Starting phenix.real_space_refine (version: dev) on Mon Feb 20 23:46:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dyr_30923/02_2023/7dyr_30923.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dyr_30923/02_2023/7dyr_30923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dyr_30923/02_2023/7dyr_30923.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dyr_30923/02_2023/7dyr_30923.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dyr_30923/02_2023/7dyr_30923.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dyr_30923/02_2023/7dyr_30923.pdb" } resolution = 2.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "Y GLU 2": "OE1" <-> "OE2" Residue "Y ARG 31": "NH1" <-> "NH2" Residue "Y GLU 57": "OE1" <-> "OE2" Residue "Y GLU 166": "OE1" <-> "OE2" Residue "Y ARG 202": "NH1" <-> "NH2" Residue "Y ARG 247": "NH1" <-> "NH2" Residue "Z ARG 54": "NH1" <-> "NH2" Residue "Z GLU 73": "OE1" <-> "OE2" Residue "Z GLU 94": "OE1" <-> "OE2" Residue "Z ARG 96": "NH1" <-> "NH2" Residue "Z ARG 131": "NH1" <-> "NH2" Residue "Z GLU 193": "OE1" <-> "OE2" Residue "Z ARG 221": "NH1" <-> "NH2" Residue "B GLU 2": "OE1" <-> "OE2" Residue "B ARG 31": "NH1" <-> "NH2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B ARG 247": "NH1" <-> "NH2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C ARG 96": "NH1" <-> "NH2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "E GLU 2": "OE1" <-> "OE2" Residue "E ARG 31": "NH1" <-> "NH2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E ARG 202": "NH1" <-> "NH2" Residue "E ARG 247": "NH1" <-> "NH2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F GLU 73": "OE1" <-> "OE2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F ARG 96": "NH1" <-> "NH2" Residue "F ARG 131": "NH1" <-> "NH2" Residue "F GLU 193": "OE1" <-> "OE2" Residue "F ARG 221": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 13326 Number of models: 1 Model: "" Number of chains: 12 Chain: "Y" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1814 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "Z" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2114 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 12, 'TRANS': 261} Chain: "A" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 502 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "B" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1814 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "C" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2114 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 12, 'TRANS': 261} Chain: "D" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 502 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "E" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1814 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "F" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2114 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 12, 'TRANS': 261} Chain: "G" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 502 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "Z" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.64, per 1000 atoms: 0.57 Number of scatterers: 13326 At special positions: 0 Unit cell: (120.954, 128.381, 85.941, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 2349 8.00 N 2229 7.00 C 8667 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.66 Conformation dependent library (CDL) restraints added in 2.0 seconds 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3156 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 3 sheets defined 77.1% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'Y' and resid 4 through 25 removed outlier: 3.634A pdb=" N ILE Y 23 " --> pdb=" O GLY Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 31 through 44 removed outlier: 4.334A pdb=" N THR Y 37 " --> pdb=" O LEU Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 61 removed outlier: 3.868A pdb=" N GLY Y 49 " --> pdb=" O ASP Y 45 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET Y 58 " --> pdb=" O GLY Y 54 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE Y 59 " --> pdb=" O THR Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 73 through 87 removed outlier: 4.183A pdb=" N ALA Y 77 " --> pdb=" O ASP Y 73 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR Y 82 " --> pdb=" O SER Y 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 91 through 98 removed outlier: 3.542A pdb=" N LEU Y 98 " --> pdb=" O ALA Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 98 through 117 Processing helix chain 'Y' and resid 117 through 129 removed outlier: 3.662A pdb=" N ASP Y 129 " --> pdb=" O ASP Y 125 " (cutoff:3.500A) Processing helix chain 'Y' and resid 132 through 143 Processing helix chain 'Y' and resid 143 through 161 removed outlier: 4.229A pdb=" N GLN Y 147 " --> pdb=" O SER Y 143 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL Y 151 " --> pdb=" O GLN Y 147 " (cutoff:3.500A) Proline residue: Y 154 - end of helix removed outlier: 3.808A pdb=" N ALA Y 159 " --> pdb=" O ALA Y 155 " (cutoff:3.500A) Processing helix chain 'Y' and resid 165 through 171 removed outlier: 3.727A pdb=" N ASN Y 169 " --> pdb=" O SER Y 165 " (cutoff:3.500A) Processing helix chain 'Y' and resid 176 through 202 removed outlier: 4.323A pdb=" N ASN Y 183 " --> pdb=" O THR Y 179 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET Y 188 " --> pdb=" O ILE Y 184 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL Y 190 " --> pdb=" O GLY Y 186 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL Y 191 " --> pdb=" O GLY Y 187 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL Y 192 " --> pdb=" O MET Y 188 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY Y 193 " --> pdb=" O ILE Y 189 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR Y 194 " --> pdb=" O VAL Y 190 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG Y 202 " --> pdb=" O ILE Y 198 " (cutoff:3.500A) Processing helix chain 'Y' and resid 207 through 220 removed outlier: 3.635A pdb=" N TYR Y 211 " --> pdb=" O MET Y 207 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR Y 220 " --> pdb=" O THR Y 216 " (cutoff:3.500A) Processing helix chain 'Y' and resid 223 through 241 Processing helix chain 'Z' and resid 18 through 28 removed outlier: 3.549A pdb=" N ARG Z 22 " --> pdb=" O GLN Z 18 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL Z 24 " --> pdb=" O ASP Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 29 through 31 No H-bonds generated for 'chain 'Z' and resid 29 through 31' Processing helix chain 'Z' and resid 41 through 49 Processing helix chain 'Z' and resid 49 through 57 removed outlier: 3.784A pdb=" N ARG Z 55 " --> pdb=" O PRO Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 62 through 72 removed outlier: 3.594A pdb=" N HIS Z 71 " --> pdb=" O ALA Z 67 " (cutoff:3.500A) Processing helix chain 'Z' and resid 82 through 99 Processing helix chain 'Z' and resid 106 through 127 removed outlier: 3.715A pdb=" N GLY Z 116 " --> pdb=" O VAL Z 112 " (cutoff:3.500A) Proline residue: Z 117 - end of helix removed outlier: 3.512A pdb=" N ASP Z 123 " --> pdb=" O ALA Z 119 " (cutoff:3.500A) Proline residue: Z 124 - end of helix Processing helix chain 'Z' and resid 129 through 145 removed outlier: 4.375A pdb=" N SER Z 144 " --> pdb=" O GLY Z 140 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY Z 145 " --> pdb=" O ILE Z 141 " (cutoff:3.500A) Processing helix chain 'Z' and resid 147 through 180 removed outlier: 3.520A pdb=" N VAL Z 160 " --> pdb=" O LEU Z 156 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA Z 163 " --> pdb=" O LEU Z 159 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP Z 178 " --> pdb=" O SER Z 174 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL Z 180 " --> pdb=" O GLY Z 176 " (cutoff:3.500A) Processing helix chain 'Z' and resid 181 through 183 No H-bonds generated for 'chain 'Z' and resid 181 through 183' Processing helix chain 'Z' and resid 186 through 211 removed outlier: 3.777A pdb=" N LYS Z 190 " --> pdb=" O GLY Z 186 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN Z 208 " --> pdb=" O GLY Z 204 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR Z 211 " --> pdb=" O VAL Z 207 " (cutoff:3.500A) Processing helix chain 'Z' and resid 234 through 242 Processing helix chain 'Z' and resid 244 through 260 Processing helix chain 'Z' and resid 263 through 281 removed outlier: 3.632A pdb=" N ILE Z 267 " --> pdb=" O ASN Z 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 24 Processing helix chain 'A' and resid 28 through 52 removed outlier: 3.680A pdb=" N ALA A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.634A pdb=" N ILE B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 44 removed outlier: 4.334A pdb=" N THR B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 61 removed outlier: 3.868A pdb=" N GLY B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET B 58 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 4.183A pdb=" N ALA B 77 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR B 82 " --> pdb=" O SER B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 98 removed outlier: 3.543A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 117 Processing helix chain 'B' and resid 117 through 129 removed outlier: 3.662A pdb=" N ASP B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 143 Processing helix chain 'B' and resid 143 through 161 removed outlier: 4.229A pdb=" N GLN B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Proline residue: B 154 - end of helix removed outlier: 3.808A pdb=" N ALA B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 171 removed outlier: 3.726A pdb=" N ASN B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 202 removed outlier: 4.323A pdb=" N ASN B 183 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL B 192 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY B 193 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG B 202 " --> pdb=" O ILE B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 220 removed outlier: 3.635A pdb=" N TYR B 211 " --> pdb=" O MET B 207 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B 220 " --> pdb=" O THR B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 241 Processing helix chain 'C' and resid 18 through 28 removed outlier: 3.549A pdb=" N ARG C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 24 " --> pdb=" O ASP C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 49 through 57 removed outlier: 3.784A pdb=" N ARG C 55 " --> pdb=" O PRO C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 72 removed outlier: 3.595A pdb=" N HIS C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 99 Processing helix chain 'C' and resid 106 through 127 removed outlier: 3.715A pdb=" N GLY C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Proline residue: C 117 - end of helix removed outlier: 3.512A pdb=" N ASP C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Proline residue: C 124 - end of helix Processing helix chain 'C' and resid 129 through 145 removed outlier: 4.375A pdb=" N SER C 144 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY C 145 " --> pdb=" O ILE C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 180 removed outlier: 3.520A pdb=" N VAL C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA C 163 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C 180 " --> pdb=" O GLY C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 183 No H-bonds generated for 'chain 'C' and resid 181 through 183' Processing helix chain 'C' and resid 186 through 211 removed outlier: 3.777A pdb=" N LYS C 190 " --> pdb=" O GLY C 186 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR C 211 " --> pdb=" O VAL C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 242 Processing helix chain 'C' and resid 244 through 260 Processing helix chain 'C' and resid 263 through 281 removed outlier: 3.632A pdb=" N ILE C 267 " --> pdb=" O ASN C 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 24 Processing helix chain 'D' and resid 28 through 52 removed outlier: 3.680A pdb=" N ALA D 33 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY D 38 " --> pdb=" O LEU D 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 25 removed outlier: 3.634A pdb=" N ILE E 23 " --> pdb=" O GLY E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 44 removed outlier: 4.334A pdb=" N THR E 37 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 61 removed outlier: 3.869A pdb=" N GLY E 49 " --> pdb=" O ASP E 45 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET E 58 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 87 removed outlier: 4.183A pdb=" N ALA E 77 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR E 82 " --> pdb=" O SER E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 98 removed outlier: 3.542A pdb=" N LEU E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 Processing helix chain 'E' and resid 117 through 129 removed outlier: 3.662A pdb=" N ASP E 129 " --> pdb=" O ASP E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 143 Processing helix chain 'E' and resid 143 through 161 removed outlier: 4.229A pdb=" N GLN E 147 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL E 151 " --> pdb=" O GLN E 147 " (cutoff:3.500A) Proline residue: E 154 - end of helix removed outlier: 3.808A pdb=" N ALA E 159 " --> pdb=" O ALA E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 171 removed outlier: 3.726A pdb=" N ASN E 169 " --> pdb=" O SER E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 202 removed outlier: 4.323A pdb=" N ASN E 183 " --> pdb=" O