Starting phenix.real_space_refine on Sat Jan 20 01:43:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dyr_30923/01_2024/7dyr_30923.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dyr_30923/01_2024/7dyr_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_30923/01_2024/7dyr_30923.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dyr_30923/01_2024/7dyr_30923.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dyr_30923/01_2024/7dyr_30923.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dyr_30923/01_2024/7dyr_30923.pdb" } resolution = 2.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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. 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 6.94, per 1000 atoms: 0.52 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: 5.92 Conformation dependent library (CDL) restraints added in 2.5 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: 1.22 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: 3.80 Time building geometry restraints manager: 6.24 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: 7016 17.78 - 35.56: 644 35.56 - 53.34: 194 53.34 - 71.12: 29 71.12 - 88.90: 4 Dihedral angle restraints: 7887 sinusoidal: 2913 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 7884 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1715 0.052 - 0.104: 424 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 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: 7.360 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: 13.280 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 37.840 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 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= 0.508 Angle : 0.779 9.857 18498 Z= 0.420 Chirality : 0.047 0.261 2226 Planarity : 0.006 0.091 2328 Dihedral : 15.446 88.905 4731 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 % Allowed : 20.33 % Favored : 76.11 % 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: 0.10 (0.21), residues: 1773 helix: 0.95 (0.15), residues: 1290 sheet: None (None), residues: 0 loop : -2.35 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 138 HIS 0.004 0.001 HIS Y 122 PHE 0.011 0.001 PHE C 47 TYR 0.027 0.003 TYR A 73 ARG 0.004 0.000 ARG Z 54 *********************** 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 : 1.559 Fit side-chains REVERT: Y 26 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7372 (mm-30) REVERT: Y 64 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7793 (mtp) REVERT: Y 125 ASP cc_start: 0.7292 (OUTLIER) cc_final: 0.6963 (m-30) REVERT: Y 176 GLU cc_start: 0.7067 (tp30) cc_final: 0.6789 (tm-30) REVERT: Z 17 THR cc_start: 0.7504 (m) cc_final: 0.7291 (p) REVERT: Z 38 GLU cc_start: 0.8653 (tt0) cc_final: 0.7953 (tt0) REVERT: Z 60 ASN cc_start: 0.6699 (m-40) cc_final: 0.6131 (t0) REVERT: Z 73 GLU cc_start: 0.7538 (mm-30) cc_final: 0.6989 (mt-10) REVERT: Z 94 GLU cc_start: 0.7693 (tt0) cc_final: 0.7217 (tt0) REVERT: Z 175 LYS cc_start: 0.7153 (tptm) cc_final: 0.6931 (tptp) REVERT: Z 223 THR cc_start: 0.7583 (OUTLIER) cc_final: 0.7239 (m) REVERT: Z 230 HIS cc_start: 0.7483 (m90) cc_final: 0.7028 (m90) REVERT: A 50 ASP cc_start: 0.6889 (m-30) cc_final: 0.6620 (m-30) REVERT: A 55 ASN cc_start: 0.8150 (p0) cc_final: 0.7944 (p0) REVERT: B 26 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7269 (mm-30) REVERT: B 64 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8029 (mtp) REVERT: B 125 ASP cc_start: 0.7305 (m-30) cc_final: 0.6880 (m-30) REVERT: B 201 MET cc_start: 0.8138 (mtm) cc_final: 0.7772 (mtp) REVERT: C 15 LYS cc_start: 0.8126 (ptpp) cc_final: 0.7833 (ptpp) REVERT: C 17 THR cc_start: 0.7845 (m) cc_final: 0.7635 (p) REVERT: C 20 ASP cc_start: 0.7632 (m-30) cc_final: 0.7260 (m-30) REVERT: C 22 ARG cc_start: 0.6328 (mtp180) cc_final: 0.6116 (mtm110) REVERT: C 38 GLU cc_start: 0.8625 (tt0) cc_final: 0.8073 (tt0) REVERT: C 60 ASN cc_start: 0.6867 (m-40) cc_final: 0.6507 (t0) REVERT: C 73 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7205 (mt-10) REVERT: D 50 ASP cc_start: 0.7159 (m-30) cc_final: 0.6647 (m-30) REVERT: D 55 ASN cc_start: 0.8316 (p0) cc_final: 0.7979 (p0) REVERT: E 3 ILE cc_start: 0.7863 (mt) cc_final: 0.7514 (mm) REVERT: E 4 THR cc_start: 0.7488 (p) cc_final: 0.7264 (t) REVERT: E 130 ASN cc_start: 0.8118 (m110) cc_final: 0.7796 (m-40) REVERT: E 142 SER cc_start: 0.8355 (OUTLIER) cc_final: 0.8125 (p) REVERT: E 176 GLU cc_start: 0.7063 (tp30) cc_final: 0.6785 (tm-30) REVERT: E 180 ASN cc_start: 0.7838 (m-40) cc_final: 0.7495 (m-40) REVERT: E 244 LYS cc_start: 0.8311 (ttpt) cc_final: 0.7980 (ttpp) REVERT: F 17 THR cc_start: 0.7743 (m) cc_final: 0.7460 (p) REVERT: F 38 GLU cc_start: 0.8654 (tt0) cc_final: 0.8036 (tt0) REVERT: F 60 ASN cc_start: 0.6881 (m-40) cc_final: 0.6221 (t0) REVERT: F 73 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7015 (mt-10) REVERT: F 95 GLN cc_start: 0.7180 (mp10) cc_final: 0.6768 (mp-120) REVERT: F 102 ILE cc_start: 0.7209 (OUTLIER) cc_final: 0.6931 (mm) REVERT: F 108 ASN cc_start: 0.7986 (m-40) cc_final: 0.7752 (m-40) REVERT: F 189 GLN cc_start: 0.6671 (OUTLIER) cc_final: 0.6427 (pt0) REVERT: F 193 GLU cc_start: 0.7609 (tt0) cc_final: 0.7397 (tt0) REVERT: F 259 ARG cc_start: 0.6852 (tpp80) cc_final: 0.6457 (ttp80) REVERT: F 281 CYS cc_start: 0.7790 (m) cc_final: 0.7579 (m) REVERT: G 19 TRP cc_start: 0.6334 (t60) cc_final: 0.6107 (t60) outliers start: 49 outliers final: 13 residues processed: 317 average time/residue: 1.1507 time to fit residues: 399.9085 Evaluate side-chains 241 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 221 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 64 MET Chi-restraints excluded: chain Y residue 125 ASP Chi-restraints excluded: chain Y residue 142 SER Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 220 SER Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 232 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.5980 chunk 131 optimal weight: 0.0980 chunk 73 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 158 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 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 158 ASN ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 13590 Z= 0.250 Angle : 0.611 6.253 18498 Z= 0.324 Chirality : 0.043 0.176 2226 Planarity : 0.006 0.088 2328 Dihedral : 5.937 54.891 1904 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.49 % Favored : 93.34 % Rotamer: Outliers : 3.63 % Allowed : 17.07 % Favored : 79.30 % 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: 0.62 (0.21), residues: 1773 helix: 1.34 (0.15), residues: 1305 sheet: None (None), residues: 0 loop : -2.31 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 127 HIS 0.002 0.001 HIS G 51 PHE 0.013 0.001 PHE C 157 TYR 0.026 0.002 TYR A 73 ARG 0.004 0.001 ARG C 131 *********************** 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 288 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 238 time to evaluate : 1.482 Fit side-chains revert: symmetry clash REVERT: Y 22 SER cc_start: 0.7686 (t) cc_final: 0.7439 (p) REVERT: Y 125 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6556 (m-30) REVERT: Y 196 MET cc_start: 0.7617 (mtp) cc_final: 0.7407 (mtp) REVERT: Z 38 GLU cc_start: 0.8708 (tt0) cc_final: 0.8058 (tt0) REVERT: Z 223 THR cc_start: 0.7433 (OUTLIER) cc_final: 0.7076 (m) REVERT: Z 230 HIS cc_start: 0.7337 (m90) cc_final: 0.6889 (m90) REVERT: Z 259 ARG cc_start: 0.6837 (ttm110) cc_final: 0.6569 (ttp80) REVERT: A 55 ASN cc_start: 0.8083 (p0) cc_final: 0.7844 (p0) REVERT: B 26 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7161 (mm-30) REVERT: B 125 ASP cc_start: 0.7128 (m-30) cc_final: 0.6692 (m-30) REVERT: B 244 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7631 (ttpp) REVERT: C 15 LYS cc_start: 0.8082 (ptpp) cc_final: 0.7858 (ptpp) REVERT: C 17 THR cc_start: 0.7942 (m) cc_final: 0.7536 (p) REVERT: C 38 GLU cc_start: 0.8622 (tt0) cc_final: 0.8137 (tt0) REVERT: C 60 ASN cc_start: 0.6560 (m-40) cc_final: 0.6065 (t0) REVERT: C 73 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7009 (mt-10) REVERT: E 176 GLU cc_start: 0.7055 (tp30) cc_final: 0.6678 (tm-30) REVERT: E 244 LYS cc_start: 0.8164 (ttpt) cc_final: 0.7913 (ttpp) REVERT: F 38 GLU cc_start: 0.8688 (tt0) cc_final: 0.8123 (tt0) REVERT: F 60 ASN cc_start: 0.6942 (m-40) cc_final: 0.6353 (t0) REVERT: F 95 GLN cc_start: 0.7035 (mp10) cc_final: 0.6690 (mp-120) REVERT: F 183 MET cc_start: 0.6400 (mmm) cc_final: 0.6077 (mmm) REVERT: F 189 GLN cc_start: 0.6653 (OUTLIER) cc_final: 0.6279 (pt0) REVERT: F 281 CYS cc_start: 0.7819 (m) cc_final: 0.7503 (m) outliers start: 50 outliers final: 17 residues processed: 273 average time/residue: 1.1975 time to fit residues: 357.5521 Evaluate side-chains 236 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 215 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 125 ASP Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 56 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 43 optimal weight: 0.3980 chunk 158 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 140 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 60 ASN A 11 ASN 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** F 29 ASN F 108 ASN F 158 ASN ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 13590 Z= 0.273 Angle : 0.610 7.799 18498 Z= 0.322 Chirality : 0.043 0.184 2226 Planarity : 0.006 0.089 2328 Dihedral : 5.559 51.105 1889 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.37 % Favored : 93.46 % Rotamer: Outliers : 3.34 % Allowed : 17.72 % Favored : 78.94 % 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 (0.21), residues: 1773 helix: 1.39 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : -2.45 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Z 127 HIS 0.003 0.001 HIS Z 71 PHE 0.013 0.001 PHE F 47 TYR 0.028 0.002 TYR A 73 ARG 0.002 0.000 ARG E 114 *********************** 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 274 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 228 time to evaluate : 1.532 Fit side-chains revert: symmetry clash REVERT: Y 22 SER cc_start: 0.7715 (t) cc_final: 0.7507 (p) REVERT: Y 125 ASP cc_start: 0.7135 (m-30) cc_final: 0.6673 (m-30) REVERT: Y 176 GLU cc_start: 0.7150 (tp30) cc_final: 0.6727 (tm-30) REVERT: Y 196 MET cc_start: 0.7580 (mtp) cc_final: 0.7373 (mtp) REVERT: Z 38 GLU cc_start: 0.8729 (tt0) cc_final: 0.8515 (tt0) REVERT: Z 60 ASN cc_start: 0.6547 (m-40) cc_final: 0.5619 (t0) REVERT: Z 94 GLU cc_start: 0.7389 (tt0) cc_final: 0.7056 (tt0) REVERT: Z 223 THR cc_start: 0.7408 (OUTLIER) cc_final: 0.6997 (m) REVERT: Z 230 HIS cc_start: 0.7380 (m90) cc_final: 0.6940 (m90) REVERT: A 55 ASN cc_start: 0.8041 (p0) cc_final: 0.7780 (p0) REVERT: B 26 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7169 (mm-30) REVERT: B 125 ASP cc_start: 0.7148 (m-30) cc_final: 0.6727 (m-30) REVERT: C 15 LYS cc_start: 0.8062 (ptpp) cc_final: 0.7856 (ptpp) REVERT: C 38 GLU cc_start: 0.8574 (tt0) cc_final: 0.8121 (tt0) REVERT: C 73 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6941 (mt-10) REVERT: D 29 LEU cc_start: 0.5819 (OUTLIER) cc_final: 0.5607 (tm) REVERT: E 64 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.8106 (mtp) REVERT: E 176 GLU cc_start: 0.7023 (tp30) cc_final: 0.6611 (tm-30) REVERT: E 244 LYS cc_start: 0.8148 (ttpt) cc_final: 0.7881 (ttpp) REVERT: F 38 GLU cc_start: 0.8692 (tt0) cc_final: 0.8170 (tt0) REVERT: F 95 GLN cc_start: 0.7106 (mp10) cc_final: 0.6779 (mp-120) REVERT: F 183 MET cc_start: 0.6496 (mmm) cc_final: 0.6137 (mmm) REVERT: F 189 GLN cc_start: 0.6599 (OUTLIER) cc_final: 0.6227 (pt0) REVERT: F 281 CYS cc_start: 0.7808 (m) cc_final: 0.7478 (m) REVERT: G 19 TRP cc_start: 0.6326 (t60) cc_final: 0.6023 (t60) outliers start: 46 outliers final: 25 residues processed: 262 average time/residue: 1.2269 time to fit residues: 350.7702 Evaluate side-chains 246 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 217 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 161 SER Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 48 SER Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 150 optimal weight: 0.2980 chunk 45 optimal weight: 0.4980 chunk 140 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 16 ASN B 180 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** F 108 ASN ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 ASN G 15 