Starting phenix.real_space_refine on Tue Aug 6 07:28:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xno_33321/08_2024/7xno_33321.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xno_33321/08_2024/7xno_33321.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xno_33321/08_2024/7xno_33321.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xno_33321/08_2024/7xno_33321.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xno_33321/08_2024/7xno_33321.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xno_33321/08_2024/7xno_33321.cif" } resolution = 2.54 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= 0.019 sd= 0.085 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 87 5.16 5 C 10398 2.51 5 N 2613 2.21 5 O 2790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 21": "OE1" <-> "OE2" Residue "Y ASP 25": "OD1" <-> "OD2" Residue "Z GLU 29": "OE1" <-> "OE2" Residue "Z ASP 93": "OD1" <-> "OD2" Residue "B ASP 4": "OD1" <-> "OD2" Residue "C GLU 21": "OE1" <-> "OE2" Residue "D PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 25": "OD1" <-> "OD2" Residue "D GLU 133": "OE1" <-> "OE2" Residue "E ASP 93": "OD1" <-> "OD2" Residue "F ASP 27": "OD1" <-> "OD2" Residue "F GLU 39": "OE1" <-> "OE2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "H GLU 21": "OE1" <-> "OE2" Residue "I ASP 93": "OD1" <-> "OD2" Residue "J GLU -7": "OE1" <-> "OE2" Residue "J ASP 4": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 15888 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 299 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "Y" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1785 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain: "Z" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2335 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 12, 'TRANS': 288} Chain: "B" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 865 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "C" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 299 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "D" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1785 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain: "E" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2335 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 12, 'TRANS': 288} Chain: "F" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 865 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "G" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 299 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "H" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1785 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain: "I" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2335 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 12, 'TRANS': 288} Chain: "J" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 865 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} 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: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "I" 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: 9.40, per 1000 atoms: 0.59 Number of scatterers: 15888 At special positions: 0 Unit cell: (130.711, 124.808, 100.353, 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 87 16.00 O 2790 8.00 N 2613 7.00 C 10398 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 10 " - pdb=" SG CYS A 15 " distance=2.03 Simple disulfide: pdb=" SG CYS C 10 " - pdb=" SG CYS C 15 " distance=2.03 Simple disulfide: pdb=" SG CYS G 10 " - pdb=" SG CYS G 15 " distance=2.03 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: 6.99 Conformation dependent library (CDL) restraints added in 3.1 seconds 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3762 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 6 sheets defined 77.3% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 18 through 40 Processing helix chain 'Y' and resid 4 through 25 removed outlier: 3.735A pdb=" N ILE Y 23 " --> pdb=" O GLY Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 31 through 44 Processing helix chain 'Y' and resid 45 through 60 Processing helix chain 'Y' and resid 73 through 88 removed outlier: 3.636A pdb=" N ALA Y 77 " --> pdb=" O ASP Y 73 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 132 removed outlier: 4.177A pdb=" N VAL Y 103 " --> pdb=" O ILE Y 99 " (cutoff:3.500A) Proline residue: Y 104 - end of helix removed outlier: 4.118A pdb=" N THR Y 121 " --> pdb=" O ARG Y 117 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLY Y 122 " --> pdb=" O THR Y 118 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE Y 123 " --> pdb=" O LEU Y 119 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 164 removed outlier: 3.636A pdb=" N ILE Y 139 " --> pdb=" O ASN Y 135 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE Y 154 " --> pdb=" O GLN Y 150 " (cutoff:3.500A) Proline residue: Y 157 - end of helix Processing helix chain 'Y' and resid 165 through 175 Processing helix chain 'Y' and resid 177 through 204 removed outlier: 4.484A pdb=" N VAL Y 192 " --> pdb=" O GLY Y 188 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ALA Y 193 " --> pdb=" O GLY Y 189 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL Y 194 " --> pdb=" O MET Y 190 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY Y 195 " --> pdb=" O VAL Y 191 " (cutoff:3.500A) Processing helix chain 'Y' and resid 208 through 219 Processing helix chain 'Y' and resid 225 through 246 removed outlier: 3.925A pdb=" N GLN Y 246 " --> pdb=" O ALA Y 242 " (cutoff:3.500A) Processing helix chain 'Z' and resid 8 through 19 Processing helix chain 'Z' and resid 20 through 24 removed outlier: 4.596A pdb=" N GLN Z 23 " --> pdb=" O THR Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 32 through 40 Processing helix chain 'Z' and resid 40 through 48 Processing helix chain 'Z' and resid 52 through 62 Processing helix chain 'Z' and resid 71 through 88 removed outlier: 4.377A pdb=" N ILE Z 75 " --> pdb=" O VAL Z 71 " (cutoff:3.500A) Processing helix chain 'Z' and resid 94 through 117 removed outlier: 3.600A pdb=" N GLN Z 98 " --> pdb=" O ASP Z 94 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY Z 106 " --> pdb=" O VAL Z 102 " (cutoff:3.500A) Proline residue: Z 107 - end of helix Proline residue: Z 114 - end of helix Processing helix chain 'Z' and resid 119 through 134 removed outlier: 3.705A pdb=" N ILE Z 123 " --> pdb=" O THR Z 119 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER Z 134 " --> pdb=" O SER Z 130 " (cutoff:3.500A) Processing helix chain 'Z' and resid 137 through 166 removed outlier: 3.857A pdb=" N ILE Z 141 " --> pdb=" O ILE Z 137 " (cutoff:3.500A) Processing helix chain 'Z' and resid 167 through 173 removed outlier: 3.632A pdb=" N GLU Z 171 " --> pdb=" O SER Z 167 " (cutoff:3.500A) Processing helix chain 'Z' and resid 176 through 201 removed outlier: 3.708A pdb=" N ASP Z 180 " --> pdb=" O GLY Z 176 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL Z 201 " --> pdb=" O VAL Z 197 " (cutoff:3.500A) Processing helix chain 'Z' and resid 215 through 219 removed outlier: 3.950A pdb=" N PHE Z 219 " --> pdb=" O LYS Z 216 " (cutoff:3.500A) Processing helix chain 'Z' and resid 228 through 241 Processing helix chain 'Z' and resid 253 through 261 removed outlier: 3.642A pdb=" N LEU Z 260 " --> pdb=" O ASN Z 256 " (cutoff:3.500A) Processing helix chain 'Z' and resid 263 through 279 Processing helix chain 'Z' and resid 282 through 300 Processing helix chain 'B' and resid -14 through -3 Processing helix chain 'B' and resid 4 through 20 Processing helix chain 'B' and resid 21 through 26 Processing helix chain 'B' and resid 27 through 43 removed outlier: 3.625A pdb=" N GLN B 43 " --> pdb=" O GLU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 65 Processing helix chain 'B' and resid 70 through 77 Processing helix chain 'C' and resid 18 through 40 Processing helix chain 'D' and resid 4 through 25 removed outlier: 3.713A pdb=" N ILE D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 44 Processing helix chain 'D' and resid 45 through 60 Processing helix chain 'D' and resid 73 through 88 removed outlier: 3.629A pdb=" N ALA D 77 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 132 removed outlier: 4.179A pdb=" N VAL D 103 " --> pdb=" O ILE D 99 " (cutoff:3.500A) Proline residue: D 104 - end of helix removed outlier: 4.144A pdb=" N THR D 121 " --> pdb=" O ARG D 117 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLY D 122 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 164 removed outlier: 3.607A pdb=" N ILE D 139 " --> pdb=" O ASN D 135 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE D 154 " --> pdb=" O GLN D 150 " (cutoff:3.500A) Proline residue: D 157 - end of helix Processing helix chain 'D' and resid 165 through 175 Processing helix chain 'D' and resid 177 through 204 removed outlier: 4.505A pdb=" N VAL D 192 " --> pdb=" O GLY D 188 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ALA D 193 " --> pdb=" O GLY D 189 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY D 195 " --> pdb=" O VAL D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 219 Processing helix chain 'D' and resid 225 through 246 removed outlier: 3.925A pdb=" N GLN D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 19 Processing helix chain 'E' and resid 20 through 24 removed outlier: 4.586A pdb=" N GLN E 23 " --> pdb=" O THR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 40 removed outlier: 3.544A pdb=" N LEU E 40 " --> pdb=" O TRP E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 48 Processing helix chain 'E' and resid 52 through 62 Processing helix chain 'E' and resid 71 through 88 removed outlier: 4.363A pdb=" N ILE E 75 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 117 removed outlier: 3.579A pdb=" N GLN E 98 " --> pdb=" O ASP E 94 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY E 106 " --> pdb=" O VAL E 102 " (cutoff:3.500A) Proline residue: E 107 - end of helix Proline residue: E 114 - end of helix Processing helix chain 'E' and resid 119 through 134 removed outlier: 3.677A pdb=" N ILE E 123 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER E 134 " --> pdb=" O SER E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 166 removed outlier: 3.855A pdb=" N ILE E 141 " --> pdb=" O ILE E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 173 removed outlier: 3.517A pdb=" N GLU E 171 " --> pdb=" O SER E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 201 removed outlier: 3.615A pdb=" N ASP E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL E 201 " --> pdb=" O VAL E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 219 removed outlier: 3.957A pdb=" N PHE E 219 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 241 Processing helix chain 'E' and resid 253 through 261 removed outlier: 3.627A pdb=" N LEU E 260 " --> pdb=" O ASN E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 279 Processing helix chain 'E' and resid 282 through 300 Processing helix chain 'F' and resid -14 through -3 Processing helix chain 'F' and resid 4 through 20 Processing helix chain 'F' and resid 21 through 26 Processing helix chain 'F' and resid 27 through 43 removed outlier: 3.575A pdb=" N GLN F 43 " --> pdb=" O GLU F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 65 Processing helix chain 'F' and resid 70 through 77 Processing helix chain 'G' and resid 18 through 40 Processing helix chain 'H' and resid 4 through 25 removed outlier: 3.702A pdb=" N ILE H 23 " --> pdb=" O GLY H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 44 Processing helix chain 'H' and resid 45 through 60 Processing helix chain 'H' and resid 73 through 88 removed outlier: 3.632A pdb=" N ALA H 77 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 132 removed outlier: 4.175A pdb=" N VAL H 103 " --> pdb=" O ILE H 99 " (cutoff:3.500A) Proline residue: H 104 - end of helix removed outlier: 4.186A pdb=" N THR H 121 " --> pdb=" O ARG H 117 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLY H 122 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE H 123 " --> pdb=" O LEU H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 164 removed outlier: 3.650A pdb=" N ILE H 139 " --> pdb=" O ASN H 135 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE H 154 " --> pdb=" O GLN H 150 " (cutoff:3.500A) Proline residue: H 157 - end of helix Processing helix chain 'H' and resid 165 through 175 Processing helix chain 'H' and resid 177 through 204 removed outlier: 4.509A pdb=" N VAL H 192 " --> pdb=" O GLY H 188 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ALA H 193 " --> pdb=" O GLY H 189 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N VAL H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY H 195 " --> pdb=" O VAL H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 219 Processing helix chain 'H' and resid 225 through 246 removed outlier: 3.861A pdb=" N GLN H 246 " --> pdb=" O ALA H 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 19 Processing helix chain 'I' and resid 20 through 24 removed outlier: 4.591A pdb=" N GLN I 23 " --> pdb=" O THR I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 40 removed outlier: 3.567A pdb=" N LEU I 40 " --> pdb=" O TRP I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 48 Processing helix chain 'I' and resid 52 through 62 Processing helix chain 'I' and resid 71 through 88 removed outlier: 4.371A pdb=" N ILE I 75 " --> pdb=" O VAL I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 117 removed outlier: 3.635A pdb=" N GLN I 98 " --> pdb=" O ASP I 94 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY I 106 " --> pdb=" O VAL I 102 " (cutoff:3.500A) Proline residue: I 107 - end of helix Proline residue: I 114 - end of helix Processing helix chain 'I' and resid 119 through 134 removed outlier: 3.653A pdb=" N ILE I 123 " --> pdb=" O THR I 119 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER I 134 " --> pdb=" O SER I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 166 removed outlier: 3.849A pdb=" N ILE I 141 " --> pdb=" O ILE I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 173 removed outlier: 3.603A pdb=" N GLU I 171 " --> pdb=" O SER I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 201 removed outlier: 3.707A pdb=" N ASP I 180 " --> pdb=" O GLY I 176 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL I 201 " --> pdb=" O VAL I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 219 removed outlier: 3.971A pdb=" N PHE I 219 " --> pdb=" O LYS I 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 241 Processing helix chain 'I' and resid 253 through 261 removed outlier: 3.654A pdb=" N LEU I 260 " --> pdb=" O ASN I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 263 through 279 Processing helix chain 'I' and resid 282 through 300 Processing helix chain 'J' and resid -14 through -3 Processing helix chain 'J' and resid 4 through 20 Processing helix chain 'J' and resid 21 through 26 Processing helix chain 'J' and resid 27 through 43 removed outlier: 3.629A pdb=" N GLN J 43 " --> pdb=" O GLU J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 65 Processing helix chain 'J' and resid 70 through 77 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 Processing sheet with id=AA2, first strand: chain 'Z' and resid 208 through 213 Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 3 Processing sheet with id=AA4, first strand: chain 'E' and resid 208 through 213 Processing sheet with id=AA5, first strand: chain 'G' and resid 2 through 3 Processing sheet with id=AA6, first strand: chain 'I' and resid 208 through 213 1129 hydrogen bonds defined for protein. 3360 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.96 Time building geometry restraints manager: 7.60 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: 4903 1.34 - 1.46: 2977 1.46 - 1.58: 8173 1.58 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 16209 Sorted by residual: bond pdb=" C THR J 82 " pdb=" N PRO J 83 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.04e+00 bond pdb=" C THR B 82 " pdb=" N PRO B 83 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 1.00e+00 bond pdb=" C THR F 82 " pdb=" N PRO F 83 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 9.85e-01 bond pdb=" C2 MAN I 401 " pdb=" O2 MAN I 401 " ideal model delta sigma weight residual 1.407 1.426 -0.019 2.00e-02 2.50e+03 9.26e-01 bond pdb=" C2 MAN E 401 " pdb=" O2 MAN E 401 " ideal model delta sigma weight residual 1.407 1.426 -0.019 2.00e-02 2.50e+03 9.06e-01 ... (remaining 16204 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.19: 364 106.19 - 113.20: 9153 113.20 - 120.21: 5660 120.21 - 127.22: 6621 127.22 - 134.23: 195 Bond angle restraints: 21993 Sorted by residual: angle pdb=" N ASP Y 73 " pdb=" CA ASP Y 73 " pdb=" C ASP Y 73 " ideal model delta sigma weight residual 111.02 115.78 -4.76 1.25e+00 6.40e-01 1.45e+01 angle pdb=" N MET E 31 " pdb=" CA MET E 31 " pdb=" C MET E 31 " ideal model delta sigma weight residual 111.02 114.75 -3.73 1.22e+00 6.72e-01 9.34e+00 angle pdb=" N MET I 31 " pdb=" CA MET I 31 " pdb=" C MET I 31 " ideal model delta sigma weight residual 111.02 114.64 -3.62 1.22e+00 6.72e-01 8.80e+00 angle pdb=" N THR Z 206 " pdb=" CA THR Z 206 " pdb=" C THR Z 206 " ideal model delta sigma weight residual 109.81 115.51 -5.70 2.21e+00 2.05e-01 6.66e+00 angle pdb=" N THR I 206 " pdb=" CA THR I 206 " pdb=" C THR I 206 " ideal model delta sigma weight residual 109.81 115.51 -5.70 2.21e+00 2.05e-01 6.65e+00 ... (remaining 21988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 8828 17.76 - 35.51: 627 35.51 - 53.27: 99 53.27 - 71.02: 19 71.02 - 88.78: 12 Dihedral angle restraints: 9585 sinusoidal: 3696 harmonic: 5889 Sorted by residual: dihedral pdb=" CA PRO J 83 " pdb=" C PRO J 83 " pdb=" N LYS J 84 " pdb=" CA LYS J 84 " ideal model delta harmonic sigma weight residual -180.00 -154.20 -25.80 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA PRO F 83 " pdb=" C PRO F 83 " pdb=" N LYS F 84 " pdb=" CA LYS F 84 " ideal model delta harmonic sigma weight residual -180.00 -154.27 -25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA PRO B 83 " pdb=" C PRO B 83 " pdb=" N LYS B 84 " pdb=" CA LYS B 84 " ideal model delta harmonic sigma weight residual -180.00 -154.61 -25.39 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 9582 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1553 0.027 - 0.054: 595 0.054 - 0.081: 331 0.081 - 0.108: 112 0.108 - 0.135: 31 Chirality restraints: 2622 Sorted by residual: chirality pdb=" CA ILE Z 92 " pdb=" N ILE Z 92 " pdb=" C ILE Z 92 " pdb=" CB ILE Z 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA ILE I 92 " pdb=" N ILE I 92 " pdb=" C ILE I 92 " pdb=" CB ILE I 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA ILE E 92 " pdb=" N ILE E 92 " pdb=" C ILE E 92 " pdb=" CB ILE E 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 2619 not shown) Planarity restraints: 2691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP J 86 " 0.031 2.00e-02 2.50e+03 2.94e-02 2.16e+01 pdb=" CG TRP J 86 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP J 86 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP J 86 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J 86 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP J 86 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP J 86 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 86 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 86 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP J 86 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 86 " 0.031 2.00e-02 2.50e+03 2.91e-02 2.12e+01 pdb=" CG TRP F 86 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP F 86 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP F 86 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 86 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP F 86 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 86 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 86 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 86 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP F 86 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 86 " 0.030 2.00e-02 2.50e+03 2.82e-02 1.99e+01 pdb=" CG TRP B 86 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP B 86 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP B 86 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 86 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 86 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 86 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 86 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 86 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP B 86 " 0.001 2.00e-02 2.50e+03 ... (remaining 2688 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2006 2.75 - 3.29: 16260 3.29 - 3.83: 28296 3.83 - 4.36: 32947 4.36 - 4.90: 57398 Nonbonded interactions: 136907 Sorted by model distance: nonbonded pdb=" OD2 ASP D 128 " pdb=" NH2 ARG E 30 " model vdw 2.215 3.120 nonbonded pdb=" O VAL D 217 " pdb=" OG1 THR D 220 " model vdw 2.235 3.040 nonbonded pdb=" OH TYR I 48 " pdb=" OE1 GLU I 83 " model vdw 2.237 3.040 nonbonded pdb=" OH TYR Z 48 " pdb=" OE1 GLU Z 83 " model vdw 2.238 3.040 nonbonded pdb=" OH TYR E 48 " pdb=" OE1 GLU E 83 " model vdw 2.242 3.040 ... (remaining 136902 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'Y' } ncs_group { reference = chain 'E' selection = chain 'I' 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: 1.650 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: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 45.590 Find NCS groups from input model: 0.510 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: 0.010 Load rotamer database and sin/cos tables:11.530 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 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 : 0.002 0.024 16209 Z= 0.157 Angle : 0.527 6.889 21993 Z= 0.283 Chirality : 0.039 0.135 2622 Planarity : 0.004 0.042 2691 Dihedral : 12.886 88.781 5814 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.46 % Favored : 95.44 % Rotamer: Outliers : 0.12 % Allowed : 0.06 % Favored : 99.82 % 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: 1.92 (0.19), residues: 2061 helix: 2.15 (0.14), residues: 1494 sheet: None (None), residues: 0 loop : -1.18 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.002 TRP J 86 HIS 0.003 0.001 HIS I 68 PHE 0.009 0.001 PHE E 219 TYR 0.008 0.001 TYR F 14 ARG 0.002 0.000 ARG Z 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 187 time to evaluate : 1.849 Fit side-chains REVERT: A 13 LYS cc_start: 0.8306 (pptt) cc_final: 0.7788 (pmtt) REVERT: B 4 ASP cc_start: 0.7964 (p0) cc_final: 0.7580 (p0) REVERT: D 246 GLN cc_start: 0.7588 (pt0) cc_final: 0.7058 (pp30) REVERT: E 52 GLU cc_start: 0.7236 (mp0) cc_final: 0.6764 (mp0) REVERT: J 65 ASN cc_start: 0.7427 (t0) cc_final: 0.7063 (t0) outliers start: 2 outliers final: 2 residues processed: 189 average time/residue: 1.4864 time to fit residues: 307.4158 Evaluate side-chains 154 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain J residue 5 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 8.9990 chunk 154 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 185 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 246 GLN Z 98 GLN ** B -6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F -6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 ASN I 98 GLN ** J -6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.058 16209 Z= 0.554 Angle : 0.729 8.001 21993 Z= 0.386 Chirality : 0.052 0.231 2622 Planarity : 0.006 0.057 2691 Dihedral : 5.381 29.180 2254 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.00 % Favored : 94.81 % Rotamer: Outliers : 1.93 % Allowed : 7.23 % Favored : 90.84 % 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: 0.81 (0.18), residues: 2061 helix: 1.22 (0.13), residues: 1530 sheet: None (None), residues: 0 loop : -1.40 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP E 26 HIS 0.006 0.001 HIS I 61 PHE 0.014 0.002 PHE I 65 TYR 0.016 0.002 TYR E 157 ARG 0.004 0.001 ARG A 2 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 164 time to evaluate : 1.792 Fit side-chains REVERT: A 13 LYS cc_start: 0.8386 (pptt) cc_final: 0.7850 (ptpp) REVERT: Z 169 ILE cc_start: 0.7211 (OUTLIER) cc_final: 0.6670 (pp) REVERT: B 4 ASP cc_start: 0.7146 (p0) cc_final: 0.6776 (p0) REVERT: B 44 ASN cc_start: 0.8401 (OUTLIER) cc_final: 0.8159 (m110) REVERT: D 92 LYS cc_start: 0.8510 (mtpp) cc_final: 0.8303 (ttpp) REVERT: D 246 GLN cc_start: 0.7618 (pt0) cc_final: 0.7056 (pp30) REVERT: E 52 GLU cc_start: 0.7382 (mp0) cc_final: 0.6896 (mp0) REVERT: F 4 ASP cc_start: 0.7088 (p0) cc_final: 0.6844 (p0) REVERT: H 182 ASP cc_start: 0.8172 (m-30) cc_final: 0.7954 (m-30) REVERT: I 168 LYS cc_start: 0.6872 (ttpt) cc_final: 0.6615 (tttm) REVERT: J 4 ASP cc_start: 0.7327 (p0) cc_final: 0.7045 (p0) outliers start: 32 outliers final: 8 residues processed: 181 average time/residue: 1.5076 time to fit residues: 298.1345 Evaluate side-chains 160 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 169 ILE Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 117 TRP Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 198 MET Chi-restraints excluded: chain I residue 117 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 126 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 185 optimal weight: 8.9990 chunk 200 optimal weight: 0.9980 chunk 165 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 246 GLN Z 98 GLN ** F -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 ASN I 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16209 Z= 0.195 Angle : 0.518 6.321 21993 Z= 0.280 Chirality : 0.041 0.148 2622 Planarity : 0.005 0.049 2691 Dihedral : 4.655 27.318 2250 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.42 % Favored : 95.49 % Rotamer: Outliers : 1.51 % Allowed : 8.92 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.19), residues: 2061 helix: 1.89 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.40 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 26 HIS 0.002 0.001 HIS I 61 PHE 0.007 0.001 PHE I 219 TYR 0.019 0.001 TYR B 5 ARG 0.001 0.000 ARG E 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 1.784 Fit side-chains REVERT: A 13 LYS cc_start: 0.8354 (pptt) cc_final: 0.7772 (ptpp) REVERT: Z 169 ILE cc_start: 0.7063 (OUTLIER) cc_final: 0.6609 (pp) REVERT: B 44 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.8134 (m110) REVERT: E 50 THR cc_start: 0.7868 (t) cc_final: 0.7648 (t) REVERT: E 52 GLU cc_start: 0.7360 (mp0) cc_final: 0.7068 (mp0) REVERT: E 169 ILE cc_start: 0.7088 (OUTLIER) cc_final: 0.6833 (pp) REVERT: J 65 ASN cc_start: 0.7427 (t0) cc_final: 0.7102 (t0) outliers start: 25 outliers final: 6 residues processed: 179 average time/residue: 1.4653 time to fit residues: 287.6064 Evaluate side-chains 161 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 152 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 169 ILE Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain E residue 117 TRP Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 117 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 20 optimal weight: 0.2980 chunk 88 optimal weight: 0.0670 chunk 124 optimal weight: 0.8980 chunk 186 optimal weight: 20.0000 chunk 197 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 176 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN Y 246 GLN Z 98 GLN C 11 ASN D 246 GLN F -2 GLN F 66 ASN I 98 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16209 Z= 0.139 Angle : 0.478 7.717 21993 Z= 0.256 Chirality : 0.039 0.147 2622 Planarity : 0.005 0.048 2691 Dihedral : 4.275 25.247 2250 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.71 % Favored : 95.15 % Rotamer: Outliers : 1.33 % Allowed : 10.01 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.19), residues: 2061 helix: 2.21 (0.13), residues: 1515 sheet: None (None), residues: 0 loop : -1.28 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 142 HIS 0.001 0.000 HIS Z 298 PHE 0.006 0.001 PHE F 61 TYR 0.012 0.001 TYR B 5 ARG 0.002 0.000 ARG Z 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 168 time to evaluate : 1.656 Fit side-chains REVERT: A 13 LYS cc_start: 0.8320 (pptt) cc_final: 0.7749 (ptpp) REVERT: Z 169 ILE cc_start: 0.6883 (OUTLIER) cc_final: 0.6494 (pp) REVERT: B 44 ASN cc_start: 0.8388 (OUTLIER) cc_final: 0.8149 (m110) REVERT: D 128 ASP cc_start: 0.7382 (m-30) cc_final: 0.7170 (m-30) REVERT: E 50 THR cc_start: 0.7821 (t) cc_final: 0.7557 (t) REVERT: E 52 GLU cc_start: 0.7252 (mp0) cc_final: 0.6933 (mp0) REVERT: E 169 ILE cc_start: 0.6965 (OUTLIER) cc_final: 0.6576 (pp) REVERT: H 137 ARG cc_start: 0.7095 (mmp-170) cc_final: 0.6839 (mmp80) REVERT: J 65 ASN cc_start: 0.7431 (t0) cc_final: 0.7116 (t0) REVERT: J 68 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8117 (mt-10) outliers start: 22 outliers final: 10 residues processed: 182 average time/residue: 1.5575 time to fit residues: 309.4149 Evaluate side-chains 167 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 154 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 25 ASP Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Z residue 169 ILE Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain F residue -14 SER Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 214 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 168 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 100 optimal weight: 0.6980 chunk 176 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN Y 246 GLN Z 98 GLN C 11 ASN F 66 ASN H 150 GLN I 98 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16209 Z= 0.214 Angle : 0.517 6.764 21993 Z= 0.276 Chirality : 0.041 0.150 2622 Planarity : 0.005 0.046 2691 Dihedral : 4.429 24.443 2250 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.66 % Favored : 95.20 % Rotamer: Outliers : 1.57 % Allowed : 10.73 % Favored : 87.70 % 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: 1.94 (0.19), residues: 2061 helix: 2.15 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.25 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 26 HIS 0.004 0.001 HIS Z 61 PHE 0.007 0.001 PHE I 65 TYR 0.010 0.001 TYR B 5 ARG 0.002 0.000 ARG H 153 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 160 time to evaluate : 1.722 Fit side-chains REVERT: A 13 LYS cc_start: 0.8383 (pptt) cc_final: 0.7789 (ptpp) REVERT: Y 137 ARG cc_start: 0.7211 (mmp80) cc_final: 0.6989 (mmp-170) REVERT: Z 169 ILE cc_start: 0.6940 (OUTLIER) cc_final: 0.6505 (pp) REVERT: B 44 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.8147 (m110) REVERT: D 206 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.5838 (tptp) REVERT: E 169 ILE cc_start: 0.7079 (OUTLIER) cc_final: 0.6696 (pp) REVERT: H 133 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.7006 (mt-10) REVERT: J 1 MET cc_start: 0.5886 (mmm) cc_final: 0.5363 (mmt) REVERT: J 44 ASN cc_start: 0.8359 (OUTLIER) cc_final: 0.8144 (m110) REVERT: J 65 ASN cc_start: 0.7473 (t0) cc_final: 0.7158 (t0) REVERT: J 68 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8165 (mt-10) outliers start: 26 outliers final: 10 residues processed: 174 average time/residue: 1.5118 time to fit residues: 287.6787 Evaluate side-chains 171 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 155 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Z residue 169 ILE Chi-restraints excluded: chain Z residue 214 LEU Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 92 LYS Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain F residue -14 SER Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 133 GLU Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain J residue 44 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 197 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN Y 246 GLN Z 98 GLN C 11 ASN F 66 ASN I 98 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16209 Z= 0.230 Angle : 0.529 6.670 21993 Z= 0.283 Chirality : 0.042 0.158 2622 Planarity : 0.005 0.047 2691 Dihedral : 4.517 25.705 2250 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.29 % Favored : 94.57 % Rotamer: Outliers : 1.87 % Allowed : 11.09 % Favored : 87.04 % 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: 1.84 (0.19), residues: 2061 helix: 2.02 (0.13), residues: 1527 sheet: None (None), residues: 0 loop : -1.18 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 26 HIS 0.004 0.001 HIS I 61 PHE 0.007 0.001 PHE I 65 TYR 0.008 0.001 TYR B 5 ARG 0.002 0.000 ARG Z 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 161 time to evaluate : 1.726 Fit side-chains REVERT: A 13 LYS cc_start: 0.8452 (pptt) cc_final: 0.7867 (ptpp) REVERT: Y 137 ARG cc_start: 0.7154 (mmp80) cc_final: 0.6934 (mmp-170) REVERT: Z 169 ILE cc_start: 0.7083 (OUTLIER) cc_final: 0.6635 (pp) REVERT: B 44 ASN cc_start: 0.8391 (OUTLIER) cc_final: 0.8144 (m110) REVERT: D 206 LYS cc_start: 0.7400 (OUTLIER) cc_final: 0.5842 (tptp) REVERT: E 52 GLU cc_start: 0.7154 (mp0) cc_final: 0.6816 (mp0) REVERT: E 169 ILE cc_start: 0.7062 (OUTLIER) cc_final: 0.6656 (pp) REVERT: H 133 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.7040 (mt-10) REVERT: J 4 ASP cc_start: 0.7352 (p0) cc_final: 0.7059 (p0) REVERT: J 44 ASN cc_start: 0.8367 (OUTLIER) cc_final: 0.8140 (m110) REVERT: J 65 ASN cc_start: 0.7481 (t0) cc_final: 0.7158 (t0) outliers start: 31 outliers final: 13 residues processed: 180 average time/residue: 1.4328 time to fit residues: 282.7845 Evaluate side-chains 178 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 159 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 169 ILE Chi-restraints excluded: chain Z residue 214 LEU Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 92 LYS Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 117 TRP Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain F residue -14 SER Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 133 GLU Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain J residue 44 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 112 optimal weight: 0.1980 chunk 144 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 166 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 196 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN Y 246 GLN Z 98 GLN C 11 ASN E 248 HIS F 66 ASN I 98 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16209 Z= 0.142 Angle : 0.474 6.468 21993 Z= 0.254 Chirality : 0.039 0.140 2622 Planarity : 0.004 0.047 2691 Dihedral : 4.249 25.536 2250 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.42 % Favored : 95.44 % Rotamer: Outliers : 1.33 % Allowed : 12.00 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.19), residues: 2061 helix: 2.32 (0.13), residues: 1497 sheet: None (None), residues: 0 loop : -1.31 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 142 HIS 0.002 0.000 HIS Z 298 PHE 0.006 0.001 PHE I 219 TYR 0.009 0.001 TYR B 5 ARG 0.002 0.000 ARG H 153 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 166 time to evaluate : 1.621 Fit side-chains REVERT: A 13 LYS cc_start: 0.8355 (pptt) cc_final: 0.7775 (ptpp) REVERT: Y 133 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6882 (mt-10) REVERT: Y 137 ARG cc_start: 0.7056 (mmp80) cc_final: 0.6841 (mmp-170) REVERT: Z 169 ILE cc_start: 0.6908 (OUTLIER) cc_final: 0.6491 (pp) REVERT: B 44 ASN cc_start: 0.8386 (OUTLIER) cc_final: 0.8149 (m110) REVERT: D 245 LYS cc_start: 0.7684 (mmtp) cc_final: 0.6939 (mttt) REVERT: E 52 GLU cc_start: 0.7139 (mp0) cc_final: 0.6939 (mp0) REVERT: E 169 ILE cc_start: 0.6990 (OUTLIER) cc_final: 0.6515 (pp) REVERT: H 133 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6971 (mt-10) REVERT: J 65 ASN cc_start: 0.7476 (t0) cc_final: 0.7153 (t0) outliers start: 22 outliers final: 13 residues processed: 177 average time/residue: 1.5014 time to fit residues: 289.9913 Evaluate side-chains 175 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 25 ASP Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 169 ILE Chi-restraints excluded: chain Z residue 214 LEU Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain F residue -14 SER Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 133 GLU Chi-restraints excluded: chain I residue 214 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.9552 > 50: distance: 12 - 16: 29.857 distance: 16 - 17: 12.862 distance: 16 - 182: 31.346 distance: 17 - 18: 52.162 distance: 17 - 20: 40.672 distance: 18 - 19: 54.755 distance: 18 - 23: 50.531 distance: 19 - 179: 24.960 distance: 20 - 21: 19.429 distance: 20 - 22: 28.998 distance: 23 - 24: 41.151 distance: 24 - 25: 55.851 distance: 24 - 27: 56.014 distance: 25 - 26: 47.884 distance: 25 - 32: 68.546 distance: 27 - 28: 23.142 distance: 28 - 29: 32.662 distance: 29 - 30: 35.131 distance: 30 - 31: 45.802 distance: 32 - 33: 39.993 distance: 33 - 34: 41.407 distance: 33 - 36: 43.637 distance: 34 - 35: 56.210 distance: 34 - 40: 43.409 distance: 36 - 37: 25.954 distance: 37 - 38: 17.043 distance: 37 - 39: 5.523 distance: 40 - 41: 40.849 distance: 41 - 42: 57.194 distance: 41 - 44: 55.969 distance: 42 - 43: 40.616 distance: 42 - 48: 38.734 distance: 43 - 61: 36.528 distance: 45 - 46: 55.732 distance: 45 - 47: 59.588 distance: 48 - 49: 37.278 distance: 50 - 51: 56.599 distance: 50 - 57: 57.760 distance: 52 - 53: 56.563 distance: 53 - 54: 56.938 distance: 54 - 55: 56.415 distance: 55 - 56: 49.663 distance: 57 - 58: 62.667 distance: 58 - 59: 61.421 distance: 59 - 60: 41.567 distance: 59 - 61: 46.914 distance: 61 - 62: 56.309 distance: 62 - 63: 38.479 distance: 63 - 64: 36.990 distance: 63 - 66: 18.034 distance: 66 - 67: 40.341 distance: 67 - 68: 48.964 distance: 67 - 70: 25.654 distance: 68 - 69: 40.504 distance: 68 - 77: 38.681 distance: 70 - 71: 30.008 distance: 71 - 72: 11.023 distance: 71 - 73: 12.542 distance: 72 - 74: 29.309 distance: 73 - 75: 23.760 distance: 74 - 76: 34.992 distance: 75 - 76: 21.704 distance: 77 - 78: 69.487 distance: 78 - 79: 56.609 distance: 78 - 81: 51.153 distance: 79 - 80: 41.206 distance: 79 - 85: 55.956 distance: 81 - 82: 44.066 distance: 81 - 83: 41.924 distance: 82 - 84: 56.955 distance: 85 - 86: 39.877 distance: 86 - 87: 66.015 distance: 86 - 89: 43.769 distance: 87 - 88: 33.019 distance: 87 - 93: 32.445 distance: 89 - 90: 36.779 distance: 90 - 91: 39.028 distance: 90 - 92: 32.971