3J G 500 " pdb=" C2' U3J G 500 " ideal model delta sigma weight residual 1.296 1.598 -0.302 2.00e-02 2.50e+03 2.28e+02 bond pdb=" C2 U3J G 500 " pdb=" O2 U3J G 500 " ideal model delta sigma weight residual 1.185 1.421 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C3' U3J G 500 " pdb=" C4' U3J G 500 " ideal model delta sigma weight residual 1.566 1.336 0.230 2.00e-02 2.50e+03 1.33e+02 ... (remaining 9064 not shown) Histogram of bond angle deviations from ideal: 100.53 - 107.68: 290 107.68 - 114.83: 5483 114.83 - 121.99: 4695 121.99 - 129.14: 1798 129.14 - 136.30: 44 Bond angle restraints: 12310 Sorted by residual: angle pdb=" O1A GDP F 500 " pdb=" PA GDP F 500 " pdb=" O2A GDP F 500 " ideal model delta sigma weight residual 109.50 120.12 -10.62 3.00e+00 1.11e-01 1.25e+01 angle pdb=" N ARG C 85 " pdb=" CA ARG C 85 " pdb=" C ARG C 85 " ideal model delta sigma weight residual 114.56 110.22 4.34 1.27e+00 6.20e-01 1.17e+01 angle pdb=" N VAL G 331 " pdb=" CA VAL G 331 " pdb=" C VAL G 331 " ideal model delta sigma weight residual 111.67 108.67 3.00 9.50e-01 1.11e+00 9.97e+00 angle pdb=" CA ARG C 85 " pdb=" C ARG C 85 " pdb=" N LEU C 86 " ideal model delta sigma weight residual 119.26 116.40 2.86 1.14e+00 7.69e-01 6.30e+00 angle pdb=" C VAL B 86 " pdb=" N ALA B 87 " pdb=" CA ALA B 87 " ideal model delta sigma weight residual 121.54 125.95 -4.41 1.91e+00 2.74e-01 5.33e+00 ... (remaining 12305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.17: 5360 32.17 - 64.33: 94 64.33 - 96.50: 6 96.50 - 128.67: 1 128.67 - 160.84: 1 Dihedral angle restraints: 5462 sinusoidal: 2036 harmonic: 3426 Sorted by residual: dihedral pdb=" C5' GDP F 500 " pdb=" O5' GDP F 500 " pdb=" PA GDP F 500 " pdb=" O3A GDP F 500 " ideal model delta sinusoidal sigma weight residual 179.98 81.38 98.60 1 2.00e+01 2.50e-03 2.76e+01 dihedral pdb=" C5' U3J G 500 " pdb=" O5' U3J G 500 " pdb=" PA U3J G 500 " pdb=" O2A U3J G 500 " ideal model delta sinusoidal sigma weight residual 84.94 -75.90 160.84 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" CA HIS E 161 " pdb=" C HIS E 161 " pdb=" N ASP E 162 " pdb=" CA ASP E 162 " ideal model delta harmonic sigma weight residual 180.00 160.59 19.41 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 5459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 989 0.037 - 0.073: 328 0.073 - 0.110: 104 0.110 - 0.146: 26 0.146 - 0.183: 1 Chirality restraints: 1448 Sorted by residual: chirality pdb=" C2' U3J G 500 " pdb=" C1' U3J G 500 " pdb=" C3' U3J G 500 " pdb=" O2' U3J G 500 " both_signs ideal model delta sigma weight residual False 2.36 2.55 -0.18 2.00e-01 2.50e+01 8.36e-01 chirality pdb=" CA VAL F 272 " pdb=" N VAL F 272 " pdb=" C VAL F 272 " pdb=" CB VAL F 272 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE F 181 " pdb=" N ILE F 181 " pdb=" C ILE F 181 " pdb=" CB ILE F 181 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 1445 not shown) Planarity restraints: 1571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 86 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO C 87 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 87 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 87 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR H 76 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.38e+00 pdb=" N PRO H 77 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO H 77 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 77 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 181 " -0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO F 182 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO F 182 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO F 182 " -0.015 5.00e-02 4.00e+02 ... (remaining 1568 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1038 2.75 - 3.29: 9137 3.29 - 3.82: 14597 3.82 - 4.36: 15876 4.36 - 4.90: 27971 Nonbonded interactions: 68619 Sorted by model distance: nonbonded pdb=" O GLY G 73 " pdb=" OG SER G 76 " model vdw 2.210 2.440 nonbonded pdb=" O THR C 57 " pdb=" OG SER C 61 " model vdw 2.230 2.440 nonbonded pdb=" O LEU G 69 " pdb=" OG SER G 72 " model vdw 2.257 2.440 nonbonded pdb=" O PHE C 49 " pdb=" OG1 THR C 52 " model vdw 2.261 2.440 nonbonded pdb=" CD1 ILE A 124 " pdb=" SG CYS E 148 " model vdw 2.273 3.820 ... (remaining 68614 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 46 5.16 5 C 5660 2.51 5 N 1515 2.21 5 O 1687 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.510 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.090 Process input model: 26.020 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 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: 35.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.378 9069 Z= 0.640 Angle : 0.499 10.616 12310 Z= 0.266 Chirality : 0.041 0.183 1448 Planarity : 0.003 0.047 1571 Dihedral : 12.830 160.836 3228 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.71 % Favored : 95.20 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.22), residues: 1146 helix: -0.39 (0.22), residues: 461 sheet: -2.70 (0.31), residues: 228 loop : -2.89 (0.25), residues: 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2295 time to fit residues: 57.1651 Evaluate side-chains 102 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.104 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.4980 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 57 optimal weight: 0.0010 chunk 45 optimal weight: 0.0870 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 53 optimal weight: 0.0060 chunk 65 optimal weight: 0.6980 chunk 102 optimal weight: 10.0000 overall best weight: 0.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN F 115 GLN G 197 GLN G 245 ASN G 253 ASN H 49 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.070 9069 Z= 0.160 Angle : 0.578 10.549 12310 Z= 0.279 Chirality : 0.042 0.169 1448 Planarity : 0.003 0.041 1571 Dihedral : 6.693 157.759 1248 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.24), residues: 1146 helix: 0.74 (0.24), residues: 459 sheet: -2.20 (0.32), residues: 228 loop : -2.44 (0.27), residues: 459 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 127 average time/residue: 0.1992 time to fit residues: 35.7470 Evaluate side-chains 105 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 1.122 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0865 time to fit residues: 2.8468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 85 optimal weight: 0.0570 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN B 61 ASN ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 245 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9069 Z= 0.207 Angle : 0.571 8.181 12310 Z= 0.280 Chirality : 0.042 0.175 1448 Planarity : 0.004 0.110 1571 Dihedral : 6.700 155.267 1248 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer Outliers : 2.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.25), residues: 1146 helix: 1.12 (0.24), residues: 460 sheet: -1.99 (0.33), residues: 231 loop : -2.16 (0.28), residues: 455 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 126 average time/residue: 0.2089 time to fit residues: 37.2010 Evaluate side-chains 101 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 1.155 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.0830 time to fit residues: 2.9534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.6980 chunk 77 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 109 optimal weight: 30.0000 chunk 97 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 90 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.082 9069 Z= 0.177 Angle : 0.570 10.780 12310 Z= 0.277 Chirality : 0.042 0.171 1448 Planarity : 0.003 0.058 1571 Dihedral : 6.557 152.108 1248 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.26), residues: 1146 helix: 1.24 (0.25), residues: 465 sheet: -1.89 (0.34), residues: 228 loop : -2.03 (0.29), residues: 453 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 107 average time/residue: 0.2009 time to fit residues: 30.6971 Evaluate side-chains 99 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 1.033 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0925 time to fit residues: 2.8442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 27 optimal weight: 0.0970 chunk 36 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.108 9069 Z= 0.175 Angle : 0.545 6.891 12310 Z= 0.268 Chirality : 0.042 0.170 1448 Planarity : 0.004 0.053 1571 Dihedral : 6.427 150.381 1248 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.26), residues: 1146 helix: 1.39 (0.25), residues: 466 sheet: -1.76 (0.34), residues: 227 loop : -1.96 (0.29), residues: 453 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 113 average time/residue: 0.1954 time to fit residues: 31.6469 Evaluate side-chains 100 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 1.119 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0843 time to fit residues: 2.8315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 90 optimal weight: 0.3980 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.123 9069 Z= 0.191 Angle : 0.567 8.065 12310 Z= 0.278 Chirality : 0.042 0.172 1448 Planarity : 0.003 0.050 1571 Dihedral : 6.330 149.291 1248 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.26), residues: 1146 helix: 1.47 (0.25), residues: 463 sheet: -1.70 (0.34), residues: 227 loop : -1.95 (0.29), residues: 456 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 106 average time/residue: 0.1952 time to fit residues: 30.2791 Evaluate side-chains 97 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 1.120 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0774 time to fit residues: 2.6206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.147 9069 Z= 0.204 Angle : 0.572 8.629 12310 Z= 0.282 Chirality : 0.042 0.171 1448 Planarity : 0.003 0.048 1571 Dihedral : 5.776 148.124 1248 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.26), residues: 1146 helix: 1.51 (0.25), residues: 463 sheet: -1.66 (0.34), residues: 225 loop : -1.86 (0.29), residues: 458 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 106 average time/residue: 0.1996 time to fit residues: 30.4502 Evaluate side-chains 93 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 1.109 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0852 time to fit residues: 2.1261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 85 optimal weight: 0.0170 chunk 99 optimal weight: 0.0670 chunk 104 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.566 9069 Z= 0.588 Angle : 0.962 73.883 12310 Z= 0.416 Chirality : 0.042 0.179 1448 Planarity : 0.004 0.070 1571 Dihedral : 5.717 147.454 1248 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.26), residues: 1146 helix: 1.46 (0.25), residues: 463 sheet: -1.61 (0.35), residues: 219 loop : -1.84 (0.29), residues: 464 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 103 average time/residue: 0.2041 time to fit residues: 30.7009 Evaluate side-chains 95 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 1.107 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0915 time to fit residues: 2.5083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 HIS G 245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.566 9069 Z= 0.718 Angle : 1.017 73.882 12310 Z= 0.469 Chirality : 0.042 0.179 1448 Planarity : 0.005 0.143 1571 Dihedral : 5.717 147.454 1248 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.26), residues: 1146 helix: 1.46 (0.25), residues: 463 sheet: -1.61 (0.35), residues: 219 loop : -1.84 (0.29), residues: 464 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.1934 time to fit residues: 25.7185 Evaluate side-chains 89 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 103 optimal weight: 0.4980 chunk 89 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 27 optimal weight: 0.0050 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.566 9069 Z= 0.718 Angle : 1.017 73.882 12310 Z= 0.469 Chirality : 0.042 0.179 1448 Planarity : 0.005 0.143 1571 Dihedral : 5.717 147.454 1248 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.26), residues: 1146 helix: 1.46 (0.25), residues: 463 sheet: -1.61 (0.35), residues: 219 loop : -1.84 (0.29), residues: 464 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.1869 time to fit residues: 25.0248 Evaluate side-chains 89 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.132 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.0020 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 0.0770 chunk 64 optimal weight: 0.5980 overall best weight: 0.5348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.082512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.067431 restraints weight = 36042.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.069430 restraints weight = 20866.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.070791 restraints weight = 14311.433| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.566 9069 Z= 0.718 Angle : 1.017 73.882 12310 Z= 0.469 Chirality : 0.042 0.179 1448 Planarity : 0.005 0.143 1571 Dihedral : 5.717 147.454 1248 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.26), residues: 1146 helix: 1.46 (0.25), residues: 463 sheet: -1.61 (0.35), residues: 219 loop : -1.84 (0.29), residues: 464 =============================================================================== Job complete usr+sys time: 1725.13 seconds wall clock time: 32 minutes 27.40 seconds (1947.40 seconds total)