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2224 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= 0.255 Angle : 0.595 7.891 18498 Z= 0.315 Chirality : 0.042 0.180 2226 Planarity : 0.006 0.090 2328 Dihedral : 5.469 56.369 1887 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.43 % Favored : 93.40 % Rotamer: Outliers : 3.70 % Allowed : 17.28 % Favored : 79.01 % 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: 0.86 (0.21), residues: 1773 helix: 1.52 (0.15), residues: 1326 sheet: None (None), residues: 0 loop : -2.43 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Z 127 HIS 0.003 0.001 HIS Z 71 PHE 0.013 0.001 PHE F 47 TYR 0.028 0.002 TYR A 73 ARG 0.003 0.000 ARG Z 259 *********************** 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 276 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 225 time to evaluate : 1.870 Fit side-chains revert: symmetry clash REVERT: Y 22 SER cc_start: 0.7703 (t) cc_final: 0.7492 (p) REVERT: Y 58 MET cc_start: 0.7790 (mmm) cc_final: 0.7436 (mmp) REVERT: Y 125 ASP cc_start: 0.7137 (m-30) cc_final: 0.6169 (m-30) REVERT: Y 176 GLU cc_start: 0.7229 (tp30) cc_final: 0.6721 (tm-30) REVERT: Z 94 GLU cc_start: 0.7383 (tt0) cc_final: 0.7053 (tt0) REVERT: Z 223 THR cc_start: 0.7515 (OUTLIER) cc_final: 0.7050 (m) REVERT: Z 230 HIS cc_start: 0.7402 (m90) cc_final: 0.7015 (m-70) REVERT: A 16 ASN cc_start: 0.7527 (OUTLIER) cc_final: 0.7226 (m-40) REVERT: A 55 ASN cc_start: 0.7946 (p0) cc_final: 0.7695 (p0) REVERT: B 26 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7120 (mm-30) REVERT: B 125 ASP cc_start: 0.7147 (m-30) cc_final: 0.6704 (m-30) REVERT: C 15 LYS cc_start: 0.8052 (ptpp) cc_final: 0.7851 (ptpp) REVERT: C 38 GLU cc_start: 0.8573 (tt0) cc_final: 0.8145 (tt0) REVERT: D 29 LEU cc_start: 0.6168 (OUTLIER) cc_final: 0.5880 (tm) REVERT: E 64 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.8101 (mtp) REVERT: E 73 ASP cc_start: 0.8021 (t70) cc_final: 0.7756 (t70) REVERT: E 176 GLU cc_start: 0.7067 (tp30) cc_final: 0.6637 (tm-30) REVERT: E 244 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7826 (ttpp) REVERT: F 14 LYS cc_start: 0.7105 (mtmp) cc_final: 0.6889 (mppt) REVERT: F 38 GLU cc_start: 0.8695 (tt0) cc_final: 0.8205 (tt0) REVERT: F 95 GLN cc_start: 0.7026 (mp10) cc_final: 0.6675 (mp-120) REVERT: F 183 MET cc_start: 0.6506 (mmm) cc_final: 0.6140 (mmm) REVERT: F 189 GLN cc_start: 0.6568 (OUTLIER) cc_final: 0.6202 (pt0) REVERT: F 281 CYS cc_start: 0.7649 (m) cc_final: 0.7365 (m) REVERT: G 19 TRP cc_start: 0.6407 (t60) cc_final: 0.6042 (t60) outliers start: 51 outliers final: 29 residues processed: 259 average time/residue: 1.1777 time to fit residues: 334.4004 Evaluate side-chains 252 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 217 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 161 SER Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 48 SER Chi-restraints excluded: chain Z residue 61 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 56 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ** D 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 ASN ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 ASN G 15 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 13590 Z= 0.283 Angle : 0.611 10.040 18498 Z= 0.322 Chirality : 0.043 0.191 2226 Planarity : 0.006 0.090 2328 Dihedral : 5.529 59.258 1887 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.60 % Favored : 93.23 % Rotamer: Outliers : 3.70 % Allowed : 17.43 % Favored : 78.87 % 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: 0.92 (0.21), residues: 1773 helix: 1.58 (0.15), residues: 1323 sheet: None (None), residues: 0 loop : -2.42 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 127 HIS 0.003 0.001 HIS Z 71 PHE 0.014 0.001 PHE F 47 TYR 0.029 0.002 TYR A 73 ARG 0.003 0.000 ARG E 114 *********************** 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 273 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 222 time to evaluate : 1.425 Fit side-chains revert: symmetry clash REVERT: Y 22 SER cc_start: 0.7735 (t) cc_final: 0.7437 (p) REVERT: Y 47 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.7109 (mtmt) REVERT: Y 58 MET cc_start: 0.7805 (mmm) cc_final: 0.7528 (mmp) REVERT: Y 125 ASP cc_start: 0.7179 (m-30) cc_final: 0.6238 (m-30) REVERT: Z 94 GLU cc_start: 0.7383 (tt0) cc_final: 0.7074 (tt0) REVERT: Z 223 THR cc_start: 0.7525 (OUTLIER) cc_final: 0.7054 (m) REVERT: Z 230 HIS cc_start: 0.7383 (m90) cc_final: 0.7037 (m-70) REVERT: A 16 ASN cc_start: 0.7477 (m110) cc_final: 0.7212 (m-40) REVERT: A 29 LEU cc_start: 0.6160 (OUTLIER) cc_final: 0.5913 (tm) REVERT: A 55 ASN cc_start: 0.7950 (p0) cc_final: 0.7683 (p0) REVERT: B 26 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7108 (mm-30) REVERT: B 47 LYS cc_start: 0.7505 (mtpt) cc_final: 0.7169 (tttp) REVERT: B 125 ASP cc_start: 0.7141 (m-30) cc_final: 0.6668 (m-30) REVERT: C 38 GLU cc_start: 0.8569 (tt0) cc_final: 0.8143 (tt0) REVERT: D 29 LEU cc_start: 0.6240 (OUTLIER) cc_final: 0.5878 (tm) REVERT: E 47 LYS cc_start: 0.7600 (mmmm) cc_final: 0.7387 (tttt) REVERT: E 64 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.8081 (mtp) REVERT: E 73 ASP cc_start: 0.8064 (t70) cc_final: 0.7733 (t70) REVERT: E 176 GLU cc_start: 0.7093 (tp30) cc_final: 0.6664 (tm-30) REVERT: E 244 LYS cc_start: 0.8104 (ttpt) cc_final: 0.7841 (ttpp) REVERT: F 14 LYS cc_start: 0.7095 (mtmp) cc_final: 0.6870 (mppt) REVERT: F 38 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8200 (tt0) REVERT: F 60 ASN cc_start: 0.6830 (OUTLIER) cc_final: 0.6173 (m-40) REVERT: F 95 GLN cc_start: 0.7005 (mp10) cc_final: 0.6653 (mp-120) REVERT: F 183 MET cc_start: 0.6511 (mmm) cc_final: 0.6143 (mmm) REVERT: F 189 GLN cc_start: 0.6553 (OUTLIER) cc_final: 0.6191 (pt0) REVERT: F 281 CYS cc_start: 0.7646 (m) cc_final: 0.7368 (m) REVERT: G 19 TRP cc_start: 0.6454 (t60) cc_final: 0.6067 (t60) outliers start: 51 outliers final: 30 residues processed: 259 average time/residue: 1.2156 time to fit residues: 344.7769 Evaluate side-chains 252 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 214 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 161 SER Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 48 SER Chi-restraints excluded: chain Z residue 61 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 55 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 98 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 162 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN 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** F 108 ASN ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 ASN G 15 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 13590 Z= 0.267 Angle : 0.600 7.112 18498 Z= 0.317 Chirality : 0.043 0.185 2226 Planarity : 0.006 0.090 2328 Dihedral : 5.523 55.925 1887 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.43 % Favored : 93.40 % Rotamer: Outliers : 3.78 % Allowed : 17.65 % Favored : 78.58 % 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: 1.08 (0.21), residues: 1773 helix: 1.69 (0.15), residues: 1326 sheet: None (None), residues: 0 loop : -2.40 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 127 HIS 0.003 0.001 HIS Z 71 PHE 0.014 0.001 PHE F 47 TYR 0.027 0.002 TYR A 73 ARG 0.002 0.000 ARG E 114 *********************** 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 278 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 226 time to evaluate : 1.677 Fit side-chains revert: symmetry clash REVERT: Y 22 SER cc_start: 0.7730 (t) cc_final: 0.7438 (p) REVERT: Y 47 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.7176 (mtmt) REVERT: Y 58 MET cc_start: 0.7805 (mmm) cc_final: 0.7451 (mmp) REVERT: Y 125 ASP cc_start: 0.7116 (m-30) cc_final: 0.6066 (m-30) REVERT: Y 244 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7536 (ttpp) REVERT: Z 187 PHE cc_start: 0.7327 (t80) cc_final: 0.7021 (t80) REVERT: Z 230 HIS cc_start: 0.7384 (m90) cc_final: 0.7025 (m-70) REVERT: A 29 LEU cc_start: 0.6254 (OUTLIER) cc_final: 0.6015 (tm) REVERT: A 55 ASN cc_start: 0.7877 (p0) cc_final: 0.7613 (p0) REVERT: B 26 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7101 (mm-30) REVERT: B 47 LYS cc_start: 0.7533 (mtpt) cc_final: 0.7206 (tttp) REVERT: B 125 ASP cc_start: 0.7086 (m-30) cc_final: 0.6619 (m-30) REVERT: C 38 GLU cc_start: 0.8558 (tt0) cc_final: 0.8149 (tt0) REVERT: D 29 LEU cc_start: 0.6202 (OUTLIER) cc_final: 0.5815 (tm) REVERT: E 64 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.8083 (mtp) REVERT: E 73 ASP cc_start: 0.8004 (t70) cc_final: 0.7673 (t70) REVERT: E 176 GLU cc_start: 0.7023 (tp30) cc_final: 0.6540 (tm-30) REVERT: E 244 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7841 (ttpp) REVERT: F 14 LYS cc_start: 0.7061 (mtmp) cc_final: 0.6827 (mppt) REVERT: F 38 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8200 (tt0) REVERT: F 60 ASN cc_start: 0.6763 (OUTLIER) cc_final: 0.6088 (m-40) REVERT: F 95 GLN cc_start: 0.6967 (mp10) cc_final: 0.6628 (mp-120) REVERT: F 183 MET cc_start: 0.6554 (mmm) cc_final: 0.6149 (mmm) REVERT: F 189 GLN cc_start: 0.6524 (OUTLIER) cc_final: 0.6170 (pt0) REVERT: F 281 CYS cc_start: 0.7619 (m) cc_final: 0.7348 (m) REVERT: G 19 TRP cc_start: 0.6399 (t60) cc_final: 0.5997 (t60) outliers start: 52 outliers final: 32 residues processed: 263 average time/residue: 1.1819 time to fit residues: 341.4212 Evaluate side-chains 258 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 217 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 161 SER Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 244 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 48 SER Chi-restraints excluded: chain Z residue 61 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 55 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 141 optimal weight: 0.2980 chunk 94 optimal weight: 0.5980 chunk 167 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 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 15 ASN A 16 ASN C 108 ASN ** D 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 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: 0.7253 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 13590 Z= 0.238 Angle : 0.583 7.954 18498 Z= 0.308 Chirality : 0.042 0.174 2226 Planarity : 0.006 0.089 2328 Dihedral : 5.451 56.802 1887 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.54 % Favored : 93.29 % Rotamer: Outliers : 3.78 % Allowed : 18.01 % Favored : 78.21 % 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: 1.22 (0.21), residues: 1773 helix: 1.79 (0.15), residues: 1323 sheet: None (None), residues: 0 loop : -2.31 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 127 HIS 0.002 0.001 HIS Z 71 PHE 0.014 0.001 PHE F 47 TYR 0.025 0.002 TYR A 73 ARG 0.006 0.000 ARG F 259 *********************** 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 279 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 227 time to evaluate : 1.646 Fit side-chains revert: symmetry clash REVERT: Y 22 SER cc_start: 0.7727 (t) cc_final: 0.7449 (p) REVERT: Y 47 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7229 (mtmt) REVERT: Y 58 MET cc_start: 0.7813 (mmm) cc_final: 0.7563 (mmp) REVERT: Y 125 ASP cc_start: 0.7160 (m-30) cc_final: 0.6080 (m-30) REVERT: Y 244 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7446 (ttpp) REVERT: Z 187 PHE cc_start: 0.7190 (t80) cc_final: 0.6932 (t80) REVERT: A 55 ASN cc_start: 0.7850 (p0) cc_final: 0.7582 (p0) REVERT: B 26 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7107 (mm-30) REVERT: B 47 LYS cc_start: 0.7495 (mtpt) cc_final: 0.7138 (tttp) REVERT: B 73 ASP cc_start: 0.7838 (t70) cc_final: 0.7619 (OUTLIER) REVERT: B 125 ASP cc_start: 0.7069 (m-30) cc_final: 0.6625 (m-30) REVERT: C 38 GLU cc_start: 0.8550 (tt0) cc_final: 0.8164 (tt0) REVERT: D 29 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.5835 (tm) REVERT: E 64 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8110 (mtp) REVERT: E 73 ASP cc_start: 0.7928 (t70) cc_final: 0.7688 (t70) REVERT: E 176 GLU cc_start: 0.7092 (tp30) cc_final: 0.6575 (tm-30) REVERT: E 244 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7825 (ttpp) REVERT: F 14 LYS cc_start: 0.7056 (mtmp) cc_final: 0.6816 (mppt) REVERT: F 38 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8197 (tt0) REVERT: F 60 ASN cc_start: 0.6565 (OUTLIER) cc_final: 0.5864 (m-40) REVERT: F 95 GLN cc_start: 0.6953 (mp10) cc_final: 