THR E 179 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET E 188 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL E 190 " --> pdb=" O GLY E 186 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL E 191 " --> pdb=" O GLY E 187 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL E 192 " --> pdb=" O MET E 188 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY E 193 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR E 194 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG E 202 " --> pdb=" O ILE E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 220 removed outlier: 3.635A pdb=" N TYR E 211 " --> pdb=" O MET E 207 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR E 220 " --> pdb=" O THR E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 241 Processing helix chain 'F' and resid 18 through 28 removed outlier: 3.549A pdb=" N ARG F 22 " --> pdb=" O GLN F 18 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL F 24 " --> pdb=" O ASP F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 41 through 49 Processing helix chain 'F' and resid 49 through 57 removed outlier: 3.784A pdb=" N ARG F 55 " --> pdb=" O PRO F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 72 removed outlier: 3.594A pdb=" N HIS F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 99 Processing helix chain 'F' and resid 106 through 127 removed outlier: 3.716A pdb=" N GLY F 116 " --> pdb=" O VAL F 112 " (cutoff:3.500A) Proline residue: F 117 - end of helix removed outlier: 3.512A pdb=" N ASP F 123 " --> pdb=" O ALA F 119 " (cutoff:3.500A) Proline residue: F 124 - end of helix Processing helix chain 'F' and resid 129 through 145 removed outlier: 4.375A pdb=" N SER F 144 " --> pdb=" O GLY F 140 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY F 145 " --> pdb=" O ILE F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 180 removed outlier: 3.520A pdb=" N VAL F 160 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA F 163 " --> pdb=" O LEU F 159 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP F 178 " --> pdb=" O SER F 174 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 183 No H-bonds generated for 'chain 'F' and resid 181 through 183' Processing helix chain 'F' and resid 186 through 211 removed outlier: 3.777A pdb=" N LYS F 190 " --> pdb=" O GLY F 186 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN F 208 " --> pdb=" O GLY F 204 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR F 211 " --> pdb=" O VAL F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 242 Processing helix chain 'F' and resid 244 through 260 Processing helix chain 'F' and resid 263 through 281 removed outlier: 3.632A pdb=" N ILE F 267 " --> pdb=" O ASN F 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 24 Processing helix chain 'G' and resid 28 through 52 removed outlier: 3.680A pdb=" N ALA G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU G 34 " --> pdb=" O GLY G 30 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Z' and resid 218 through 221 removed outlier: 7.009A pdb=" N THR Z 232 " --> pdb=" O VAL Z 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 218 through 221 removed outlier: 7.009A pdb=" N THR C 232 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 218 through 221 removed outlier: 7.009A pdb=" N THR F 232 " --> pdb=" O VAL F 219 " (cutoff:3.500A) 888 hydrogen bonds defined for protein. 2664 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: 4.00 Time building geometry restraints manager: 6.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4269 1.34 - 1.46: 2665 1.46 - 1.58: 6509 1.58 - 1.70: 0 1.70 - 1.82: 147 Bond restraints: 13590 Sorted by residual: bond pdb=" N GLN F 41 " pdb=" CA GLN F 41 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.29e-02 6.01e+03 3.59e+00 bond pdb=" N GLN C 41 " pdb=" CA GLN C 41 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.29e-02 6.01e+03 3.22e+00 bond pdb=" CB PRO Z 132 " pdb=" CG PRO Z 132 " ideal model delta sigma weight residual 1.492 1.406 0.086 5.00e-02 4.00e+02 2.93e+00 bond pdb=" CB PRO C 132 " pdb=" CG PRO C 132 " ideal model delta sigma weight residual 1.492 1.407 0.085 5.00e-02 4.00e+02 2.92e+00 bond pdb=" CB PRO F 132 " pdb=" CG PRO F 132 " ideal model delta sigma weight residual 1.492 1.407 0.085 5.00e-02 4.00e+02 2.91e+00 ... (remaining 13585 not shown) Histogram of bond angle deviations from ideal: 99.66 - 106.58: 407 106.58 - 113.50: 7725 113.50 - 120.42: 5520 120.42 - 127.34: 4699 127.34 - 134.27: 147 Bond angle restraints: 18498 Sorted by residual: angle pdb=" N VAL E 156 " pdb=" CA VAL E 156 " pdb=" C VAL E 156 " ideal model delta sigma weight residual 111.81 108.08 3.73 8.60e-01 1.35e+00 1.88e+01 angle pdb=" N VAL Y 156 " pdb=" CA VAL Y 156 " pdb=" C VAL Y 156 " ideal model delta sigma weight residual 111.81 108.08 3.73 8.60e-01 1.35e+00 1.88e+01 angle pdb=" N VAL B 156 " pdb=" CA VAL B 156 " pdb=" C VAL B 156 " ideal model delta sigma weight residual 111.81 108.09 3.72 8.60e-01 1.35e+00 1.87e+01 angle pdb=" C GLN Z 41 " pdb=" CA GLN Z 41 " pdb=" CB GLN Z 41 " ideal model delta sigma weight residual 111.48 105.78 5.70 1.59e+00 3.96e-01 1.29e+01 angle pdb=" CA TYR A 73 " pdb=" CB TYR A 73 " pdb=" CG TYR A 73 " ideal model delta sigma weight residual 113.90 107.46 6.44 1.80e+00 3.09e-01 1.28e+01 ... (remaining 18493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 7049 17.78 - 35.56: 644 35.56 - 53.34: 194 53.34 - 71.12: 29 71.12 - 88.90: 4 Dihedral angle restraints: 7920 sinusoidal: 2946 harmonic: 4974 Sorted by residual: dihedral pdb=" CA ILE B 174 " pdb=" C ILE B 174 " pdb=" N PRO B 175 " pdb=" CA PRO B 175 " ideal model delta harmonic sigma weight residual -180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA ILE E 174 " pdb=" C ILE E 174 " pdb=" N PRO E 175 " pdb=" CA PRO E 175 " ideal model delta harmonic sigma weight residual -180.00 -158.30 -21.70 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA ILE Y 174 " pdb=" C ILE Y 174 " pdb=" N PRO Y 175 " pdb=" CA PRO Y 175 " ideal model delta harmonic sigma weight residual -180.00 -158.30 -21.70 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 7917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1718 0.052 - 0.104: 421 0.104 - 0.157: 78 0.157 - 0.209: 8 0.209 - 0.261: 1 Chirality restraints: 2226 Sorted by residual: chirality pdb=" CA ASP Z 103 " pdb=" N ASP Z 103 " pdb=" C ASP Z 103 " pdb=" CB ASP Z 103 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA PRO B 72 " pdb=" N PRO B 72 " pdb=" C PRO B 72 " pdb=" CB PRO B 72 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA PRO Y 72 " pdb=" N PRO Y 72 " pdb=" C PRO Y 72 " pdb=" CB PRO Y 72 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.16e-01 ... (remaining 2223 not shown) Planarity restraints: 2328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA Y 71 " 0.060 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO Y 72 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO Y 72 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO Y 72 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 71 " 0.060 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO B 72 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 72 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 72 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 71 " -0.060 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO E 72 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO E 72 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO E 72 " -0.050 5.00e-02 4.00e+02 ... (remaining 2325 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2180 2.74 - 3.28: 13533 3.28 - 3.82: 22248 3.82 - 4.36: 26647 4.36 - 4.90: 46236 Nonbonded interactions: 110844 Sorted by model distance: nonbonded pdb=" OD2 ASP Y 125 " pdb=" NH2 ARG Z 39 " model vdw 2.205 2.520 nonbonded pdb=" OD2 ASP E 125 " pdb=" NH2 ARG F 39 " model vdw 2.205 2.520 nonbonded pdb=" OD2 ASP B 125 " pdb=" NH2 ARG C 39 " model vdw 2.206 2.520 nonbonded pdb=" N ASN G 67 " pdb=" OD1 ASN G 67 " model vdw 2.275 2.520 nonbonded pdb=" N ASN D 67 " pdb=" OD1 ASN D 67 " model vdw 2.275 2.520 ... (remaining 110839 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 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'Y' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'Z' } 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: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 8667 2.51 5 N 2229 2.21 5 O 2349 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 14.910 Check model and map are aligned: 0.180 Process input model: 36.460 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.130 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 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 : 0.008 0.086 13590 Z= 0.509 Angle : 0.769 9.857 18498 Z= 0.418 Chirality : 0.047 0.261 2226 Planarity : 0.006 0.091 2328 Dihedral : 15.399 88.905 4764 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.22 % Favored : 92.50 % Rotamer Outliers : 3.56 % 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: 0.10 (0.21), residues: 1773 helix: 0.95 (0.15), residues: 1290 sheet: None (None), residues: 0 loop : -2.35 (0.26), residues: 483 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 285 time to evaluate : 1.373 Fit side-chains outliers start: 49 outliers final: 13 residues processed: 317 average time/residue: 1.2092 time to fit residues: 419.4932 Evaluate side-chains 228 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 215 time to evaluate : 1.550 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 2.0257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 1.9990 chunk 131 optimal weight: 0.4980 chunk 73 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 136 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 158 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 29 ASN ** Z 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 15 ASN A 42 GLN A 46 GLN C 108 ASN C 158 ASN D 15 ASN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 ASN F 158 ASN F 189 GLN G 15 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 13590 Z= 0.284 Angle : 0.634 6.525 18498 Z= 0.337 Chirality : 0.044 0.184 2226 Planarity : 0.006 0.089 2328 Dihedral : 4.600 23.460 1908 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.60 % Favored : 93.23 % Rotamer Outliers : 4.50 % 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: 0.59 (0.21), residues: 1773 helix: 1.32 (0.15), residues: 1305 sheet: None (None), residues: 0 loop : -2.32 (0.27), residues: 468 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 230 time to evaluate : 1.318 Fit side-chains outliers start: 62 outliers final: 27 residues processed: 276 average time/residue: 1.2351 time to fit residues: 371.9563 Evaluate side-chains 238 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 211 time to evaluate : 1.512 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 20 residues processed: 7 average time/residue: 0.5233 time to fit residues: 6.3705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 131 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 126 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 180 ASN A 11 ASN A 15 ASN A 16 ASN C 108 ASN D 11 ASN F 29 ASN F 108 ASN F 158 ASN F 189 GLN G 15 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 13590 Z= 0.281 Angle : 0.617 7.291 18498 Z= 0.327 Chirality : 0.043 0.186 2226 Planarity : 0.006 0.091 2328 Dihedral : 4.584 28.105 1908 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.20 % Favored : 93.63 % Rotamer Outliers : 3.99 % 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: 0.66 (0.21), residues: 1773 helix: 1.38 (0.15), residues: 1314 sheet: None (None), residues: 0 loop : -2.40 (0.27), residues: 459 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 227 time to evaluate : 1.556 Fit side-chains outliers start: 55 outliers final: 31 residues processed: 270 average time/residue: 1.2345 time to fit residues: 363.9686 Evaluate side-chains 243 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 212 time to evaluate : 1.516 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 23 residues processed: 8 average time/residue: 0.5902 time to fit residues: 7.4593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.4980 chunk 119 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 150 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 140 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 42 GLN B 180 ASN C 98 ASN C 108 ASN D 11 ASN ** D 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 ASN F 108 ASN G 11 ASN G 15 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 13590 Z= 0.228 Angle : 0.579 8.051 18498 Z= 0.305 Chirality : 0.042 0.172 2226 Planarity : 0.006 0.090 2328 Dihedral : 4.477 31.641 1908 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.03 % Favored : 93.80 % Rotamer Outliers : 3.56 % 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: 0.90 (0.21), residues: 1773 helix: 1.59 (0.15), residues: 1311 sheet: None (None), residues: 0 loop : -2.43 (0.26), residues: 462 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 226 time to evaluate : 1.561 Fit side-chains outliers start: 49 outliers final: 33 residues processed: 267 average time/residue: 1.2372 time to fit residues: 361.6319 Evaluate side-chains 247 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 214 time to evaluate : 1.549 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 27 residues processed: 6 average time/residue: 0.4966 time to fit residues: 5.8110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 0.0980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN C 98 ASN C 108 ASN E 180 ASN F 108 ASN F 189 GLN G 11 ASN G 15 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 13590 Z= 0.296 Angle : 0.615 6.777 18498 Z= 0.327 Chirality : 0.044 0.193 2226 Planarity : 0.006 0.091 2328 Dihedral : 4.630 42.942 1908 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.71 % Favored : 93.12 % Rotamer Outliers : 3.41 % 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: 0.93 (0.21), residues: 1773 helix: 1.62 (0.15), residues: 1314 sheet: None (None), residues: 0 loop : -2.48 (0.26), residues: 459 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 220 time to evaluate : 1.655 Fit side-chains outliers start: 47 outliers final: 27 residues processed: 258 average time/residue: 1.2510 time to fit residues: 352.4499 Evaluate side-chains 238 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 211 time to evaluate : 1.489 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 22 residues processed: 5 average time/residue: 0.2186 time to fit residues: 3.6697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 0.5980 chunk 33 optimal weight: 0.0970 chunk 98 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 162 optimal weight: 0.0170 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN C 108 ASN D 11 ASN ** D 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 ASN F 108 ASN G 11 ASN G 15 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 13590 Z= 0.197 Angle : 0.553 7.191 18498 Z= 0.293 Chirality : 0.041 0.164 2226 Planarity : 0.006 0.090 2328 Dihedral : 4.479 49.725 1908 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.92 % Favored : 93.91 % Rotamer Outliers : 3.34 % 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: 1.24 (0.21), residues: 1773 helix: 1.84 (0.15), residues: 1317 sheet: None (None), residues: 0 loop : -2.36 (0.27), residues: 456 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 234 time to evaluate : 1.498 Fit side-chains outliers start: 46 outliers final: 32 residues processed: 272 average time/residue: 1.1639 time to fit residues: 347.1453 Evaluate side-chains 250 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 218 time to evaluate : 1.480 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 27 residues processed: 5 average time/residue: 0.2154 time to fit residues: 3.4460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 167 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 61 ASN A 15 ASN C 98 ASN C 108 ASN ** D 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 ASN F 108 ASN G 11 ASN G 15 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 13590 Z= 0.284 Angle : 0.607 10.860 18498 Z= 0.322 Chirality : 0.043 0.187 2226 Planarity : 0.006 0.090 2328 Dihedral : 4.631 58.880 1908 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.99 % Favored : 92.84 % Rotamer Outliers : 3.12 % 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: 1.17 (0.21), residues: 1773 helix: 1.78 (0.15), residues: 1317 sheet: None (None), residues: 0 loop : -2.33 (0.27), residues: 456 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 216 time to evaluate : 1.542 Fit side-chains outliers start: 43 outliers final: 31 residues processed: 252 average time/residue: 1.2139 time to fit residues: 334.7623 Evaluate side-chains 246 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 215 time to evaluate : 1.529 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 26 residues processed: 5 average time/residue: 0.3994 time to fit residues: 4.5397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 2.9990 chunk 50 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 106 optimal weight: 0.0040 chunk 114 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 131 optimal weight: 0.6980 chunk 152 optimal weight: 0.0980 chunk 160 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 61 ASN Z 189 GLN A 15 ASN C 71 HIS C 108 ASN ** D 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 ASN G 11 ASN G 15 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 13590 Z= 0.196 Angle : 0.555 11.551 18498 Z= 0.293 Chirality : 0.041 0.160 2226 Planarity : 0.006 0.089 2328 Dihedral : 4.478 57.264 1908 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.87 % Favored : 93.97 % Rotamer Outliers : 3.20 % 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: 1.42 (0.21), residues: 1773 helix: 1.97 (0.15), residues: 1317 sheet: None (None), residues: 0 loop : -2.27 (0.27), residues: 456 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 227 time to evaluate : 1.454 Fit side-chains outliers start: 44 outliers final: 25 residues processed: 262 average time/residue: 1.1988 time to fit residues: 345.7916 Evaluate side-chains 242 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 217 time to evaluate : 1.476 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 24 residues processed: 1 average time/residue: 0.2623 time to fit residues: 2.3522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.2980 chunk 160 optimal weight: 2.9990 chunk 94 optimal weight: 0.2980 chunk 68 optimal weight: 0.1980 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 141 optimal weight: 0.6980 chunk 147 optimal weight: 0.0980 chunk 155 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 165 optimal weight: 0.3980 overall best weight: 0.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 189 GLN A 15 ASN C 98 ASN C 108 ASN ** D 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 ASN G 11 ASN G 15 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 13590 Z= 0.179 Angle : 0.537 7.639 18498 Z= 0.285 Chirality : 0.040 0.159 2226 Planarity : 0.005 0.086 2328 Dihedral : 4.292 51.386 1908 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.92 % Favored : 93.91 % Rotamer Outliers : 2.61 % 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: 1.60 (0.21), residues: 1773 helix: 2.11 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : -2.28 (0.27), residues: 453 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 232 time to evaluate : 1.445 Fit side-chains outliers start: 36 outliers final: 28 residues processed: 264 average time/residue: 1.1893 time to fit residues: 344.7095 Evaluate side-chains 250 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 222 time to evaluate : 1.589 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 27 residues processed: 1 average time/residue: 0.2662 time to fit residues: 2.4432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 1.9990 chunk 78 optimal weight: 0.3980 chunk 114 optimal weight: 0.7980 chunk 173 optimal weight: 0.9980 chunk 159 optimal weight: 0.5980 chunk 138 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 147 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN C 98 ASN C 108 ASN F 76 ASN F 108 ASN G 11 ASN G 15 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 13590 Z= 0.242 Angle : 0.592 8.887 18498 Z= 0.313 Chirality : 0.042 0.178 2226 Planarity : 0.006 0.083 2328 Dihedral : 4.366 42.358 1908 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.43 % Favored : 93.40 % Rotamer Outliers : 2.40 % 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: 1.49 (0.21), residues: 1773 helix: 2.04 (0.15), residues: 1314 sheet: None (None), residues: 0 loop : -2.28 (0.27), residues: 459 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 220 time to evaluate : 1.488 Fit side-chains outliers start: 33 outliers final: 26 residues processed: 252 average time/residue: 1.2350 time to fit residues: 340.4478 Evaluate side-chains 241 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 215 time to evaluate : 1.388 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 25 residues processed: 1 average time/residue: 0.2503 time to fit residues: 2.3586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 20 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 138 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 chunk 141 optimal weight: 0.5980 chunk 17 optimal weight: 0.0770 chunk 25 optimal weight: 0.4980 chunk 121 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 189 GLN B 172 ASN C 108 ASN F 108 ASN G 11 ASN G 15 ASN G 74 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.102244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.077469 restraints weight = 17920.359| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.67 r_work: 0.2894 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 13590 Z= 0.202 Angle : 0.570 10.717 18498 Z= 0.301 Chirality : 0.041 0.162 2226 Planarity : 0.006 0.084 2328 Dihedral : 4.266 34.384 1908 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.87 % Favored : 93.97 % Rotamer Outliers : 2.32 % 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: 1.58 (0.21), residues: 1773 helix: 2.11 (0.15), residues: 1311 sheet: None (None), residues: 0 loop : -2.23 (0.27), residues: 462 =============================================================================== Job complete usr+sys time: 5709.87 seconds wall clock time: 101 minutes 22.29 seconds (6082.29 seconds total)