Starting phenix.real_space_refine on Sat Jan 20 17:25:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xno_33321/01_2024/7xno_33321.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xno_33321/01_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_33321/01_2024/7xno_33321.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xno_33321/01_2024/7xno_33321.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xno_33321/01_2024/7xno_33321.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xno_33321/01_2024/7xno_33321.pdb" } 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-1.21-5211/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: 8.61, per 1000 atoms: 0.54 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: 6.63 Conformation dependent library (CDL) restraints added in 2.9 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: 1.58 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: 4.99 Time building geometry restraints manager: 7.12 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: 8762 17.76 - 35.51: 627 35.51 - 53.27: 99 53.27 - 71.02: 19 71.02 - 88.78: 12 Dihedral angle restraints: 9519 sinusoidal: 3630 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 9516 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 2.520 nonbonded pdb=" O VAL D 217 " pdb=" OG1 THR D 220 " model vdw 2.235 2.440 nonbonded pdb=" OH TYR I 48 " pdb=" OE1 GLU I 83 " model vdw 2.237 2.440 nonbonded pdb=" OH TYR Z 48 " pdb=" OE1 GLU Z 83 " model vdw 2.238 2.440 nonbonded pdb=" OH TYR E 48 " pdb=" OE1 GLU E 83 " model vdw 2.242 2.440 ... (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 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: 6.210 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: 0.020 Extract box with map and model: 8.390 Check model and map are aligned: 0.260 Set scattering table: 0.140 Process input model: 44.920 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.100 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:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.810 ------------------------------------------------------------------------------- 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 : 12.942 88.781 5748 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 : 2.059 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: 1.5816 time to fit residues: 325.8043 Evaluate side-chains 154 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 1.958 ------------------------------------------------------------------------------- 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: 9.9990 chunk 154 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 185 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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** D 246 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.063 16209 Z= 0.625 Angle : 0.769 8.470 21993 Z= 0.403 Chirality : 0.054 0.252 2622 Planarity : 0.007 0.059 2691 Dihedral : 5.195 28.788 2188 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.05 % Favored : 94.71 % Rotamer: Outliers : 2.35 % Allowed : 6.87 % Favored : 90.78 % 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 (0.18), residues: 2061 helix: 1.07 (0.13), residues: 1530 sheet: None (None), residues: 0 loop : -1.43 (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 E 61 PHE 0.015 0.002 PHE I 65 TYR 0.018 0.003 TYR E 157 ARG 0.007 0.001 ARG Z 151 *********************** 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 198 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 159 time to evaluate : 2.240 Fit side-chains REVERT: A 13 LYS cc_start: 0.8390 (pptt) cc_final: 0.7836 (ptpp) REVERT: Z 169 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.6707 (pp) REVERT: B 4 ASP cc_start: 0.7225 (p0) cc_final: 0.6868 (p0) REVERT: B 44 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.8168 (m110) REVERT: D 92 LYS cc_start: 0.8514 (mtpp) cc_final: 0.8282 (ttpp) REVERT: E 52 GLU cc_start: 0.7326 (mp0) cc_final: 0.6828 (mp0) REVERT: F 4 ASP cc_start: 0.7234 (p0) cc_final: 0.6947 (p0) REVERT: H 182 ASP cc_start: 0.8202 (m-30) cc_final: 0.7957 (m-30) REVERT: J -7 GLU cc_start: 0.7426 (tt0) cc_final: 0.7126 (tt0) REVERT: J 4 ASP cc_start: 0.7403 (p0) cc_final: 0.7074 (p0) REVERT: J 82 THR cc_start: 0.7392 (m) cc_final: 0.7170 (p) outliers start: 39 outliers final: 14 residues processed: 179 average time/residue: 1.6578 time to fit residues: 324.5746 Evaluate side-chains 165 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 149 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 33 VAL 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 15 THR Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 117 TRP Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 198 MET Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain J residue 15 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 126 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 185 optimal weight: 6.9990 chunk 200 optimal weight: 0.7980 chunk 165 optimal weight: 0.9990 chunk 184 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 148 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8247 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16209 Z= 0.157 Angle : 0.500 6.673 21993 Z= 0.267 Chirality : 0.040 0.189 2622 Planarity : 0.005 0.044 2691 Dihedral : 4.607 26.902 2184 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.17 % Favored : 95.78 % Rotamer: Outliers : 1.21 % Allowed : 8.92 % Favored : 89.87 % 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: 1.70 (0.19), residues: 2061 helix: 1.98 (0.13), residues: 1509 sheet: None (None), residues: 0 loop : -1.33 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 26 HIS 0.002 0.000 HIS I 61 PHE 0.006 0.001 PHE Z 219 TYR 0.019 0.001 TYR B 5 ARG 0.001 0.000 ARG E 54 *********************** 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 177 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 157 time to evaluate : 1.817 Fit side-chains REVERT: A 13 LYS cc_start: 0.8388 (pptt) cc_final: 0.7842 (ptpp) REVERT: Y 137 ARG cc_start: 0.7125 (mmp-170) cc_final: 0.6923 (mmp80) REVERT: Z 169 ILE cc_start: 0.6961 (OUTLIER) cc_final: 0.6515 (pp) REVERT: B 44 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.8151 (m110) REVERT: D 245 LYS cc_start: 0.7723 (mmtp) cc_final: 0.7010 (mttt) REVERT: E 52 GLU cc_start: 0.7310 (mp0) cc_final: 0.6729 (mp0) REVERT: E 169 ILE cc_start: 0.7092 (OUTLIER) cc_final: 0.6784 (pp) REVERT: F 1 MET cc_start: 0.6097 (mmm) cc_final: 0.5886 (mpt) REVERT: H 137 ARG cc_start: 0.7037 (mmp-170) cc_final: 0.6630 (mmp-170) REVERT: J 65 ASN cc_start: 0.7441 (t0) cc_final: 0.7090 (t0) outliers start: 20 outliers final: 2 residues processed: 169 average time/residue: 1.4815 time to fit residues: 273.8784 Evaluate side-chains 155 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 150 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 169 ILE Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 0.7980 chunk 139 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 186 optimal weight: 20.0000 chunk 197 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 ** B -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F -6 ASN ** F -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 ASN I 98 GLN J -6 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1219 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= 0.187 Angle : 0.511 7.773 21993 Z= 0.271 Chirality : 0.041 0.146 2622 Planarity : 0.005 0.042 2691 Dihedral : 4.471 25.172 2184 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.61 % Favored : 95.25 % Rotamer: Outliers : 1.21 % Allowed : 10.49 % Favored : 88.31 % 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: 1.85 (0.19), residues: 2061 helix: 2.09 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.29 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 26 HIS 0.003 0.001 HIS I 61 PHE 0.007 0.001 PHE I 65 TYR 0.012 0.001 TYR B 5 ARG 0.002 0.000 ARG Z 86 *********************** 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 176 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 156 time to evaluate : 1.980 Fit side-chains REVERT: A 13 LYS cc_start: 0.8399 (pptt) cc_final: 0.7852 (ptpp) REVERT: Y 137 ARG cc_start: 0.7172 (mmp-170) cc_final: 0.6953 (mmp80) REVERT: Z 169 ILE cc_start: 0.6946 (OUTLIER) cc_final: 0.6495 (pp) REVERT: B 44 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.8131 (m110) REVERT: E 52 GLU cc_start: 0.7236 (mp0) cc_final: 0.6983 (mp0) REVERT: E 169 ILE cc_start: 0.7094 (OUTLIER) cc_final: 0.6751 (pp) REVERT: J 44 ASN cc_start: 0.8337 (OUTLIER) cc_final: 0.8128 (m110) REVERT: J 65 ASN cc_start: 0.7458 (t0) cc_final: 0.7109 (t0) outliers start: 20 outliers final: 9 residues processed: 170 average time/residue: 1.5043 time to fit residues: 279.8413 Evaluate side-chains 166 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 153 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 -6 ASN 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 F residue -14 SER Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain J residue 44 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 146 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 168 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 B -6 ASN ** B -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 ASN F -6 ASN ** F -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 ASN I 98 GLN J -6 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16209 Z= 0.149 Angle : 0.477 7.064 21993 Z= 0.254 Chirality : 0.039 0.147 2622 Planarity : 0.004 0.041 2691 Dihedral : 4.333 25.809 2184 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.46 % Favored : 95.39 % Rotamer: Outliers : 1.63 % Allowed : 11.15 % Favored : 87.22 % 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: 2.05 (0.19), residues: 2061 helix: 2.24 (0.13), residues: 1515 sheet: None (None), residues: 0 loop : -1.27 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 26 HIS 0.002 0.000 HIS I 61 PHE 0.006 0.001 PHE E 219 TYR 0.011 0.001 TYR B 5 ARG 0.001 0.000 ARG Z 86 *********************** 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 196 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 169 time to evaluate : 1.760 Fit side-chains REVERT: A 13 LYS cc_start: 0.8392 (pptt) cc_final: 0.7842 (ptpp) REVERT: Z 169 ILE cc_start: 0.6887 (OUTLIER) cc_final: 0.6475 (pp) REVERT: B 44 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.8137 (m110) REVERT: D 206 LYS cc_start: 0.7236 (OUTLIER) cc_final: 0.5719 (tptp) REVERT: D 245 LYS cc_start: 0.7682 (mmtp) cc_final: 0.6943 (mttt) REVERT: E 169 ILE cc_start: 0.7028 (OUTLIER) cc_final: 0.6570 (pp) REVERT: H 137 ARG cc_start: 0.7100 (mmp-170) cc_final: 0.6880 (mmp80) REVERT: J 65 ASN cc_start: 0.7435 (t0) cc_final: 0.7112 (t0) outliers start: 27 outliers final: 13 residues processed: 182 average time/residue: 1.5531 time to fit residues: 310.5474 Evaluate side-chains 177 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 160 time to evaluate : 2.128 ------------------------------------------------------------------------------- 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 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 25 ASP Chi-restraints excluded: chain D residue 33 VAL 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 F residue 27 ASP Chi-restraints excluded: chain G residue 13 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.7980 chunk 177 optimal weight: 0.0570 chunk 38 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 197 optimal weight: 0.8980 chunk 163 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 overall best weight: 1.2700 ------------------------------------------------------------------------------- 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 ** B -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 ASN F -6 ASN ** F -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 ASN I 98 GLN J -6 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16209 Z= 0.166 Angle : 0.488 6.610 21993 Z= 0.260 Chirality : 0.040 0.150 2622 Planarity : 0.004 0.041 2691 Dihedral : 4.300 24.180 2184 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.51 % Favored : 95.34 % Rotamer: Outliers : 1.75 % Allowed : 11.87 % Favored : 86.38 % 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: 2.26 (0.13), residues: 1515 sheet: None (None), residues: 0 loop : -1.26 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 26 HIS 0.003 0.000 HIS I 61 PHE 0.006 0.001 PHE I 219 TYR 0.009 0.001 TYR B 5 ARG 0.001 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 189 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 160 time to evaluate : 1.920 Fit side-chains REVERT: A 13 LYS cc_start: 0.8394 (pptt) cc_final: 0.7829 (ptpp) REVERT: Z 169 ILE cc_start: 0.6913 (OUTLIER) cc_final: 0.6500 (pp) REVERT: B 44 ASN cc_start: 0.8385 (OUTLIER) cc_final: 0.8136 (m110) REVERT: D 206 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.5780 (tptp) REVERT: D 245 LYS cc_start: 0.7680 (mmtp) cc_final: 0.6934 (mttt) REVERT: E 52 GLU cc_start: 0.7074 (mp0) cc_final: 0.6619 (mp0) REVERT: E 169 ILE cc_start: 0.7029 (OUTLIER) cc_final: 0.6538 (pp) REVERT: H 133 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6977 (mt-10) REVERT: H 137 ARG cc_start: 0.7133 (mmp-170) cc_final: 0.6732 (mmp-170) REVERT: J 4 ASP cc_start: 0.7395 (p0) cc_final: 0.7064 (p0) REVERT: J 44 ASN cc_start: 0.8360 (OUTLIER) cc_final: 0.8152 (m110) REVERT: J 65 ASN cc_start: 0.7495 (t0) cc_final: 0.7156 (t0) outliers start: 29 outliers final: 11 residues processed: 176 average time/residue: 1.5240 time to fit residues: 292.5674 Evaluate side-chains 176 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 159 time to evaluate : 1.845 ------------------------------------------------------------------------------- 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 27 ASP Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain D residue 33 VAL 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 F residue 27 ASP Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 133 GLU Chi-restraints excluded: chain I residue 117 TRP 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: 2.9990 chunk 22 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 B -6 ASN ** B -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 ASN F -6 ASN ** F -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 ASN I 98 GLN J -6 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16209 Z= 0.211 Angle : 0.515 6.359 21993 Z= 0.274 Chirality : 0.041 0.151 2622 Planarity : 0.005 0.043 2691 Dihedral : 4.417 24.770 2184 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.80 % Favored : 95.05 % Rotamer: Outliers : 1.99 % Allowed : 12.00 % Favored : 86.02 % 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: 1.97 (0.19), residues: 2061 helix: 2.12 (0.13), residues: 1527 sheet: None (None), residues: 0 loop : -1.14 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 26 HIS 0.004 0.001 HIS I 61 PHE 0.008 0.001 PHE I 65 TYR 0.007 0.001 TYR B 5 ARG 0.002 0.000 ARG Z 86 *********************** 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 191 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 158 time to evaluate : 1.899 Fit side-chains REVERT: A 13 LYS cc_start: 0.8426 (pptt) cc_final: 0.7857 (ptpp) REVERT: Z 169 ILE cc_start: 0.6998 (OUTLIER) cc_final: 0.6547 (pp) REVERT: B 44 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.8136 (m110) REVERT: D 206 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.5766 (tptp) REVERT: D 245 LYS cc_start: 0.7718 (mmtp) cc_final: 0.6935 (mttt) REVERT: E 52 GLU cc_start: 0.7147 (mp0) cc_final: 0.6659 (mp0) REVERT: E 169 ILE cc_start: 0.7049 (OUTLIER) cc_final: 0.6618 (pp) REVERT: H 133 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6999 (mt-10) REVERT: H 137 ARG cc_start: 0.7185 (mmp-170) cc_final: 0.6779 (mmp-170) REVERT: J 44 ASN cc_start: 0.8365 (OUTLIER) cc_final: 0.8160 (m110) REVERT: J 65 ASN cc_start: 0.7509 (t0) cc_final: 0.7174 (t0) outliers start: 33 outliers final: 12 residues processed: 179 average time/residue: 1.4959 time to fit residues: 292.4597 Evaluate side-chains 179 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 161 time to evaluate : 1.964 ------------------------------------------------------------------------------- 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 96 THR 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 G residue 13 LYS Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 133 GLU Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain J residue 44 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 B -6 ASN ** B -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 ASN F -6 ASN ** F -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 ASN I 98 GLN J -6 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16209 Z= 0.304 Angle : 0.575 7.284 21993 Z= 0.304 Chirality : 0.044 0.181 2622 Planarity : 0.005 0.044 2691 Dihedral : 4.634 25.593 2184 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.19 % Favored : 94.66 % Rotamer: Outliers : 2.11 % Allowed : 12.18 % Favored : 85.71 % 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: 1.63 (0.19), residues: 2061 helix: 1.86 (0.13), residues: 1527 sheet: None (None), residues: 0 loop : -1.24 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 26 HIS 0.004 0.001 HIS E 61 PHE 0.009 0.001 PHE Y 211 TYR 0.010 0.002 TYR I 28 ARG 0.002 0.000 ARG E 86 *********************** REFINEMENT MACRO_CYCLE 8 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 194 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 159 time to evaluate : 2.085 Fit side-chains REVERT: A 13 LYS cc_start: 0.8462 (pptt) cc_final: 0.7879 (ptpp) REVERT: Y 137 ARG cc_start: 0.7136 (mmp80) cc_final: 0.6934 (mmp-170) REVERT: Z 169 ILE cc_start: 0.7074 (OUTLIER) cc_final: 0.6553 (pp) REVERT: B 44 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.8146 (m110) REVERT: D 206 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.5889 (tptp) REVERT: E 52 GLU cc_start: 0.7178 (mp0) cc_final: 0.6826 (mp0) REVERT: E 169 ILE cc_start: 0.7163 (OUTLIER) cc_final: 0.6883 (pp) REVERT: F 1 MET cc_start: 0.5296 (OUTLIER) cc_final: 0.4928 (mpt) REVERT: H 133 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7105 (mt-10) REVERT: I 168 LYS cc_start: 0.6801 (ttpt) cc_final: 0.6572 (tttm) REVERT: J 4 ASP cc_start: 0.7479 (p0) cc_final: 0.7122 (p0) REVERT: J 65 ASN cc_start: 0.7522 (t0) cc_final: 0.7175 (t0) outliers start: 35 outliers final: 12 residues processed: 179 average time/residue: 1.5312 time to fit residues: 301.1049 Evaluate side-chains 176 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 158 time to evaluate : 1.803 ------------------------------------------------------------------------------- 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 44 ASN Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 94 ASP 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 1 MET Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 133 GLU Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 214 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 7.9990 chunk 171 optimal weight: 0.7980 chunk 183 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 chunk 182 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F -6 ASN ** F -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 ASN I 98 GLN J -6 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16209 Z= 0.170 Angle : 0.493 7.185 21993 Z= 0.264 Chirality : 0.040 0.146 2622 Planarity : 0.004 0.042 2691 Dihedral : 4.426 26.137 2184 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.00 % Favored : 94.91 % Rotamer: Outliers : 1.51 % Allowed : 12.66 % Favored : 85.83 % 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 (0.13), residues: 1515 sheet: None (None), residues: 0 loop : -1.31 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 26 HIS 0.003 0.001 HIS I 61 PHE 0.006 0.001 PHE I 219 TYR 0.008 0.001 TYR B 5 ARG 0.001 0.000 ARG I 86 *********************** REFINEMENT MACRO_CYCLE 9 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 185 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 160 time to evaluate : 1.808 Fit side-chains REVERT: A 13 LYS cc_start: 0.8429 (pptt) cc_final: 0.7857 (ptpp) REVERT: Z 169 ILE cc_start: 0.7015 (OUTLIER) cc_final: 0.6541 (pp) REVERT: B 44 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.8146 (m110) REVERT: D 206 LYS cc_start: 0.7312 (OUTLIER) cc_final: 0.5821 (tptp) REVERT: D 245 LYS cc_start: 0.7754 (mmtp) cc_final: 0.6961 (mttt) REVERT: E 52 GLU cc_start: 0.7166 (mp0) cc_final: 0.6536 (mp0) REVERT: E 169 ILE cc_start: 0.7022 (OUTLIER) cc_final: 0.6676 (pp) REVERT: F 4 ASP cc_start: 0.6933 (p0) cc_final: 0.6731 (p0) REVERT: H 133 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.7060 (mt-10) REVERT: I 168 LYS cc_start: 0.6735 (ttpt) cc_final: 0.6513 (tttm) REVERT: J 4 ASP cc_start: 0.7414 (p0) cc_final: 0.7058 (p0) REVERT: J 65 ASN cc_start: 0.7496 (t0) cc_final: 0.7125 (t0) outliers start: 25 outliers final: 13 residues processed: 177 average time/residue: 1.5378 time to fit residues: 296.9828 Evaluate side-chains 177 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 159 time to evaluate : 1.931 ------------------------------------------------------------------------------- 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 44 ASN Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 96 THR 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 G residue 13 LYS Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 133 GLU Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 2.9990 chunk 118 optimal weight: 0.0020 chunk 91 optimal weight: 8.9990 chunk 134 optimal weight: 0.8980 chunk 203 optimal weight: 6.9990 chunk 187 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 overall best weight: 1.7792 ------------------------------------------------------------------------------- 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 ** B -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 ASN F -6 ASN ** F -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 ASN I 98 GLN J -6 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16209 Z= 0.200 Angle : 0.512 7.119 21993 Z= 0.273 Chirality : 0.041 0.153 2622 Planarity : 0.005 0.041 2691 Dihedral : 4.419 24.669 2184 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.19 % Favored : 94.71 % Rotamer: Outliers : 1.51 % Allowed : 12.72 % Favored : 85.77 % 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: 1.95 (0.19), residues: 2061 helix: 2.09 (0.13), residues: 1527 sheet: None (None), residues: 0 loop : -1.14 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 26 HIS 0.003 0.001 HIS I 61 PHE 0.007 0.001 PHE I 65 TYR 0.008 0.001 TYR F 14 ARG 0.002 0.000 ARG I 86 ********************** REFINEMENT MACRO_CYCLE 10 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 184 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 159 time to evaluate : 1.906 Fit side-chains REVERT: A 13 LYS cc_start: 0.8461 (pptt) cc_final: 0.7882 (ptpp) REVERT: Z 169 ILE cc_start: 0.7017 (OUTLIER) cc_final: 0.6544 (pp) REVERT: B 44 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.8129 (m110) REVERT: D 206 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.5817 (tptp) REVERT: D 245 LYS cc_start: 0.7752 (mmtp) cc_final: 0.6949 (mttt) REVERT: E 169 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6709 (pp) REVERT: F 4 ASP cc_start: 0.6939 (p0) cc_final: 0.6733 (p0) REVERT: H 133 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.7059 (mt-10) REVERT: I 168 LYS cc_start: 0.6746 (ttpt) cc_final: 0.6399 (ttpp) REVERT: J 4 ASP cc_start: 0.7413 (p0) cc_final: 0.7048 (p0) REVERT: J 65 ASN cc_start: 0.7514 (t0) cc_final: 0.7145 (t0) outliers start: 25 outliers final: 14 residues processed: 177 average time/residue: 1.5055 time to fit residues: 291.2519 Evaluate side-chains 178 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 159 time to evaluate : 1.903 ------------------------------------------------------------------------------- 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 117 TRP 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 206 LYS Chi-restraints excluded: chain E residue 94 ASP 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 G residue 13 LYS Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 133 GLU Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 overall best weight: 3.1386 ------------------------------------------------------------------------------- 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 ** B -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 ASN F -6 ASN ** F -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN J -6 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.092554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.073469 restraints weight = 28073.196| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.72 r_work: 0.3089 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16209 Z= 0.298 Angle : 0.577 6.970 21993 Z= 0.306 Chirality : 0.044 0.179 2622 Planarity : 0.005 0.044 2691 Dihedral : 4.639 25.567 2184 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.14 % Favored : 94.71 % Rotamer: Outliers : 1.75 % Allowed : 12.48 % Favored : 85.77 % 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: 1.62 (0.19), residues: 2061 helix: 1.85 (0.13), residues: 1527 sheet: None (None), residues: 0 loop : -1.26 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 26 HIS 0.004 0.001 HIS I 61 PHE 0.008 0.001 PHE Y 211 TYR 0.009 0.002 TYR E 157 ARG 0.002 0.000 ARG E 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5306.44 seconds wall clock time: 96 minutes 6.01 seconds (5766.01 seconds total)