0.6594 (mp-120) REVERT: F 183 MET cc_start: 0.6592 (mmm) cc_final: 0.6200 (mmm) REVERT: F 189 GLN cc_start: 0.6522 (OUTLIER) cc_final: 0.6158 (pt0) REVERT: F 281 CYS cc_start: 0.7614 (m) cc_final: 0.7344 (m) REVERT: G 19 TRP cc_start: 0.6395 (t60) cc_final: 0.5958 (t60) outliers start: 52 outliers final: 28 residues processed: 264 average time/residue: 1.2111 time to fit residues: 351.7877 Evaluate side-chains 255 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 220 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 161 SER Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 244 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 56 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 114 optimal weight: 0.3980 chunk 82 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 152 optimal weight: 0.0980 chunk 160 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 A 42 GLN C 76 ASN C 108 ASN ** D 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** 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: 0.7263 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 13590 Z= 0.268 Angle : 0.608 10.747 18498 Z= 0.321 Chirality : 0.043 0.185 2226 Planarity : 0.006 0.089 2328 Dihedral : 5.483 55.666 1887 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.66 % Favored : 93.18 % Rotamer: Outliers : 3.78 % Allowed : 18.08 % Favored : 78.14 % 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: 1.21 (0.21), residues: 1773 helix: 1.78 (0.15), residues: 1323 sheet: None (None), residues: 0 loop : -2.29 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 127 HIS 0.003 0.001 HIS Z 71 PHE 0.015 0.001 PHE F 47 TYR 0.028 0.002 TYR A 73 ARG 0.005 0.000 ARG F 259 *********************** 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 273 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 221 time to evaluate : 1.436 Fit side-chains revert: symmetry clash REVERT: Y 22 SER cc_start: 0.7733 (t) cc_final: 0.7447 (p) REVERT: Y 47 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7217 (mtmt) REVERT: Y 58 MET cc_start: 0.7823 (mmm) cc_final: 0.7441 (mmp) REVERT: Y 125 ASP cc_start: 0.7134 (m-30) cc_final: 0.6084 (m-30) REVERT: Y 142 SER cc_start: 0.7782 (t) cc_final: 0.7565 (p) REVERT: Y 244 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7414 (ttpp) REVERT: Z 187 PHE cc_start: 0.7316 (t80) cc_final: 0.7056 (t80) REVERT: A 55 ASN cc_start: 0.7871 (p0) cc_final: 0.7595 (p0) REVERT: B 26 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7113 (mm-30) REVERT: B 47 LYS cc_start: 0.7539 (mtpt) cc_final: 0.7274 (tttp) REVERT: B 73 ASP cc_start: 0.7917 (t70) cc_final: 0.7658 (t70) REVERT: B 125 ASP cc_start: 0.7082 (m-30) cc_final: 0.6641 (m-30) REVERT: C 38 GLU cc_start: 0.8546 (tt0) cc_final: 0.8167 (tt0) REVERT: D 29 LEU cc_start: 0.6242 (OUTLIER) cc_final: 0.5818 (tm) REVERT: E 64 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.8074 (mtp) REVERT: E 73 ASP cc_start: 0.7981 (t70) cc_final: 0.7695 (t70) REVERT: E 176 GLU cc_start: 0.7117 (tp30) cc_final: 0.6589 (tm-30) REVERT: E 244 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7829 (ttpp) REVERT: F 14 LYS cc_start: 0.7050 (mtmp) cc_final: 0.6801 (mppt) REVERT: F 38 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8181 (tt0) REVERT: F 60 ASN cc_start: 0.6603 (OUTLIER) cc_final: 0.5908 (m-40) REVERT: F 95 GLN cc_start: 0.6951 (mp10) cc_final: 0.6599 (mp-120) REVERT: F 183 MET cc_start: 0.6654 (mmm) cc_final: 0.6311 (mmm) REVERT: F 189 GLN cc_start: 0.6530 (OUTLIER) cc_final: 0.6177 (pt0) REVERT: F 281 CYS cc_start: 0.7621 (m) cc_final: 0.7336 (m) REVERT: G 19 TRP cc_start: 0.6424 (t60) cc_final: 0.5999 (t60) outliers start: 52 outliers final: 30 residues processed: 258 average time/residue: 1.2015 time to fit residues: 339.5612 Evaluate side-chains 257 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 219 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 161 SER Chi-restraints excluded: chain Y residue 162 VAL Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 244 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 94 optimal weight: 0.1980 chunk 68 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 147 optimal weight: 0.5980 chunk 155 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 165 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 A 42 GLN C 108 ASN ** D 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** 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: 0.7253 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 13590 Z= 0.239 Angle : 0.591 11.557 18498 Z= 0.311 Chirality : 0.042 0.175 2226 Planarity : 0.006 0.089 2328 Dihedral : 5.431 57.352 1887 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.32 % Favored : 93.51 % Rotamer: Outliers : 3.78 % Allowed : 17.94 % Favored : 78.29 % 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: 1.31 (0.21), residues: 1773 helix: 1.88 (0.15), residues: 1317 sheet: None (None), residues: 0 loop : -2.29 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 138 HIS 0.002 0.001 HIS Z 71 PHE 0.015 0.001 PHE F 47 TYR 0.025 0.002 TYR A 73 ARG 0.005 0.000 ARG F 259 *********************** 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 272 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 220 time to evaluate : 1.570 Fit side-chains revert: symmetry clash REVERT: Y 22 SER cc_start: 0.7728 (t) cc_final: 0.7454 (p) REVERT: Y 47 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.7217 (mtmt) REVERT: Y 58 MET cc_start: 0.7822 (mmm) cc_final: 0.7564 (mmp) REVERT: Y 125 ASP cc_start: 0.7160 (m-30) cc_final: 0.6067 (m-30) REVERT: Y 142 SER cc_start: 0.7797 (t) cc_final: 0.7590 (p) REVERT: Y 244 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7481 (ttpp) REVERT: Z 66 GLN cc_start: 0.7448 (mm-40) cc_final: 0.6874 (mt0) REVERT: Z 187 PHE cc_start: 0.7303 (t80) cc_final: 0.7039 (t80) REVERT: A 55 ASN cc_start: 0.7839 (p0) cc_final: 0.7560 (p0) REVERT: B 26 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7097 (mm-30) REVERT: B 47 LYS cc_start: 0.7523 (mtpt) cc_final: 0.7244 (tttp) REVERT: B 125 ASP cc_start: 0.7071 (m-30) cc_final: 0.6648 (m-30) REVERT: C 38 GLU cc_start: 0.8554 (tt0) cc_final: 0.8178 (tt0) REVERT: C 61 ASN cc_start: 0.7398 (OUTLIER) cc_final: 0.7052 (p0) REVERT: D 29 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.5818 (tm) REVERT: E 64 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8104 (mtp) REVERT: E 73 ASP cc_start: 0.7887 (t70) cc_final: 0.7679 (t70) REVERT: E 176 GLU cc_start: 0.7071 (tp30) cc_final: 0.6540 (tm-30) REVERT: E 244 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7899 (ttpp) REVERT: F 14 LYS cc_start: 0.7035 (mtmp) cc_final: 0.6782 (mppt) REVERT: F 38 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8214 (tt0) REVERT: F 60 ASN cc_start: 0.6508 (OUTLIER) cc_final: 0.5783 (m-40) REVERT: F 95 GLN cc_start: 0.6948 (mp10) cc_final: 0.6598 (mp-120) REVERT: F 183 MET cc_start: 0.6647 (mmm) cc_final: 0.6315 (mmm) REVERT: F 189 GLN cc_start: 0.6519 (OUTLIER) cc_final: 0.6167 (pt0) REVERT: F 281 CYS cc_start: 0.7610 (m) cc_final: 0.7331 (m) REVERT: G 19 TRP cc_start: 0.6432 (t60) cc_final: 0.5999 (t60) outliers start: 52 outliers final: 31 residues processed: 257 average time/residue: 1.1826 time to fit residues: 332.7273 Evaluate side-chains 256 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 216 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 161 SER Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 244 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 29 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 2.9990 chunk 78 optimal weight: 0.2980 chunk 114 optimal weight: 0.5980 chunk 173 optimal weight: 2.9990 chunk 159 optimal weight: 0.5980 chunk 138 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 84 optimal weight: 0.0670 chunk 109 optimal weight: 3.9990 chunk 147 optimal weight: 0.5980 overall best weight: 0.4318 ------------------------------------------------------------------------------- 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 A 42 GLN B 172 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** F 108 ASN G 11 ASN G 15 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2669 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: