Starting phenix.real_space_refine on Fri Feb 6 18:58:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n0w_48796/02_2026/9n0w_48796.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n0w_48796/02_2026/9n0w_48796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n0w_48796/02_2026/9n0w_48796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n0w_48796/02_2026/9n0w_48796.map" model { file = "/net/cci-nas-00/data/ceres_data/9n0w_48796/02_2026/9n0w_48796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n0w_48796/02_2026/9n0w_48796.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.004 sd= 0.040 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 108 5.16 5 C 17046 2.51 5 N 4842 2.21 5 O 5130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 171 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27126 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1507 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 14, 'TRANS': 178} Chain: "C" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1507 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 14, 'TRANS': 178} Chain: "A" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1507 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 14, 'TRANS': 178} Chain: "D" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1507 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 14, 'TRANS': 178} Chain: "E" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1507 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 14, 'TRANS': 178} Chain: "F" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1507 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 14, 'TRANS': 178} Chain: "G" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1507 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 14, 'TRANS': 178} Chain: "H" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1507 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 14, 'TRANS': 178} Chain: "I" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1507 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 14, 'TRANS': 178} Chain: "J" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1507 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 14, 'TRANS': 178} Chain: "K" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1507 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 14, 'TRANS': 178} Chain: "L" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1507 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 14, 'TRANS': 178} Chain: "M" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1507 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 14, 'TRANS': 178} Chain: "N" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1507 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 14, 'TRANS': 178} Chain: "O" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1507 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 14, 'TRANS': 178} Chain: "P" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1507 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 14, 'TRANS': 178} Chain: "Q" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1507 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 14, 'TRANS': 178} Chain: "R" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1507 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 14, 'TRANS': 178} Time building chain proxies: 6.22, per 1000 atoms: 0.23 Number of scatterers: 27126 At special positions: 0 Unit cell: (165, 151.8, 85.8, 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 108 16.00 O 5130 8.00 N 4842 7.00 C 17046 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6552 Finding SS restraints... Secondary structure from input PDB file: 234 helices and 0 sheets defined 80.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'B' and resid 16 through 28 Processing helix chain 'B' and resid 34 through 49 Processing helix chain 'B' and resid 51 through 63 Processing helix chain 'B' and resid 64 through 86 Processing helix chain 'B' and resid 96 through 103 removed outlier: 3.614A pdb=" N ASN B 102 " --> pdb=" O ARG B 98 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN B 103 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 128 removed outlier: 3.699A pdb=" N PHE B 121 " --> pdb=" O TRP B 117 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) Proline residue: B 125 - end of helix Processing helix chain 'B' and resid 131 through 136 removed outlier: 3.503A pdb=" N ALA B 134 " --> pdb=" O PRO B 131 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE B 136 " --> pdb=" O TRP B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 159 removed outlier: 3.550A pdb=" N ASN B 157 " --> pdb=" O ILE B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 176 removed outlier: 4.592A pdb=" N TYR B 174 " --> pdb=" O ARG B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 194 through 202 Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'C' and resid 16 through 27 Processing helix chain 'C' and resid 34 through 49 Processing helix chain 'C' and resid 51 through 63 Processing helix chain 'C' and resid 64 through 86 Processing helix chain 'C' and resid 91 through 95 removed outlier: 3.563A pdb=" N GLY C 95 " --> pdb=" O PRO C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 101 Processing helix chain 'C' and resid 106 through 123 removed outlier: 3.808A pdb=" N PHE C 121 " --> pdb=" O TRP C 117 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 128 Processing helix chain 'C' and resid 143 through 159 Processing helix chain 'C' and resid 164 through 176 removed outlier: 4.370A pdb=" N ILE C 168 " --> pdb=" O PRO C 164 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR C 174 " --> pdb=" O ARG C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'C' and resid 194 through 202 Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'A' and resid 16 through 28 Processing helix chain 'A' and resid 34 through 49 Processing helix chain 'A' and resid 51 through 63 Processing helix chain 'A' and resid 64 through 86 removed outlier: 3.678A pdb=" N SER A 77 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 95 Processing helix chain 'A' and resid 96 through 103 removed outlier: 3.607A pdb=" N ASN A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A 103 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 121 removed outlier: 3.700A pdb=" N PHE A 121 " --> pdb=" O TRP A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.624A pdb=" N GLY A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 136 removed outlier: 3.538A pdb=" N ILE A 136 " --> pdb=" O TRP A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 159 removed outlier: 3.626A pdb=" N GLU A 149 " --> pdb=" O HIS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 176 removed outlier: 3.826A pdb=" N ILE A 168 " --> pdb=" O PRO A 164 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 188 removed outlier: 4.141A pdb=" N GLN A 186 " --> pdb=" O GLN A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 202 Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'D' and resid 16 through 28 Processing helix chain 'D' and resid 34 through 49 Processing helix chain 'D' and resid 51 through 63 Processing helix chain 'D' and resid 64 through 86 Processing helix chain 'D' and resid 96 through 103 removed outlier: 3.614A pdb=" N ASN D 102 " --> pdb=" O ARG D 98 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN D 103 " --> pdb=" O VAL D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 128 removed outlier: 3.699A pdb=" N PHE D 121 " --> pdb=" O TRP D 117 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA D 123 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) Proline residue: D 125 - end of helix Processing helix chain 'D' and resid 131 through 136 removed outlier: 3.503A pdb=" N ALA D 134 " --> pdb=" O PRO D 131 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE D 136 " --> pdb=" O TRP D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 159 removed outlier: 3.550A pdb=" N ASN D 157 " --> pdb=" O ILE D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 176 removed outlier: 4.592A pdb=" N TYR D 174 " --> pdb=" O ARG D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 194 through 202 Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'E' and resid 16 through 27 Processing helix chain 'E' and resid 34 through 49 Processing helix chain 'E' and resid 51 through 63 Processing helix chain 'E' and resid 64 through 86 Processing helix chain 'E' and resid 91 through 95 removed outlier: 3.563A pdb=" N GLY E 95 " --> pdb=" O PRO E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 101 Processing helix chain 'E' and resid 106 through 123 removed outlier: 3.807A pdb=" N PHE E 121 " --> pdb=" O TRP E 117 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA E 123 " --> pdb=" O ALA E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 128 Processing helix chain 'E' and resid 143 through 159 Processing helix chain 'E' and resid 164 through 176 removed outlier: 4.370A pdb=" N ILE E 168 " --> pdb=" O PRO E 164 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR E 174 " --> pdb=" O ARG E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 189 Processing helix chain 'E' and resid 194 through 202 Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'F' and resid 16 through 28 Processing helix chain 'F' and resid 34 through 49 Processing helix chain 'F' and resid 51 through 63 Processing helix chain 'F' and resid 64 through 86 removed outlier: 3.678A pdb=" N SER F 77 " --> pdb=" O GLN F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 95 Processing helix chain 'F' and resid 96 through 103 removed outlier: 3.607A pdb=" N ASN F 102 " --> pdb=" O ARG F 98 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN F 103 " --> pdb=" O VAL F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 121 removed outlier: 3.701A pdb=" N PHE F 121 " --> pdb=" O TRP F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 127 removed outlier: 3.624A pdb=" N GLY F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 136 removed outlier: 3.538A pdb=" N ILE F 136 " --> pdb=" O TRP F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 159 removed outlier: 3.626A pdb=" N GLU F 149 " --> pdb=" O HIS F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 176 removed outlier: 3.826A pdb=" N ILE F 168 " --> pdb=" O PRO F 164 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR F 174 " --> pdb=" O ARG F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 188 removed outlier: 4.140A pdb=" N GLN F 186 " --> pdb=" O GLN F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 202 Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'G' and resid 16 through 28 Processing helix chain 'G' and resid 34 through 49 Processing helix chain 'G' and resid 51 through 63 Processing helix chain 'G' and resid 64 through 86 Processing helix chain 'G' and resid 96 through 103 removed outlier: 3.614A pdb=" N ASN G 102 " --> pdb=" O ARG G 98 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN G 103 " --> pdb=" O VAL G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 128 removed outlier: 3.699A pdb=" N PHE G 121 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA G 122 " --> pdb=" O LEU G 118 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA G 123 " --> pdb=" O ALA G 119 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU G 124 " --> pdb=" O ALA G 120 " (cutoff:3.500A) Proline residue: G 125 - end of helix Processing helix chain 'G' and resid 131 through 136 removed outlier: 3.503A pdb=" N ALA G 134 " --> pdb=" O PRO G 131 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE G 136 " --> pdb=" O TRP G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 159 removed outlier: 3.550A pdb=" N ASN G 157 " --> pdb=" O ILE G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 176 removed outlier: 4.593A pdb=" N TYR G 174 " --> pdb=" O ARG G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 189 Processing helix chain 'G' and resid 194 through 202 Processing helix chain 'G' and resid 203 through 205 No H-bonds generated for 'chain 'G' and resid 203 through 205' Processing helix chain 'H' and resid 16 through 27 Processing helix chain 'H' and resid 34 through 49 Processing helix chain 'H' and resid 51 through 63 Processing helix chain 'H' and resid 64 through 86 Processing helix chain 'H' and resid 91 through 95 removed outlier: 3.563A pdb=" N GLY H 95 " --> pdb=" O PRO H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 101 Processing helix chain 'H' and resid 106 through 123 removed outlier: 3.807A pdb=" N PHE H 121 " --> pdb=" O TRP H 117 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA H 122 " --> pdb=" O LEU H 118 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA H 123 " --> pdb=" O ALA H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 128 Processing helix chain 'H' and resid 143 through 159 Processing helix chain 'H' and resid 164 through 176 removed outlier: 4.369A pdb=" N ILE H 168 " --> pdb=" O PRO H 164 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR H 174 " --> pdb=" O ARG H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 189 Processing helix chain 'H' and resid 194 through 202 Processing helix chain 'H' and resid 203 through 205 No H-bonds generated for 'chain 'H' and resid 203 through 205' Processing helix chain 'I' and resid 16 through 28 Processing helix chain 'I' and resid 34 through 49 Processing helix chain 'I' and resid 51 through 63 Processing helix chain 'I' and resid 64 through 86 removed outlier: 3.678A pdb=" N SER I 77 " --> pdb=" O GLN I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 95 Processing helix chain 'I' and resid 96 through 103 removed outlier: 3.607A pdb=" N ASN I 102 " --> pdb=" O ARG I 98 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN I 103 " --> pdb=" O VAL I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 121 removed outlier: 3.700A pdb=" N PHE I 121 " --> pdb=" O TRP I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 127 removed outlier: 3.623A pdb=" N GLY I 126 " --> pdb=" O ALA I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 136 removed outlier: 3.538A pdb=" N ILE I 136 " --> pdb=" O TRP I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 159 removed outlier: 3.626A pdb=" N GLU I 149 " --> pdb=" O HIS I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 176 removed outlier: 3.827A pdb=" N ILE I 168 " --> pdb=" O PRO I 164 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR I 174 " --> pdb=" O ARG I 170 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 188 removed outlier: 4.141A pdb=" N GLN I 186 " --> pdb=" O GLN I 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 194 through 202 Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'J' and resid 16 through 28 Processing helix chain 'J' and resid 34 through 49 Processing helix chain 'J' and resid 51 through 63 Processing helix chain 'J' and resid 64 through 86 Processing helix chain 'J' and resid 96 through 103 removed outlier: 3.614A pdb=" N ASN J 102 " --> pdb=" O ARG J 98 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN J 103 " --> pdb=" O VAL J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 128 removed outlier: 3.700A pdb=" N PHE J 121 " --> pdb=" O TRP J 117 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA J 122 " --> pdb=" O LEU J 118 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA J 123 " --> pdb=" O ALA J 119 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU J 124 " --> pdb=" O ALA J 120 " (cutoff:3.500A) Proline residue: J 125 - end of helix Processing helix chain 'J' and resid 131 through 136 removed outlier: 3.503A pdb=" N ALA J 134 " --> pdb=" O PRO J 131 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE J 136 " --> pdb=" O TRP J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 159 removed outlier: 3.550A pdb=" N ASN J 157 " --> pdb=" O ILE J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 176 removed outlier: 4.592A pdb=" N TYR J 174 " --> pdb=" O ARG J 170 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 189 Processing helix chain 'J' and resid 194 through 202 Processing helix chain 'J' and resid 203 through 205 No H-bonds generated for 'chain 'J' and resid 203 through 205' Processing helix chain 'K' and resid 16 through 27 Processing helix chain 'K' and resid 34 through 49 Processing helix chain 'K' and resid 51 through 63 Processing helix chain 'K' and resid 64 through 86 Processing helix chain 'K' and resid 91 through 95 removed outlier: 3.563A pdb=" N GLY K 95 " --> pdb=" O PRO K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 101 Processing helix chain 'K' and resid 106 through 123 removed outlier: 3.808A pdb=" N PHE K 121 " --> pdb=" O TRP K 117 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA K 122 " --> pdb=" O LEU K 118 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA K 123 " --> pdb=" O ALA K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 128 Processing helix chain 'K' and resid 143 through 159 Processing helix chain 'K' and resid 164 through 176 removed outlier: 4.370A pdb=" N ILE K 168 " --> pdb=" O PRO K 164 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR K 174 " --> pdb=" O ARG K 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 189 Processing helix chain 'K' and resid 194 through 202 Processing helix chain 'K' and resid 203 through 205 No H-bonds generated for 'chain 'K' and resid 203 through 205' Processing helix chain 'L' and resid 16 through 28 Processing helix chain 'L' and resid 34 through 49 Processing helix chain 'L' and resid 51 through 63 Processing helix chain 'L' and resid 64 through 86 removed outlier: 3.678A pdb=" N SER L 77 " --> pdb=" O GLN L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 95 Processing helix chain 'L' and resid 96 through 103 removed outlier: 3.607A pdb=" N ASN L 102 " --> pdb=" O ARG L 98 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN L 103 " --> pdb=" O VAL L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 121 removed outlier: 3.700A pdb=" N PHE L 121 " --> pdb=" O TRP L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 127 removed outlier: 3.624A pdb=" N GLY L 126 " --> pdb=" O ALA L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 136 removed outlier: 3.538A pdb=" N ILE L 136 " --> pdb=" O TRP L 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 159 removed outlier: 3.627A pdb=" N GLU L 149 " --> pdb=" O HIS L 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 176 removed outlier: 3.827A pdb=" N ILE L 168 " --> pdb=" O PRO L 164 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR L 174 " --> pdb=" O ARG L 170 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 188 removed outlier: 4.141A pdb=" N GLN L 186 " --> pdb=" O GLN L 182 " (cutoff:3.500A) Processing helix chain 'L' and resid 194 through 202 Processing helix chain 'L' and resid 203 through 205 No H-bonds generated for 'chain 'L' and resid 203 through 205' Processing helix chain 'M' and resid 16 through 28 Processing helix chain 'M' and resid 34 through 49 Processing helix chain 'M' and resid 51 through 63 Processing helix chain 'M' and resid 64 through 86 Processing helix chain 'M' and resid 96 through 103 removed outlier: 3.614A pdb=" N ASN M 102 " --> pdb=" O ARG M 98 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN M 103 " --> pdb=" O VAL M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 128 removed outlier: 3.699A pdb=" N PHE M 121 " --> pdb=" O TRP M 117 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA M 122 " --> pdb=" O LEU M 118 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA M 123 " --> pdb=" O ALA M 119 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'M' and resid 131 through 136 removed outlier: 3.503A pdb=" N ALA M 134 " --> pdb=" O PRO M 131 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE M 136 " --> pdb=" O TRP M 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 159 removed outlier: 3.550A pdb=" N ASN M 157 " --> pdb=" O ILE M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 165 through 176 removed outlier: 4.592A pdb=" N TYR M 174 " --> pdb=" O ARG M 170 " (cutoff:3.500A) Processing helix chain 'M' and resid 178 through 189 Processing helix chain 'M' and resid 194 through 202 Processing helix chain 'M' and resid 203 through 205 No H-bonds generated for 'chain 'M' and resid 203 through 205' Processing helix chain 'N' and resid 16 through 27 Processing helix chain 'N' and resid 34 through 49 Processing helix chain 'N' and resid 51 through 63 Processing helix chain 'N' and resid 64 through 86 Processing helix chain 'N' and resid 91 through 95 removed outlier: 3.563A pdb=" N GLY N 95 " --> pdb=" O PRO N 92 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 101 Processing helix chain 'N' and resid 106 through 123 removed outlier: 3.808A pdb=" N PHE N 121 " --> pdb=" O TRP N 117 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA N 122 " --> pdb=" O LEU N 118 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA N 123 " --> pdb=" O ALA N 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 128 Processing helix chain 'N' and resid 143 through 159 Processing helix chain 'N' and resid 164 through 176 removed outlier: 4.370A pdb=" N ILE N 168 " --> pdb=" O PRO N 164 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR N 174 " --> pdb=" O ARG N 170 " (cutoff:3.500A) Processing helix chain 'N' and resid 178 through 189 Processing helix chain 'N' and resid 194 through 202 Processing helix chain 'N' and resid 203 through 205 No H-bonds generated for 'chain 'N' and resid 203 through 205' Processing helix chain 'O' and resid 16 through 28 Processing helix chain 'O' and resid 34 through 49 Processing helix chain 'O' and resid 51 through 63 Processing helix chain 'O' and resid 64 through 86 removed outlier: 3.679A pdb=" N SER O 77 " --> pdb=" O GLN O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 91 through 95 Processing helix chain 'O' and resid 96 through 103 removed outlier: 3.607A pdb=" N ASN O 102 " --> pdb=" O ARG O 98 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN O 103 " --> pdb=" O VAL O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 121 removed outlier: 3.701A pdb=" N PHE O 121 " --> pdb=" O TRP O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 122 through 127 removed outlier: 3.624A pdb=" N GLY O 126 " --> pdb=" O ALA O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 136 removed outlier: 3.538A pdb=" N ILE O 136 " --> pdb=" O TRP O 133 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 159 removed outlier: 3.626A pdb=" N GLU O 149 " --> pdb=" O HIS O 145 " (cutoff:3.500A) Processing helix chain 'O' and resid 164 through 176 removed outlier: 3.827A pdb=" N ILE O 168 " --> pdb=" O PRO O 164 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR O 174 " --> pdb=" O ARG O 170 " (cutoff:3.500A) Processing helix chain 'O' and resid 180 through 188 removed outlier: 4.140A pdb=" N GLN O 186 " --> pdb=" O GLN O 182 " (cutoff:3.500A) Processing helix chain 'O' and resid 194 through 202 Processing helix chain 'O' and resid 203 through 205 No H-bonds generated for 'chain 'O' and resid 203 through 205' Processing helix chain 'P' and resid 16 through 28 Processing helix chain 'P' and resid 34 through 49 Processing helix chain 'P' and resid 51 through 63 Processing helix chain 'P' and resid 64 through 86 Processing helix chain 'P' and resid 96 through 103 removed outlier: 3.614A pdb=" N ASN P 102 " --> pdb=" O ARG P 98 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN P 103 " --> pdb=" O VAL P 99 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 128 removed outlier: 3.700A pdb=" N PHE P 121 " --> pdb=" O TRP P 117 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA P 122 " --> pdb=" O LEU P 118 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA P 123 " --> pdb=" O ALA P 119 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU P 124 " --> pdb=" O ALA P 120 " (cutoff:3.500A) Proline residue: P 125 - end of helix Processing helix chain 'P' and resid 131 through 136 removed outlier: 3.503A pdb=" N ALA P 134 " --> pdb=" O PRO P 131 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE P 136 " --> pdb=" O TRP P 133 " (cutoff:3.500A) Processing helix chain 'P' and resid 143 through 159 removed outlier: 3.550A pdb=" N ASN P 157 " --> pdb=" O ILE P 153 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 176 removed outlier: 4.592A pdb=" N TYR P 174 " --> pdb=" O ARG P 170 " (cutoff:3.500A) Processing helix chain 'P' and resid 178 through 189 Processing helix chain 'P' and resid 194 through 202 Processing helix chain 'P' and resid 203 through 205 No H-bonds generated for 'chain 'P' and resid 203 through 205' Processing helix chain 'Q' and resid 16 through 27 Processing helix chain 'Q' and resid 34 through 49 Processing helix chain 'Q' and resid 51 through 63 Processing helix chain 'Q' and resid 64 through 86 Processing helix chain 'Q' and resid 91 through 95 removed outlier: 3.563A pdb=" N GLY Q 95 " --> pdb=" O PRO Q 92 " (cutoff:3.500A) Processing helix chain 'Q' and resid 96 through 101 Processing helix chain 'Q' and resid 106 through 123 removed outlier: 3.807A pdb=" N PHE Q 121 " --> pdb=" O TRP Q 117 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA Q 122 " --> pdb=" O LEU Q 118 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA Q 123 " --> pdb=" O ALA Q 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 124 through 128 Processing helix chain 'Q' and resid 143 through 159 Processing helix chain 'Q' and resid 164 through 176 removed outlier: 4.370A pdb=" N ILE Q 168 " --> pdb=" O PRO Q 164 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR Q 174 " --> pdb=" O ARG Q 170 " (cutoff:3.500A) Processing helix chain 'Q' and resid 178 through 189 Processing helix chain 'Q' and resid 194 through 202 Processing helix chain 'Q' and resid 203 through 205 No H-bonds generated for 'chain 'Q' and resid 203 through 205' Processing helix chain 'R' and resid 16 through 28 Processing helix chain 'R' and resid 34 through 49 Processing helix chain 'R' and resid 51 through 63 Processing helix chain 'R' and resid 64 through 86 removed outlier: 3.679A pdb=" N SER R 77 " --> pdb=" O GLN R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 95 Processing helix chain 'R' and resid 96 through 103 removed outlier: 3.607A pdb=" N ASN R 102 " --> pdb=" O ARG R 98 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN R 103 " --> pdb=" O VAL R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 121 removed outlier: 3.700A pdb=" N PHE R 121 " --> pdb=" O TRP R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 122 through 127 removed outlier: 3.624A pdb=" N GLY R 126 " --> pdb=" O ALA R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 136 removed outlier: 3.538A pdb=" N ILE R 136 " --> pdb=" O TRP R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 143 through 159 removed outlier: 3.626A pdb=" N GLU R 149 " --> pdb=" O HIS R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 176 removed outlier: 3.826A pdb=" N ILE R 168 " --> pdb=" O PRO R 164 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR R 174 " --> pdb=" O ARG R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 188 removed outlier: 4.141A pdb=" N GLN R 186 " --> pdb=" O GLN R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 194 through 202 Processing helix chain 'R' and resid 203 through 205 No H-bonds generated for 'chain 'R' and resid 203 through 205' 1722 hydrogen bonds defined for protein. 5022 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: 4.89 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9264 1.34 - 1.46: 4338 1.46 - 1.58: 13968 1.58 - 1.69: 6 1.69 - 1.81: 162 Bond restraints: 27738 Sorted by residual: bond pdb=" CB PRO F 96 " pdb=" CG PRO F 96 " ideal model delta sigma weight residual 1.492 1.593 -0.101 5.00e-02 4.00e+02 4.11e+00 bond pdb=" CB PRO I 96 " pdb=" CG PRO I 96 " ideal model delta sigma weight residual 1.492 1.593 -0.101 5.00e-02 4.00e+02 4.10e+00 bond pdb=" CB PRO R 96 " pdb=" CG PRO R 96 " ideal model delta sigma weight residual 1.492 1.593 -0.101 5.00e-02 4.00e+02 4.10e+00 bond pdb=" CB PRO A 96 " pdb=" CG PRO A 96 " ideal model delta sigma weight residual 1.492 1.593 -0.101 5.00e-02 4.00e+02 4.10e+00 bond pdb=" CB PRO O 96 " pdb=" CG PRO O 96 " ideal model delta sigma weight residual 1.492 1.593 -0.101 5.00e-02 4.00e+02 4.09e+00 ... (remaining 27733 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 36961 1.98 - 3.97: 654 3.97 - 5.95: 113 5.95 - 7.93: 12 7.93 - 9.92: 6 Bond angle restraints: 37746 Sorted by residual: angle pdb=" CA GLN D 107 " pdb=" CB GLN D 107 " pdb=" CG GLN D 107 " ideal model delta sigma weight residual 114.10 120.44 -6.34 2.00e+00 2.50e-01 1.00e+01 angle pdb=" CA GLN P 107 " pdb=" CB GLN P 107 " pdb=" CG GLN P 107 " ideal model delta sigma weight residual 114.10 120.42 -6.32 2.00e+00 2.50e-01 9.98e+00 angle pdb=" CA GLN J 107 " pdb=" CB GLN J 107 " pdb=" CG GLN J 107 " ideal model delta sigma weight residual 114.10 120.42 -6.32 2.00e+00 2.50e-01 9.98e+00 angle pdb=" CA GLN B 107 " pdb=" CB GLN B 107 " pdb=" CG GLN B 107 " ideal model delta sigma weight residual 114.10 120.41 -6.31 2.00e+00 2.50e-01 9.96e+00 angle pdb=" CA GLN M 107 " pdb=" CB GLN M 107 " pdb=" CG GLN M 107 " ideal model delta sigma weight residual 114.10 120.40 -6.30 2.00e+00 2.50e-01 9.91e+00 ... (remaining 37741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 14815 17.91 - 35.83: 1642 35.83 - 53.74: 414 53.74 - 71.66: 79 71.66 - 89.57: 24 Dihedral angle restraints: 16974 sinusoidal: 6876 harmonic: 10098 Sorted by residual: dihedral pdb=" CA TRP P 15 " pdb=" C TRP P 15 " pdb=" N GLN P 16 " pdb=" CA GLN P 16 " ideal model delta harmonic sigma weight residual 180.00 160.78 19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA TRP D 15 " pdb=" C TRP D 15 " pdb=" N GLN D 16 " pdb=" CA GLN D 16 " ideal model delta harmonic sigma weight residual 180.00 160.82 19.18 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA TRP J 15 " pdb=" C TRP J 15 " pdb=" N GLN J 16 " pdb=" CA GLN J 16 " ideal model delta harmonic sigma weight residual 180.00 160.84 19.16 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 16971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3329 0.045 - 0.090: 672 0.090 - 0.135: 110 0.135 - 0.181: 5 0.181 - 0.226: 6 Chirality restraints: 4122 Sorted by residual: chirality pdb=" CG LEU P 169 " pdb=" CB LEU P 169 " pdb=" CD1 LEU P 169 " pdb=" CD2 LEU P 169 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CG LEU G 169 " pdb=" CB LEU G 169 " pdb=" CD1 LEU G 169 " pdb=" CD2 LEU G 169 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CG LEU B 169 " pdb=" CB LEU B 169 " pdb=" CD1 LEU B 169 " pdb=" CD2 LEU B 169 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 4119 not shown) Planarity restraints: 5040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP I 166 " -0.072 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO I 167 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO I 167 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO I 167 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP O 166 " 0.072 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO O 167 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO O 167 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO O 167 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 166 " 0.072 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO A 167 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO A 167 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 167 " 0.059 5.00e-02 4.00e+02 ... (remaining 5037 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 48 2.13 - 2.82: 8139 2.82 - 3.51: 41043 3.51 - 4.21: 62785 4.21 - 4.90: 113473 Nonbonded interactions: 225488 Sorted by model distance: nonbonded pdb=" OH TYR A 174 " pdb=" CE1 TYR D 174 " model vdw 1.437 3.340 nonbonded pdb=" OH TYR L 174 " pdb=" CE1 TYR M 174 " model vdw 1.437 3.340 nonbonded pdb=" OH TYR I 174 " pdb=" CE1 TYR J 174 " model vdw 1.437 3.340 nonbonded pdb=" OH TYR F 174 " pdb=" CE1 TYR G 174 " model vdw 1.437 3.340 nonbonded pdb=" CE1 TYR B 174 " pdb=" OH TYR R 174 " model vdw 1.437 3.340 ... (remaining 225483 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 24.010 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 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 : 0.006 0.331 27744 Z= 0.507 Angle : 0.636 9.917 37746 Z= 0.328 Chirality : 0.036 0.226 4122 Planarity : 0.008 0.108 5040 Dihedral : 16.422 89.569 10422 Min Nonbonded Distance : 1.437 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.14 % Allowed : 17.67 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.15), residues: 3438 helix: 1.44 (0.11), residues: 2448 sheet: None (None), residues: 0 loop : 0.76 (0.22), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 110 TYR 0.010 0.001 TYR K 113 PHE 0.016 0.002 PHE I 37 TRP 0.031 0.003 TRP I 133 HIS 0.005 0.001 HIS G 71 Details of bonding type rmsd covalent geometry : bond 0.00368 (27738) covalent geometry : angle 0.63562 (37746) hydrogen bonds : bond 0.13015 ( 1722) hydrogen bonds : angle 5.41572 ( 5022) Misc. bond : bond 0.33090 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 595 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 175 SER cc_start: 0.7440 (m) cc_final: 0.7142 (t) REVERT: A 17 MET cc_start: 0.7436 (tpp) cc_final: 0.6878 (tpt) REVERT: D 36 GLN cc_start: 0.6790 (tp-100) cc_final: 0.6415 (tp-100) REVERT: D 39 GLN cc_start: 0.8449 (mt0) cc_final: 0.8076 (mt0) REVERT: D 63 CYS cc_start: 0.7910 (m) cc_final: 0.7656 (m) REVERT: E 39 GLN cc_start: 0.8243 (mt0) cc_final: 0.8037 (mt0) REVERT: E 45 VAL cc_start: 0.8034 (t) cc_final: 0.7724 (m) REVERT: E 70 LEU cc_start: 0.7682 (mt) cc_final: 0.7465 (mt) REVERT: E 110 ARG cc_start: 0.8268 (ttp80) cc_final: 0.8029 (ttp80) REVERT: E 115 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7500 (mm110) REVERT: F 17 MET cc_start: 0.7624 (tpp) cc_final: 0.7408 (tpp) REVERT: F 38 MET cc_start: 0.8302 (mmm) cc_final: 0.7932 (mmp) REVERT: F 67 VAL cc_start: 0.8244 (p) cc_final: 0.7876 (t) REVERT: F 105 GLN cc_start: 0.6994 (mp10) cc_final: 0.6491 (mp10) REVERT: F 107 GLN cc_start: 0.7378 (tt0) cc_final: 0.7149 (tt0) REVERT: F 138 GLN cc_start: 0.5440 (tp40) cc_final: 0.5200 (tp-100) REVERT: F 170 ARG cc_start: 0.7368 (mtp180) cc_final: 0.7124 (mtp180) REVERT: G 29 GLN cc_start: 0.6686 (mm-40) cc_final: 0.6369 (mm-40) REVERT: G 46 GLN cc_start: 0.6478 (tp40) cc_final: 0.6177 (tp40) REVERT: H 53 LYS cc_start: 0.7796 (tttt) cc_final: 0.7364 (tttt) REVERT: H 59 LEU cc_start: 0.7889 (tp) cc_final: 0.7445 (tt) REVERT: H 107 GLN cc_start: 0.7614 (tt0) cc_final: 0.7290 (tt0) REVERT: H 110 ARG cc_start: 0.7638 (ttp80) cc_final: 0.7019 (ttp80) REVERT: H 111 ARG cc_start: 0.7298 (mmt-90) cc_final: 0.7016 (tpp80) REVERT: H 121 PHE cc_start: 0.8073 (m-80) cc_final: 0.7614 (m-80) REVERT: I 39 GLN cc_start: 0.8175 (mt0) cc_final: 0.7961 (mt0) REVERT: I 170 ARG cc_start: 0.7365 (mtp180) cc_final: 0.7070 (mtp180) REVERT: K 21 GLN cc_start: 0.7933 (mt0) cc_final: 0.7704 (mt0) REVERT: M 39 GLN cc_start: 0.7860 (mt0) cc_final: 0.7510 (mt0) REVERT: M 107 GLN cc_start: 0.7668 (tp-100) cc_final: 0.7260 (tp-100) REVERT: M 114 GLN cc_start: 0.7876 (mt0) cc_final: 0.7309 (mt0) REVERT: N 39 GLN cc_start: 0.8031 (mt0) cc_final: 0.7786 (mt0) REVERT: N 53 LYS cc_start: 0.7910 (tttt) cc_final: 0.7441 (tttt) REVERT: N 70 LEU cc_start: 0.7730 (mt) cc_final: 0.7442 (mp) REVERT: N 110 ARG cc_start: 0.8021 (ttp80) cc_final: 0.7205 (ttp80) REVERT: N 186 GLN cc_start: 0.6652 (mt0) cc_final: 0.6444 (mt0) REVERT: O 38 MET cc_start: 0.8345 (mmm) cc_final: 0.7939 (mmp) REVERT: O 46 GLN cc_start: 0.6996 (mt0) cc_final: 0.6776 (mt0) REVERT: O 67 VAL cc_start: 0.8068 (p) cc_final: 0.7625 (t) REVERT: O 169 LEU cc_start: 0.7984 (tp) cc_final: 0.7784 (tp) REVERT: O 170 ARG cc_start: 0.7068 (mtp180) cc_final: 0.6809 (mtp180) REVERT: P 39 GLN cc_start: 0.8036 (mt0) cc_final: 0.7784 (mt0) REVERT: P 70 LEU cc_start: 0.7914 (mm) cc_final: 0.7545 (mp) REVERT: P 111 ARG cc_start: 0.7375 (tpp-160) cc_final: 0.7043 (mmt-90) REVERT: Q 110 ARG cc_start: 0.8266 (ttp80) cc_final: 0.7100 (ttp80) REVERT: R 39 GLN cc_start: 0.8310 (mt0) cc_final: 0.8055 (mt0) REVERT: R 48 PHE cc_start: 0.7860 (m-80) cc_final: 0.7615 (m-80) REVERT: R 53 LYS cc_start: 0.8043 (tttt) cc_final: 0.7725 (ttmm) REVERT: R 78 LEU cc_start: 0.7797 (mp) cc_final: 0.7567 (mm) REVERT: R 133 TRP cc_start: 0.7984 (p-90) cc_final: 0.7091 (p-90) outliers start: 4 outliers final: 0 residues processed: 596 average time/residue: 0.1673 time to fit residues: 156.7727 Evaluate side-chains 570 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 570 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.0670 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 0.9980 overall best weight: 1.1720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN C 29 GLN C 157 ASN A 36 GLN A 39 GLN ** A 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 GLN D 107 GLN D 114 GLN E 29 GLN E 56 GLN E 157 ASN F 36 GLN F 71 HIS F 107 GLN G 56 GLN G 107 GLN G 114 GLN H 29 GLN H 157 ASN I 36 GLN I 39 GLN I 46 GLN I 107 GLN J 36 GLN J 107 GLN K 29 GLN K 157 ASN L 36 GLN L 39 GLN ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 107 GLN M 46 GLN M 60 GLN M 107 GLN N 29 GLN N 56 GLN N 157 ASN O 36 GLN ** O 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 107 GLN P 114 GLN Q 29 GLN Q 115 GLN Q 157 ASN R 36 GLN R 39 GLN R 107 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.189665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.161364 restraints weight = 31989.045| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.58 r_work: 0.3709 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27744 Z= 0.171 Angle : 0.635 8.310 37746 Z= 0.309 Chirality : 0.038 0.217 4122 Planarity : 0.006 0.073 5040 Dihedral : 4.113 19.739 3708 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.28 % Allowed : 16.39 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.15), residues: 3438 helix: 1.56 (0.11), residues: 2466 sheet: None (None), residues: 0 loop : 0.61 (0.23), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 110 TYR 0.030 0.003 TYR Q 61 PHE 0.015 0.002 PHE I 37 TRP 0.028 0.002 TRP B 15 HIS 0.007 0.001 HIS O 72 Details of bonding type rmsd covalent geometry : bond 0.00395 (27738) covalent geometry : angle 0.63527 (37746) hydrogen bonds : bond 0.04023 ( 1722) hydrogen bonds : angle 4.43090 ( 5022) Misc. bond : bond 0.00321 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 590 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LYS cc_start: 0.7960 (tttp) cc_final: 0.7759 (tttp) REVERT: B 74 GLN cc_start: 0.8129 (tp40) cc_final: 0.7874 (mm-40) REVERT: B 107 GLN cc_start: 0.7977 (tp-100) cc_final: 0.7191 (tp-100) REVERT: B 114 GLN cc_start: 0.8425 (mt0) cc_final: 0.8149 (mt0) REVERT: B 174 TYR cc_start: 0.8096 (t80) cc_final: 0.7866 (t80) REVERT: C 36 GLN cc_start: 0.6494 (tp-100) cc_final: 0.6129 (tp-100) REVERT: C 175 SER cc_start: 0.7506 (m) cc_final: 0.7170 (t) REVERT: A 17 MET cc_start: 0.7293 (tpp) cc_final: 0.7046 (tpt) REVERT: A 61 TYR cc_start: 0.8223 (t80) cc_final: 0.7849 (t80) REVERT: A 174 TYR cc_start: 0.7419 (t80) cc_final: 0.7004 (t80) REVERT: D 36 GLN cc_start: 0.6441 (tp-100) cc_final: 0.5980 (tp-100) REVERT: D 63 CYS cc_start: 0.7833 (m) cc_final: 0.7621 (m) REVERT: E 39 GLN cc_start: 0.8368 (mt0) cc_final: 0.8043 (mt0) REVERT: E 67 VAL cc_start: 0.8300 (OUTLIER) cc_final: 0.7915 (t) REVERT: E 110 ARG cc_start: 0.8316 (ttp80) cc_final: 0.8008 (ttp80) REVERT: F 36 GLN cc_start: 0.7198 (tp-100) cc_final: 0.6916 (tp-100) REVERT: F 39 GLN cc_start: 0.8035 (mt0) cc_final: 0.7818 (mt0) REVERT: F 67 VAL cc_start: 0.8280 (p) cc_final: 0.7907 (t) REVERT: F 107 GLN cc_start: 0.7878 (tt0) cc_final: 0.7629 (tt0) REVERT: F 170 ARG cc_start: 0.8175 (mtp180) cc_final: 0.7954 (mtp180) REVERT: G 42 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.7096 (mtm-85) REVERT: H 53 LYS cc_start: 0.7901 (tttt) cc_final: 0.7617 (tttt) REVERT: H 110 ARG cc_start: 0.7806 (ttp80) cc_final: 0.7211 (ttp80) REVERT: H 111 ARG cc_start: 0.7550 (mmt-90) cc_final: 0.7138 (tpp80) REVERT: H 121 PHE cc_start: 0.8319 (m-80) cc_final: 0.8024 (m-80) REVERT: H 198 MET cc_start: 0.6463 (mmt) cc_final: 0.5961 (mmt) REVERT: I 36 GLN cc_start: 0.6843 (tp-100) cc_final: 0.6354 (tp-100) REVERT: I 39 GLN cc_start: 0.8217 (mt0) cc_final: 0.7933 (mt0) REVERT: I 43 LEU cc_start: 0.7924 (tp) cc_final: 0.7533 (tp) REVERT: I 170 ARG cc_start: 0.8015 (mtp180) cc_final: 0.7580 (mtp180) REVERT: I 174 TYR cc_start: 0.7344 (t80) cc_final: 0.6776 (t80) REVERT: J 174 TYR cc_start: 0.7928 (t80) cc_final: 0.7342 (t80) REVERT: K 61 TYR cc_start: 0.8014 (t80) cc_final: 0.7702 (t80) REVERT: K 107 GLN cc_start: 0.7953 (tt0) cc_final: 0.7593 (tt0) REVERT: K 121 PHE cc_start: 0.8243 (m-80) cc_final: 0.7835 (m-80) REVERT: K 175 SER cc_start: 0.7500 (m) cc_final: 0.7154 (t) REVERT: L 17 MET cc_start: 0.7443 (tpp) cc_final: 0.7170 (tpt) REVERT: L 61 TYR cc_start: 0.8039 (t80) cc_final: 0.7707 (t80) REVERT: L 174 TYR cc_start: 0.7588 (t80) cc_final: 0.6768 (t80) REVERT: M 39 GLN cc_start: 0.7923 (mt0) cc_final: 0.7521 (mt0) REVERT: M 56 GLN cc_start: 0.8257 (tp40) cc_final: 0.7897 (tp40) REVERT: M 110 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7788 (ttp80) REVERT: M 114 GLN cc_start: 0.7964 (mt0) cc_final: 0.7676 (mt0) REVERT: M 174 TYR cc_start: 0.7933 (t80) cc_final: 0.7369 (t80) REVERT: N 39 GLN cc_start: 0.8100 (mt0) cc_final: 0.7811 (mt0) REVERT: N 53 LYS cc_start: 0.8052 (tttt) cc_final: 0.7707 (tttt) REVERT: N 67 VAL cc_start: 0.8160 (OUTLIER) cc_final: 0.7756 (t) REVERT: N 75 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7379 (tt) REVERT: N 80 SER cc_start: 0.7172 (m) cc_final: 0.6706 (p) REVERT: N 110 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7357 (ttp80) REVERT: N 186 GLN cc_start: 0.6766 (mt0) cc_final: 0.6487 (mt0) REVERT: O 36 GLN cc_start: 0.7167 (tp-100) cc_final: 0.6902 (tp-100) REVERT: O 67 VAL cc_start: 0.7988 (p) cc_final: 0.7534 (t) REVERT: O 105 GLN cc_start: 0.7277 (mp10) cc_final: 0.6907 (mp10) REVERT: P 26 GLU cc_start: 0.7038 (tp30) cc_final: 0.6709 (tp30) REVERT: P 70 LEU cc_start: 0.7886 (mm) cc_final: 0.7559 (mp) REVERT: P 111 ARG cc_start: 0.7662 (tpp-160) cc_final: 0.7237 (mmt-90) REVERT: Q 61 TYR cc_start: 0.7947 (t80) cc_final: 0.7627 (t80) REVERT: Q 80 SER cc_start: 0.7886 (m) cc_final: 0.7386 (p) REVERT: Q 110 ARG cc_start: 0.8285 (ttp80) cc_final: 0.7364 (ttp80) REVERT: R 36 GLN cc_start: 0.6883 (tp-100) cc_final: 0.6489 (tp-100) REVERT: R 43 LEU cc_start: 0.8164 (tp) cc_final: 0.7741 (tp) outliers start: 66 outliers final: 34 residues processed: 632 average time/residue: 0.1628 time to fit residues: 162.4552 Evaluate side-chains 616 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 578 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 15 TRP Chi-restraints excluded: chain E residue 63 CYS Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain H residue 15 TRP Chi-restraints excluded: chain H residue 29 GLN Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 36 GLN Chi-restraints excluded: chain K residue 15 TRP Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain N residue 15 TRP Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain Q residue 15 TRP Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain Q residue 105 GLN Chi-restraints excluded: chain Q residue 206 THR Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 70 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 186 optimal weight: 0.8980 chunk 276 optimal weight: 0.6980 chunk 318 optimal weight: 9.9990 chunk 289 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 45 optimal weight: 0.0770 chunk 12 optimal weight: 10.0000 chunk 249 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN A 36 GLN A 46 GLN A 71 HIS D 60 GLN F 21 GLN G 56 GLN G 114 GLN I 56 GLN J 36 GLN J 60 GLN K 56 GLN L 46 GLN ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 60 GLN M 74 GLN O 71 HIS P 60 GLN Q 115 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.194475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.165094 restraints weight = 31577.283| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.58 r_work: 0.3708 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27744 Z= 0.121 Angle : 0.581 6.639 37746 Z= 0.281 Chirality : 0.036 0.174 4122 Planarity : 0.006 0.074 5040 Dihedral : 3.976 17.897 3708 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.45 % Allowed : 16.98 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.15), residues: 3438 helix: 1.78 (0.11), residues: 2448 sheet: None (None), residues: 0 loop : 0.61 (0.22), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 111 TYR 0.022 0.001 TYR Q 61 PHE 0.013 0.002 PHE I 37 TRP 0.026 0.002 TRP B 15 HIS 0.004 0.001 HIS F 71 Details of bonding type rmsd covalent geometry : bond 0.00285 (27738) covalent geometry : angle 0.58109 (37746) hydrogen bonds : bond 0.03563 ( 1722) hydrogen bonds : angle 4.26291 ( 5022) Misc. bond : bond 0.00051 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 596 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 GLN cc_start: 0.8129 (tp40) cc_final: 0.7831 (mm-40) REVERT: B 91 ASN cc_start: 0.8374 (p0) cc_final: 0.8054 (p0) REVERT: B 107 GLN cc_start: 0.8089 (tp-100) cc_final: 0.7453 (tp-100) REVERT: B 114 GLN cc_start: 0.8403 (mt0) cc_final: 0.8147 (mt0) REVERT: B 174 TYR cc_start: 0.8155 (t80) cc_final: 0.7832 (t80) REVERT: C 36 GLN cc_start: 0.6545 (tp-100) cc_final: 0.6175 (tp-100) REVERT: C 175 SER cc_start: 0.7561 (m) cc_final: 0.7213 (t) REVERT: A 61 TYR cc_start: 0.8048 (t80) cc_final: 0.7703 (t80) REVERT: A 174 TYR cc_start: 0.7468 (t80) cc_final: 0.6986 (t80) REVERT: D 36 GLN cc_start: 0.6190 (tp-100) cc_final: 0.5657 (tp-100) REVERT: D 63 CYS cc_start: 0.7833 (m) cc_final: 0.7626 (m) REVERT: D 107 GLN cc_start: 0.7778 (tp40) cc_final: 0.7376 (tp40) REVERT: E 39 GLN cc_start: 0.8410 (mt0) cc_final: 0.8084 (mt0) REVERT: E 67 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.7915 (t) REVERT: E 110 ARG cc_start: 0.8254 (ttp80) cc_final: 0.7602 (ttp80) REVERT: F 36 GLN cc_start: 0.7180 (tp-100) cc_final: 0.6938 (tp-100) REVERT: F 67 VAL cc_start: 0.8210 (p) cc_final: 0.7846 (t) REVERT: F 107 GLN cc_start: 0.7777 (tt0) cc_final: 0.7530 (tt0) REVERT: G 42 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7202 (mtm-85) REVERT: H 110 ARG cc_start: 0.7871 (ttp80) cc_final: 0.7244 (ttp80) REVERT: H 111 ARG cc_start: 0.7632 (mmt-90) cc_final: 0.7223 (tpp80) REVERT: H 198 MET cc_start: 0.6331 (mmt) cc_final: 0.5881 (mmt) REVERT: I 36 GLN cc_start: 0.6800 (tp-100) cc_final: 0.6251 (tp-100) REVERT: I 43 LEU cc_start: 0.7936 (tp) cc_final: 0.7523 (tp) REVERT: I 167 PRO cc_start: 0.7336 (Cg_exo) cc_final: 0.6949 (Cg_endo) REVERT: I 170 ARG cc_start: 0.7872 (mtp180) cc_final: 0.7523 (mtp180) REVERT: J 110 ARG cc_start: 0.8127 (ttp80) cc_final: 0.7772 (ttp80) REVERT: J 174 TYR cc_start: 0.7954 (t80) cc_final: 0.7669 (t80) REVERT: K 53 LYS cc_start: 0.8169 (tttt) cc_final: 0.7855 (tttt) REVERT: K 54 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7312 (t0) REVERT: K 56 GLN cc_start: 0.7379 (tp-100) cc_final: 0.7059 (tp-100) REVERT: K 60 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7422 (mm-40) REVERT: K 61 TYR cc_start: 0.7990 (t80) cc_final: 0.7652 (t80) REVERT: K 80 SER cc_start: 0.7084 (m) cc_final: 0.6469 (p) REVERT: K 111 ARG cc_start: 0.8029 (tpp80) cc_final: 0.7654 (tpp80) REVERT: K 121 PHE cc_start: 0.8312 (m-80) cc_final: 0.7970 (m-80) REVERT: K 175 SER cc_start: 0.7536 (m) cc_final: 0.7175 (t) REVERT: L 61 TYR cc_start: 0.8038 (t80) cc_final: 0.7579 (t80) REVERT: L 167 PRO cc_start: 0.7786 (Cg_exo) cc_final: 0.7398 (Cg_endo) REVERT: L 174 TYR cc_start: 0.7602 (t80) cc_final: 0.6782 (t80) REVERT: M 17 MET cc_start: 0.7986 (tpp) cc_final: 0.7725 (tpp) REVERT: M 39 GLN cc_start: 0.7944 (mt0) cc_final: 0.7553 (mt0) REVERT: M 106 GLN cc_start: 0.7235 (mm-40) cc_final: 0.6828 (mm-40) REVERT: M 114 GLN cc_start: 0.7944 (mt0) cc_final: 0.7662 (mt0) REVERT: M 174 TYR cc_start: 0.7993 (t80) cc_final: 0.7405 (t80) REVERT: N 39 GLN cc_start: 0.8126 (mt0) cc_final: 0.7821 (mt0) REVERT: N 60 GLN cc_start: 0.8018 (mm-40) cc_final: 0.7787 (mm-40) REVERT: N 67 VAL cc_start: 0.8216 (OUTLIER) cc_final: 0.7787 (t) REVERT: N 70 LEU cc_start: 0.7740 (mt) cc_final: 0.7524 (mp) REVERT: N 75 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7517 (tt) REVERT: N 80 SER cc_start: 0.7193 (m) cc_final: 0.6705 (p) REVERT: N 110 ARG cc_start: 0.8089 (ttp80) cc_final: 0.7275 (ttp80) REVERT: O 15 TRP cc_start: 0.7683 (OUTLIER) cc_final: 0.7329 (m100) REVERT: O 36 GLN cc_start: 0.7120 (tp-100) cc_final: 0.6902 (tp-100) REVERT: O 67 VAL cc_start: 0.7928 (p) cc_final: 0.7439 (t) REVERT: O 105 GLN cc_start: 0.7220 (mp10) cc_final: 0.6841 (mp10) REVERT: O 138 GLN cc_start: 0.5148 (tt0) cc_final: 0.4786 (tm-30) REVERT: P 26 GLU cc_start: 0.6989 (tp30) cc_final: 0.6708 (tp30) REVERT: P 70 LEU cc_start: 0.7943 (mm) cc_final: 0.7574 (mp) REVERT: Q 80 SER cc_start: 0.7942 (m) cc_final: 0.7408 (p) REVERT: Q 110 ARG cc_start: 0.8239 (ttp80) cc_final: 0.7326 (ttp80) REVERT: R 36 GLN cc_start: 0.6960 (tp-100) cc_final: 0.6508 (tp-100) REVERT: R 43 LEU cc_start: 0.8164 (tp) cc_final: 0.7689 (tp) REVERT: R 170 ARG cc_start: 0.7929 (mtp180) cc_final: 0.7292 (mtp180) outliers start: 71 outliers final: 35 residues processed: 646 average time/residue: 0.1723 time to fit residues: 177.6794 Evaluate side-chains 621 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 580 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 TRP Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain C residue 15 TRP Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain A residue 15 TRP Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain E residue 15 TRP Chi-restraints excluded: chain E residue 63 CYS Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain F residue 15 TRP Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 15 TRP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain I residue 15 TRP Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 36 GLN Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 169 LEU Chi-restraints excluded: chain N residue 15 TRP Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain O residue 15 TRP Chi-restraints excluded: chain O residue 25 GLN Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain Q residue 105 GLN Chi-restraints excluded: chain Q residue 206 THR Chi-restraints excluded: chain R residue 15 TRP Chi-restraints excluded: chain R residue 70 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 181 optimal weight: 0.7980 chunk 184 optimal weight: 3.9990 chunk 238 optimal weight: 0.9980 chunk 246 optimal weight: 9.9990 chunk 255 optimal weight: 0.6980 chunk 264 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 282 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 292 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN C 29 GLN C 115 GLN E 29 GLN F 21 GLN G 56 GLN G 114 GLN H 29 GLN I 36 GLN K 29 GLN K 115 GLN ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 29 GLN O 56 GLN Q 115 GLN R 36 GLN R 56 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.191550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.163684 restraints weight = 32088.223| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 1.58 r_work: 0.3704 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27744 Z= 0.149 Angle : 0.579 5.892 37746 Z= 0.279 Chirality : 0.037 0.151 4122 Planarity : 0.006 0.071 5040 Dihedral : 3.901 18.728 3708 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.52 % Allowed : 17.29 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.15), residues: 3438 helix: 1.75 (0.11), residues: 2448 sheet: None (None), residues: 0 loop : 0.71 (0.22), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 111 TYR 0.013 0.001 TYR Q 61 PHE 0.016 0.002 PHE I 37 TRP 0.025 0.002 TRP B 15 HIS 0.007 0.001 HIS O 72 Details of bonding type rmsd covalent geometry : bond 0.00357 (27738) covalent geometry : angle 0.57927 (37746) hydrogen bonds : bond 0.03519 ( 1722) hydrogen bonds : angle 4.17198 ( 5022) Misc. bond : bond 0.00032 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 598 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 ASN cc_start: 0.8429 (p0) cc_final: 0.8051 (p0) REVERT: B 174 TYR cc_start: 0.8157 (t80) cc_final: 0.7831 (t80) REVERT: C 36 GLN cc_start: 0.6518 (tp-100) cc_final: 0.6156 (tp-100) REVERT: C 175 SER cc_start: 0.7527 (m) cc_final: 0.7189 (t) REVERT: A 61 TYR cc_start: 0.8041 (t80) cc_final: 0.7694 (t80) REVERT: A 174 TYR cc_start: 0.7486 (t80) cc_final: 0.7042 (t80) REVERT: D 36 GLN cc_start: 0.6284 (tp-100) cc_final: 0.5681 (tp-100) REVERT: D 150 ARG cc_start: 0.7845 (mtt-85) cc_final: 0.7628 (mtt-85) REVERT: D 159 LEU cc_start: 0.7224 (mt) cc_final: 0.7006 (mt) REVERT: E 39 GLN cc_start: 0.8515 (mt0) cc_final: 0.8220 (mt0) REVERT: E 67 VAL cc_start: 0.8334 (OUTLIER) cc_final: 0.7977 (t) REVERT: E 110 ARG cc_start: 0.8322 (ttp80) cc_final: 0.7914 (ttp80) REVERT: E 198 MET cc_start: 0.5718 (mmt) cc_final: 0.5455 (mmt) REVERT: F 36 GLN cc_start: 0.7294 (tp-100) cc_final: 0.6908 (tp-100) REVERT: F 39 GLN cc_start: 0.8055 (mt0) cc_final: 0.7658 (mt0) REVERT: F 67 VAL cc_start: 0.8231 (p) cc_final: 0.7877 (t) REVERT: F 107 GLN cc_start: 0.7770 (tt0) cc_final: 0.7527 (tt0) REVERT: G 36 GLN cc_start: 0.6184 (tp-100) cc_final: 0.5926 (tp-100) REVERT: G 42 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7339 (mtm-85) REVERT: H 34 SER cc_start: 0.8009 (t) cc_final: 0.7770 (t) REVERT: H 64 SER cc_start: 0.8273 (p) cc_final: 0.8040 (p) REVERT: H 77 SER cc_start: 0.8226 (t) cc_final: 0.7456 (m) REVERT: H 80 SER cc_start: 0.7997 (m) cc_final: 0.7465 (p) REVERT: H 110 ARG cc_start: 0.7924 (ttp80) cc_final: 0.7118 (ttp80) REVERT: H 175 SER cc_start: 0.7366 (m) cc_final: 0.6974 (t) REVERT: H 193 SER cc_start: 0.6603 (t) cc_final: 0.5652 (m) REVERT: H 198 MET cc_start: 0.6502 (mmt) cc_final: 0.5892 (mmt) REVERT: I 36 GLN cc_start: 0.6882 (tp40) cc_final: 0.6501 (tp40) REVERT: I 43 LEU cc_start: 0.7827 (tp) cc_final: 0.7569 (tp) REVERT: I 170 ARG cc_start: 0.7967 (mtp180) cc_final: 0.7559 (mtp180) REVERT: I 174 TYR cc_start: 0.7345 (t80) cc_final: 0.6645 (t80) REVERT: J 56 GLN cc_start: 0.8007 (tp-100) cc_final: 0.7207 (tp-100) REVERT: J 174 TYR cc_start: 0.7964 (t80) cc_final: 0.7272 (t80) REVERT: K 54 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7179 (t0) REVERT: K 56 GLN cc_start: 0.7304 (tp-100) cc_final: 0.6876 (tp-100) REVERT: K 75 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7783 (tt) REVERT: K 77 SER cc_start: 0.8203 (t) cc_final: 0.7388 (m) REVERT: K 80 SER cc_start: 0.7244 (m) cc_final: 0.6546 (p) REVERT: K 111 ARG cc_start: 0.7910 (tpp80) cc_final: 0.7532 (tpp80) REVERT: K 175 SER cc_start: 0.7513 (m) cc_final: 0.7137 (t) REVERT: L 61 TYR cc_start: 0.7989 (t80) cc_final: 0.7580 (t80) REVERT: L 115 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7983 (mm-40) REVERT: L 138 GLN cc_start: 0.5932 (tt0) cc_final: 0.5346 (tm-30) REVERT: L 167 PRO cc_start: 0.7845 (Cg_exo) cc_final: 0.7498 (Cg_endo) REVERT: L 174 TYR cc_start: 0.7710 (t80) cc_final: 0.6747 (t80) REVERT: M 39 GLN cc_start: 0.8134 (mt0) cc_final: 0.7722 (mt0) REVERT: M 78 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8106 (mt) REVERT: M 105 GLN cc_start: 0.7652 (mm-40) cc_final: 0.6960 (mm-40) REVERT: M 106 GLN cc_start: 0.7285 (mm-40) cc_final: 0.6904 (mm-40) REVERT: M 174 TYR cc_start: 0.7966 (t80) cc_final: 0.7352 (t80) REVERT: N 39 GLN cc_start: 0.8287 (mt0) cc_final: 0.7900 (mt0) REVERT: N 61 TYR cc_start: 0.8127 (t80) cc_final: 0.7888 (t80) REVERT: N 67 VAL cc_start: 0.8231 (OUTLIER) cc_final: 0.7853 (t) REVERT: N 70 LEU cc_start: 0.7781 (mt) cc_final: 0.7560 (mp) REVERT: N 75 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7544 (tt) REVERT: N 110 ARG cc_start: 0.8173 (ttp80) cc_final: 0.7117 (ttp80) REVERT: O 36 GLN cc_start: 0.7186 (tp-100) cc_final: 0.6889 (tp-100) REVERT: O 67 VAL cc_start: 0.8014 (p) cc_final: 0.7614 (t) REVERT: O 105 GLN cc_start: 0.7243 (mp10) cc_final: 0.6868 (mp10) REVERT: O 138 GLN cc_start: 0.5189 (tt0) cc_final: 0.4810 (tt0) REVERT: P 15 TRP cc_start: 0.7760 (OUTLIER) cc_final: 0.7483 (m100) REVERT: P 26 GLU cc_start: 0.7170 (tp30) cc_final: 0.6843 (tp30) REVERT: P 111 ARG cc_start: 0.7703 (tpp80) cc_final: 0.7009 (mmt-90) REVERT: Q 80 SER cc_start: 0.8078 (m) cc_final: 0.7523 (p) REVERT: Q 110 ARG cc_start: 0.8243 (ttp80) cc_final: 0.7308 (ttp80) REVERT: R 36 GLN cc_start: 0.6872 (tp40) cc_final: 0.6491 (tp40) REVERT: R 43 LEU cc_start: 0.8045 (tp) cc_final: 0.7736 (tp) outliers start: 73 outliers final: 46 residues processed: 645 average time/residue: 0.1794 time to fit residues: 183.7029 Evaluate side-chains 642 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 588 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 TRP Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain C residue 15 TRP Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain A residue 15 TRP Chi-restraints excluded: chain D residue 15 TRP Chi-restraints excluded: chain E residue 15 TRP Chi-restraints excluded: chain E residue 63 CYS Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain F residue 15 TRP Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain G residue 15 TRP Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 15 TRP Chi-restraints excluded: chain H residue 29 GLN Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain I residue 15 TRP Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain J residue 15 TRP Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 36 GLN Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain L residue 15 TRP Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain N residue 15 TRP Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 193 SER Chi-restraints excluded: chain O residue 25 GLN Chi-restraints excluded: chain P residue 15 TRP Chi-restraints excluded: chain Q residue 15 TRP Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain Q residue 105 GLN Chi-restraints excluded: chain R residue 15 TRP Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 151 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 234 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 104 optimal weight: 0.0980 chunk 251 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 318 optimal weight: 0.0870 chunk 126 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 55 optimal weight: 0.2980 chunk 30 optimal weight: 0.0670 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN B 107 GLN B 114 GLN A 39 GLN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN G 114 GLN J 36 GLN K 115 GLN L 21 GLN O 36 GLN ** O 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 115 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.186569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.159918 restraints weight = 32496.181| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.52 r_work: 0.3711 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 27744 Z= 0.103 Angle : 0.551 7.564 37746 Z= 0.264 Chirality : 0.035 0.177 4122 Planarity : 0.005 0.066 5040 Dihedral : 3.794 17.601 3708 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.83 % Allowed : 17.05 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.15), residues: 3438 helix: 1.95 (0.11), residues: 2430 sheet: None (None), residues: 0 loop : 0.59 (0.22), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 111 TYR 0.011 0.001 TYR M 113 PHE 0.013 0.001 PHE I 37 TRP 0.024 0.002 TRP B 15 HIS 0.004 0.001 HIS D 71 Details of bonding type rmsd covalent geometry : bond 0.00241 (27738) covalent geometry : angle 0.55128 (37746) hydrogen bonds : bond 0.03217 ( 1722) hydrogen bonds : angle 4.07095 ( 5022) Misc. bond : bond 0.00042 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 587 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 ASN cc_start: 0.8412 (p0) cc_final: 0.7997 (p0) REVERT: B 107 GLN cc_start: 0.8000 (tp40) cc_final: 0.7071 (tp40) REVERT: B 111 ARG cc_start: 0.7765 (tpp-160) cc_final: 0.7470 (tpp-160) REVERT: B 174 TYR cc_start: 0.8102 (t80) cc_final: 0.7783 (t80) REVERT: C 17 MET cc_start: 0.7392 (tpt) cc_final: 0.6788 (tpt) REVERT: C 36 GLN cc_start: 0.6454 (tp-100) cc_final: 0.6106 (tp-100) REVERT: C 175 SER cc_start: 0.7496 (m) cc_final: 0.7142 (t) REVERT: A 61 TYR cc_start: 0.7972 (t80) cc_final: 0.7602 (t80) REVERT: A 174 TYR cc_start: 0.7480 (t80) cc_final: 0.7154 (t80) REVERT: D 150 ARG cc_start: 0.7760 (mtt-85) cc_final: 0.7547 (mtt-85) REVERT: D 159 LEU cc_start: 0.7203 (mt) cc_final: 0.6967 (mt) REVERT: E 39 GLN cc_start: 0.8458 (mt0) cc_final: 0.8142 (mt0) REVERT: E 67 VAL cc_start: 0.8299 (OUTLIER) cc_final: 0.7917 (t) REVERT: E 110 ARG cc_start: 0.8240 (ttp80) cc_final: 0.7870 (ttp80) REVERT: E 198 MET cc_start: 0.5752 (mmt) cc_final: 0.5489 (mmt) REVERT: F 36 GLN cc_start: 0.7314 (tp-100) cc_final: 0.6866 (tp-100) REVERT: F 39 GLN cc_start: 0.8073 (mt0) cc_final: 0.7699 (mt0) REVERT: F 67 VAL cc_start: 0.8083 (p) cc_final: 0.7701 (t) REVERT: F 107 GLN cc_start: 0.7801 (tt0) cc_final: 0.7561 (tt0) REVERT: F 151 LEU cc_start: 0.7462 (tp) cc_final: 0.7121 (tp) REVERT: H 34 SER cc_start: 0.7959 (t) cc_final: 0.7656 (t) REVERT: H 60 GLN cc_start: 0.8058 (mt0) cc_final: 0.7810 (mt0) REVERT: H 64 SER cc_start: 0.8156 (p) cc_final: 0.7922 (p) REVERT: H 77 SER cc_start: 0.8112 (t) cc_final: 0.7341 (m) REVERT: H 80 SER cc_start: 0.8005 (m) cc_final: 0.7459 (p) REVERT: H 110 ARG cc_start: 0.7871 (ttp80) cc_final: 0.7201 (ttp80) REVERT: H 175 SER cc_start: 0.7318 (m) cc_final: 0.6957 (t) REVERT: H 193 SER cc_start: 0.6659 (OUTLIER) cc_final: 0.5629 (m) REVERT: H 198 MET cc_start: 0.6526 (mmt) cc_final: 0.5879 (mmt) REVERT: I 36 GLN cc_start: 0.6898 (tp40) cc_final: 0.6434 (tp40) REVERT: I 43 LEU cc_start: 0.7884 (tp) cc_final: 0.7535 (tp) REVERT: I 170 ARG cc_start: 0.7883 (mtp180) cc_final: 0.7457 (mtp180) REVERT: I 174 TYR cc_start: 0.7438 (t80) cc_final: 0.6701 (t80) REVERT: J 56 GLN cc_start: 0.8068 (tp-100) cc_final: 0.7218 (tp-100) REVERT: J 110 ARG cc_start: 0.8117 (ttp80) cc_final: 0.7611 (ttp80) REVERT: J 174 TYR cc_start: 0.7931 (t80) cc_final: 0.7212 (t80) REVERT: K 54 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7159 (t0) REVERT: K 56 GLN cc_start: 0.7230 (tp-100) cc_final: 0.6820 (tp-100) REVERT: K 77 SER cc_start: 0.8171 (t) cc_final: 0.7500 (m) REVERT: K 110 ARG cc_start: 0.8140 (ttp80) cc_final: 0.7751 (ttp80) REVERT: K 111 ARG cc_start: 0.7825 (tpp80) cc_final: 0.7445 (tpp80) REVERT: K 175 SER cc_start: 0.7476 (m) cc_final: 0.7080 (t) REVERT: L 61 TYR cc_start: 0.7901 (t80) cc_final: 0.7550 (t80) REVERT: L 105 GLN cc_start: 0.7041 (mp10) cc_final: 0.6626 (mp10) REVERT: L 138 GLN cc_start: 0.5542 (tt0) cc_final: 0.5292 (pt0) REVERT: L 174 TYR cc_start: 0.7534 (t80) cc_final: 0.6595 (t80) REVERT: M 39 GLN cc_start: 0.8072 (mt0) cc_final: 0.7664 (mt0) REVERT: M 78 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8122 (mt) REVERT: M 105 GLN cc_start: 0.7584 (mm-40) cc_final: 0.7038 (mm-40) REVERT: M 106 GLN cc_start: 0.7205 (mm-40) cc_final: 0.6878 (mm-40) REVERT: M 174 TYR cc_start: 0.7915 (t80) cc_final: 0.7305 (t80) REVERT: N 29 GLN cc_start: 0.7499 (mm-40) cc_final: 0.7179 (mm-40) REVERT: N 39 GLN cc_start: 0.8260 (mt0) cc_final: 0.7905 (mt0) REVERT: N 61 TYR cc_start: 0.8108 (t80) cc_final: 0.7853 (t80) REVERT: N 67 VAL cc_start: 0.8088 (OUTLIER) cc_final: 0.7667 (t) REVERT: N 70 LEU cc_start: 0.7704 (mt) cc_final: 0.7481 (mp) REVERT: N 75 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7591 (tt) REVERT: N 110 ARG cc_start: 0.8083 (ttp80) cc_final: 0.7129 (ttp80) REVERT: N 198 MET cc_start: 0.5440 (mmt) cc_final: 0.5239 (mmt) REVERT: O 36 GLN cc_start: 0.7217 (tp40) cc_final: 0.6977 (tp40) REVERT: O 67 VAL cc_start: 0.7983 (p) cc_final: 0.7532 (t) REVERT: O 105 GLN cc_start: 0.7183 (mp10) cc_final: 0.6810 (mp10) REVERT: O 138 GLN cc_start: 0.4921 (tt0) cc_final: 0.4604 (tt0) REVERT: P 15 TRP cc_start: 0.7681 (OUTLIER) cc_final: 0.7382 (m100) REVERT: P 26 GLU cc_start: 0.7111 (tp30) cc_final: 0.6827 (tp30) REVERT: P 106 GLN cc_start: 0.7025 (mm-40) cc_final: 0.6695 (mm-40) REVERT: Q 80 SER cc_start: 0.8267 (m) cc_final: 0.7733 (p) REVERT: Q 110 ARG cc_start: 0.8188 (ttp80) cc_final: 0.7270 (ttp80) REVERT: R 36 GLN cc_start: 0.6910 (tp40) cc_final: 0.6584 (tp40) REVERT: R 43 LEU cc_start: 0.8179 (tp) cc_final: 0.7655 (tp) outliers start: 82 outliers final: 49 residues processed: 647 average time/residue: 0.1700 time to fit residues: 174.7951 Evaluate side-chains 635 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 579 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 TRP Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain C residue 15 TRP Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain A residue 15 TRP Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 15 TRP Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 63 CYS Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain F residue 15 TRP Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain G residue 15 TRP Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain H residue 15 TRP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 193 SER Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain I residue 15 TRP Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 15 TRP Chi-restraints excluded: chain J residue 36 GLN Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain L residue 15 TRP Chi-restraints excluded: chain L residue 180 GLU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 169 LEU Chi-restraints excluded: chain N residue 15 TRP Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 193 SER Chi-restraints excluded: chain O residue 25 GLN Chi-restraints excluded: chain O residue 169 LEU Chi-restraints excluded: chain P residue 15 TRP Chi-restraints excluded: chain Q residue 15 TRP Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain Q residue 105 GLN Chi-restraints excluded: chain Q residue 193 SER Chi-restraints excluded: chain R residue 151 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 238 optimal weight: 0.9990 chunk 275 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 258 optimal weight: 6.9990 chunk 60 optimal weight: 0.0570 chunk 194 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 237 optimal weight: 0.8980 chunk 303 optimal weight: 0.0770 chunk 81 optimal weight: 0.6980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN B 114 GLN C 56 GLN C 115 GLN F 36 GLN I 74 GLN J 36 GLN ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 107 GLN K 115 GLN L 21 GLN P 56 GLN Q 115 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.187097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.160321 restraints weight = 32594.840| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 1.54 r_work: 0.3736 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27744 Z= 0.107 Angle : 0.558 7.349 37746 Z= 0.265 Chirality : 0.035 0.181 4122 Planarity : 0.005 0.062 5040 Dihedral : 3.708 17.204 3708 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.69 % Allowed : 17.36 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.15), residues: 3438 helix: 2.00 (0.11), residues: 2430 sheet: None (None), residues: 0 loop : 0.67 (0.22), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 111 TYR 0.018 0.001 TYR G 113 PHE 0.014 0.001 PHE A 37 TRP 0.024 0.002 TRP B 15 HIS 0.004 0.001 HIS O 72 Details of bonding type rmsd covalent geometry : bond 0.00255 (27738) covalent geometry : angle 0.55783 (37746) hydrogen bonds : bond 0.03178 ( 1722) hydrogen bonds : angle 4.01720 ( 5022) Misc. bond : bond 0.00032 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 592 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 ASN cc_start: 0.8461 (p0) cc_final: 0.7989 (p0) REVERT: B 107 GLN cc_start: 0.8048 (tp40) cc_final: 0.6951 (tp40) REVERT: B 111 ARG cc_start: 0.7757 (tpp-160) cc_final: 0.7404 (tpp-160) REVERT: B 174 TYR cc_start: 0.8035 (t80) cc_final: 0.7788 (t80) REVERT: C 36 GLN cc_start: 0.6426 (tp-100) cc_final: 0.5972 (tp-100) REVERT: C 56 GLN cc_start: 0.7173 (tp-100) cc_final: 0.6810 (tp-100) REVERT: C 175 SER cc_start: 0.7542 (m) cc_final: 0.7208 (t) REVERT: A 17 MET cc_start: 0.7896 (tpt) cc_final: 0.7158 (tpt) REVERT: A 61 TYR cc_start: 0.7962 (t80) cc_final: 0.7571 (t80) REVERT: A 174 TYR cc_start: 0.7418 (t80) cc_final: 0.7169 (t80) REVERT: D 39 GLN cc_start: 0.8109 (mt0) cc_final: 0.7738 (mt0) REVERT: D 136 ILE cc_start: 0.6907 (mt) cc_final: 0.6647 (mp) REVERT: D 150 ARG cc_start: 0.7815 (mtt-85) cc_final: 0.7603 (mtt-85) REVERT: D 159 LEU cc_start: 0.7234 (mt) cc_final: 0.6970 (mt) REVERT: E 39 GLN cc_start: 0.8475 (mt0) cc_final: 0.8115 (mt0) REVERT: E 67 VAL cc_start: 0.8242 (OUTLIER) cc_final: 0.7898 (t) REVERT: E 110 ARG cc_start: 0.8240 (ttp80) cc_final: 0.7870 (ttp80) REVERT: E 198 MET cc_start: 0.5609 (mmt) cc_final: 0.5347 (mmt) REVERT: F 17 MET cc_start: 0.7638 (tpp) cc_final: 0.7398 (tpt) REVERT: F 36 GLN cc_start: 0.7321 (tp40) cc_final: 0.6968 (tp40) REVERT: F 39 GLN cc_start: 0.8070 (mt0) cc_final: 0.7735 (mt0) REVERT: F 67 VAL cc_start: 0.8108 (p) cc_final: 0.7704 (t) REVERT: F 107 GLN cc_start: 0.7820 (tt0) cc_final: 0.7571 (tt0) REVERT: F 151 LEU cc_start: 0.7503 (tp) cc_final: 0.7169 (tp) REVERT: G 114 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7314 (tt0) REVERT: H 34 SER cc_start: 0.7896 (t) cc_final: 0.7564 (t) REVERT: H 60 GLN cc_start: 0.8115 (mt0) cc_final: 0.7884 (mt0) REVERT: H 64 SER cc_start: 0.8186 (p) cc_final: 0.7951 (p) REVERT: H 77 SER cc_start: 0.8196 (t) cc_final: 0.7452 (m) REVERT: H 80 SER cc_start: 0.8056 (m) cc_final: 0.7497 (p) REVERT: H 110 ARG cc_start: 0.7875 (ttp80) cc_final: 0.7188 (ttp80) REVERT: H 175 SER cc_start: 0.7395 (m) cc_final: 0.7005 (t) REVERT: I 36 GLN cc_start: 0.6837 (tp40) cc_final: 0.6352 (tp40) REVERT: I 43 LEU cc_start: 0.7900 (tp) cc_final: 0.7549 (tp) REVERT: I 170 ARG cc_start: 0.7992 (mtp180) cc_final: 0.7590 (mtp180) REVERT: I 174 TYR cc_start: 0.7290 (t80) cc_final: 0.6702 (t80) REVERT: J 56 GLN cc_start: 0.8066 (tp-100) cc_final: 0.7215 (tp-100) REVERT: J 110 ARG cc_start: 0.8097 (ttp80) cc_final: 0.7517 (ttp80) REVERT: J 174 TYR cc_start: 0.7926 (t80) cc_final: 0.7251 (t80) REVERT: K 54 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7182 (t0) REVERT: K 56 GLN cc_start: 0.7190 (tp-100) cc_final: 0.6752 (tp-100) REVERT: K 77 SER cc_start: 0.8204 (t) cc_final: 0.7566 (m) REVERT: K 110 ARG cc_start: 0.8147 (ttp80) cc_final: 0.7739 (ttp80) REVERT: K 175 SER cc_start: 0.7499 (m) cc_final: 0.7097 (t) REVERT: L 61 TYR cc_start: 0.7913 (t80) cc_final: 0.7533 (t80) REVERT: L 105 GLN cc_start: 0.7040 (mp10) cc_final: 0.6631 (mp10) REVERT: L 138 GLN cc_start: 0.5407 (tt0) cc_final: 0.4914 (tm-30) REVERT: L 167 PRO cc_start: 0.7782 (Cg_exo) cc_final: 0.7456 (Cg_endo) REVERT: L 174 TYR cc_start: 0.7498 (t80) cc_final: 0.6931 (t80) REVERT: M 39 GLN cc_start: 0.8061 (mt0) cc_final: 0.7622 (mt0) REVERT: M 56 GLN cc_start: 0.8142 (tp40) cc_final: 0.7930 (tp40) REVERT: M 105 GLN cc_start: 0.7573 (mm-40) cc_final: 0.7052 (mm-40) REVERT: M 106 GLN cc_start: 0.7230 (mm-40) cc_final: 0.6893 (mm-40) REVERT: M 174 TYR cc_start: 0.7877 (t80) cc_final: 0.7522 (t80) REVERT: N 29 GLN cc_start: 0.7478 (mm-40) cc_final: 0.7180 (mm-40) REVERT: N 39 GLN cc_start: 0.8285 (mt0) cc_final: 0.7910 (mt0) REVERT: N 61 TYR cc_start: 0.8092 (t80) cc_final: 0.7880 (t80) REVERT: N 67 VAL cc_start: 0.8064 (OUTLIER) cc_final: 0.7686 (t) REVERT: N 70 LEU cc_start: 0.7736 (mt) cc_final: 0.7520 (mp) REVERT: N 75 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7656 (tt) REVERT: N 110 ARG cc_start: 0.8133 (ttp80) cc_final: 0.7175 (ttp80) REVERT: O 36 GLN cc_start: 0.7313 (tp40) cc_final: 0.6994 (tp40) REVERT: O 67 VAL cc_start: 0.7973 (p) cc_final: 0.7537 (t) REVERT: O 105 GLN cc_start: 0.7238 (mp10) cc_final: 0.6839 (mp10) REVERT: O 138 GLN cc_start: 0.4888 (tt0) cc_final: 0.4677 (tt0) REVERT: P 15 TRP cc_start: 0.7690 (OUTLIER) cc_final: 0.7368 (m100) REVERT: P 24 LYS cc_start: 0.8263 (tptm) cc_final: 0.7931 (tptm) REVERT: P 26 GLU cc_start: 0.7119 (tp30) cc_final: 0.6863 (tp30) REVERT: P 106 GLN cc_start: 0.7015 (mm-40) cc_final: 0.6647 (mm-40) REVERT: Q 80 SER cc_start: 0.8333 (m) cc_final: 0.7818 (p) REVERT: Q 110 ARG cc_start: 0.8185 (ttp80) cc_final: 0.7302 (ttp80) REVERT: R 36 GLN cc_start: 0.6755 (tp40) cc_final: 0.6409 (tp40) REVERT: R 43 LEU cc_start: 0.8159 (tp) cc_final: 0.7593 (tp) REVERT: R 60 GLN cc_start: 0.7567 (mm-40) cc_final: 0.7324 (mt0) outliers start: 78 outliers final: 49 residues processed: 644 average time/residue: 0.1602 time to fit residues: 165.8152 Evaluate side-chains 640 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 585 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 TRP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain A residue 15 TRP Chi-restraints excluded: chain D residue 15 TRP Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 15 TRP Chi-restraints excluded: chain E residue 29 GLN Chi-restraints excluded: chain E residue 63 CYS Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain F residue 15 TRP Chi-restraints excluded: chain G residue 15 TRP Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 193 SER Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain I residue 15 TRP Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 15 TRP Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 107 GLN Chi-restraints excluded: chain K residue 193 SER Chi-restraints excluded: chain L residue 15 TRP Chi-restraints excluded: chain M residue 15 TRP Chi-restraints excluded: chain M residue 169 LEU Chi-restraints excluded: chain N residue 15 TRP Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 193 SER Chi-restraints excluded: chain O residue 25 GLN Chi-restraints excluded: chain O residue 100 GLN Chi-restraints excluded: chain O residue 169 LEU Chi-restraints excluded: chain P residue 15 TRP Chi-restraints excluded: chain Q residue 15 TRP Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain Q residue 105 GLN Chi-restraints excluded: chain Q residue 193 SER Chi-restraints excluded: chain R residue 15 TRP Chi-restraints excluded: chain R residue 151 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 304 optimal weight: 0.9980 chunk 52 optimal weight: 0.4980 chunk 126 optimal weight: 9.9990 chunk 131 optimal weight: 20.0000 chunk 226 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 276 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 333 optimal weight: 0.9990 chunk 79 optimal weight: 0.0770 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN D 60 GLN D 73 GLN G 114 GLN H 29 GLN J 73 GLN K 29 GLN K 115 GLN L 73 GLN Q 115 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.187025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.160161 restraints weight = 32409.139| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 1.52 r_work: 0.3719 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27744 Z= 0.118 Angle : 0.563 7.200 37746 Z= 0.268 Chirality : 0.035 0.203 4122 Planarity : 0.005 0.061 5040 Dihedral : 3.685 17.696 3708 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.80 % Allowed : 17.81 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.15), residues: 3438 helix: 1.95 (0.11), residues: 2448 sheet: None (None), residues: 0 loop : 0.74 (0.22), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 110 TYR 0.010 0.001 TYR N 61 PHE 0.015 0.001 PHE R 37 TRP 0.026 0.002 TRP F 133 HIS 0.005 0.001 HIS O 72 Details of bonding type rmsd covalent geometry : bond 0.00287 (27738) covalent geometry : angle 0.56254 (37746) hydrogen bonds : bond 0.03184 ( 1722) hydrogen bonds : angle 3.98713 ( 5022) Misc. bond : bond 0.00020 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 591 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 ASN cc_start: 0.8453 (p0) cc_final: 0.8005 (p0) REVERT: B 107 GLN cc_start: 0.8070 (tp40) cc_final: 0.7030 (tp40) REVERT: B 111 ARG cc_start: 0.7773 (tpp-160) cc_final: 0.7394 (tpp-160) REVERT: B 174 TYR cc_start: 0.8094 (t80) cc_final: 0.7633 (t80) REVERT: C 36 GLN cc_start: 0.6406 (tp-100) cc_final: 0.5955 (tp-100) REVERT: C 56 GLN cc_start: 0.7096 (tp-100) cc_final: 0.6674 (tp-100) REVERT: C 175 SER cc_start: 0.7497 (m) cc_final: 0.7157 (t) REVERT: A 17 MET cc_start: 0.7908 (tpt) cc_final: 0.7114 (tpt) REVERT: A 61 TYR cc_start: 0.8014 (t80) cc_final: 0.7599 (t80) REVERT: A 174 TYR cc_start: 0.7718 (t80) cc_final: 0.7283 (t80) REVERT: D 136 ILE cc_start: 0.6979 (mt) cc_final: 0.6658 (mp) REVERT: D 150 ARG cc_start: 0.7711 (mtt-85) cc_final: 0.7472 (mtt-85) REVERT: D 159 LEU cc_start: 0.7054 (mt) cc_final: 0.6815 (mt) REVERT: E 39 GLN cc_start: 0.8481 (mt0) cc_final: 0.8209 (mt0) REVERT: E 67 VAL cc_start: 0.8258 (OUTLIER) cc_final: 0.7871 (t) REVERT: E 69 SER cc_start: 0.7630 (p) cc_final: 0.7273 (t) REVERT: E 110 ARG cc_start: 0.8262 (ttp80) cc_final: 0.7849 (ttp80) REVERT: E 198 MET cc_start: 0.5880 (mmt) cc_final: 0.5571 (mmt) REVERT: F 17 MET cc_start: 0.7723 (tpp) cc_final: 0.7510 (tpt) REVERT: F 36 GLN cc_start: 0.7492 (tp40) cc_final: 0.7029 (tp40) REVERT: F 39 GLN cc_start: 0.8084 (mt0) cc_final: 0.7776 (mt0) REVERT: F 67 VAL cc_start: 0.8121 (p) cc_final: 0.7750 (t) REVERT: F 107 GLN cc_start: 0.7818 (tt0) cc_final: 0.7590 (tt0) REVERT: F 151 LEU cc_start: 0.7693 (tp) cc_final: 0.7393 (tp) REVERT: G 114 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7681 (mt0) REVERT: H 34 SER cc_start: 0.7953 (t) cc_final: 0.7622 (t) REVERT: H 60 GLN cc_start: 0.8066 (mt0) cc_final: 0.7788 (mt0) REVERT: H 64 SER cc_start: 0.8196 (p) cc_final: 0.7944 (p) REVERT: H 77 SER cc_start: 0.8148 (t) cc_final: 0.7357 (m) REVERT: H 80 SER cc_start: 0.8064 (m) cc_final: 0.7487 (p) REVERT: H 110 ARG cc_start: 0.7898 (ttp80) cc_final: 0.7105 (ttp80) REVERT: H 175 SER cc_start: 0.7301 (m) cc_final: 0.6946 (t) REVERT: I 36 GLN cc_start: 0.6902 (tp40) cc_final: 0.6375 (tp40) REVERT: I 43 LEU cc_start: 0.7934 (tp) cc_final: 0.7568 (tp) REVERT: I 170 ARG cc_start: 0.7691 (mtp180) cc_final: 0.7258 (mtp180) REVERT: I 174 TYR cc_start: 0.7577 (t80) cc_final: 0.6682 (t80) REVERT: J 56 GLN cc_start: 0.8064 (tp-100) cc_final: 0.7298 (tp-100) REVERT: J 110 ARG cc_start: 0.8058 (ttp80) cc_final: 0.7352 (ttp80) REVERT: J 174 TYR cc_start: 0.7935 (t80) cc_final: 0.7057 (t80) REVERT: K 24 LYS cc_start: 0.7931 (tttp) cc_final: 0.7731 (tttm) REVERT: K 54 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7124 (t0) REVERT: K 56 GLN cc_start: 0.7157 (tp-100) cc_final: 0.6728 (tp-100) REVERT: K 77 SER cc_start: 0.8071 (t) cc_final: 0.7378 (m) REVERT: K 110 ARG cc_start: 0.8208 (ttp80) cc_final: 0.7735 (ttp80) REVERT: K 175 SER cc_start: 0.7475 (m) cc_final: 0.7083 (t) REVERT: L 61 TYR cc_start: 0.7972 (t80) cc_final: 0.7588 (t80) REVERT: L 105 GLN cc_start: 0.7012 (mp10) cc_final: 0.6618 (mp10) REVERT: L 167 PRO cc_start: 0.7748 (Cg_exo) cc_final: 0.7411 (Cg_endo) REVERT: L 174 TYR cc_start: 0.7743 (t80) cc_final: 0.7123 (t80) REVERT: M 39 GLN cc_start: 0.8086 (mt0) cc_final: 0.7838 (mt0) REVERT: M 105 GLN cc_start: 0.7629 (mm-40) cc_final: 0.7158 (mm-40) REVERT: M 106 GLN cc_start: 0.7267 (mm-40) cc_final: 0.6917 (mm-40) REVERT: M 174 TYR cc_start: 0.7849 (t80) cc_final: 0.7431 (t80) REVERT: M 193 SER cc_start: 0.6781 (p) cc_final: 0.6565 (p) REVERT: N 29 GLN cc_start: 0.7283 (mm-40) cc_final: 0.6991 (mm-40) REVERT: N 39 GLN cc_start: 0.8361 (mt0) cc_final: 0.7987 (mt0) REVERT: N 61 TYR cc_start: 0.8125 (t80) cc_final: 0.7889 (t80) REVERT: N 67 VAL cc_start: 0.8203 (OUTLIER) cc_final: 0.7789 (t) REVERT: N 70 LEU cc_start: 0.7702 (mt) cc_final: 0.7470 (mp) REVERT: N 75 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7575 (tt) REVERT: N 110 ARG cc_start: 0.8184 (ttp80) cc_final: 0.7807 (ttp80) REVERT: O 36 GLN cc_start: 0.7323 (tp40) cc_final: 0.6974 (tp40) REVERT: O 67 VAL cc_start: 0.7989 (p) cc_final: 0.7560 (t) REVERT: O 105 GLN cc_start: 0.7122 (mp10) cc_final: 0.6772 (mp10) REVERT: O 138 GLN cc_start: 0.4935 (tt0) cc_final: 0.4656 (tt0) REVERT: O 170 ARG cc_start: 0.7862 (mtp180) cc_final: 0.7613 (mtp180) REVERT: P 15 TRP cc_start: 0.7756 (OUTLIER) cc_final: 0.7441 (m100) REVERT: P 24 LYS cc_start: 0.8323 (tptm) cc_final: 0.8007 (tptm) REVERT: P 26 GLU cc_start: 0.7270 (tp30) cc_final: 0.7013 (tp30) REVERT: P 106 GLN cc_start: 0.7046 (mm-40) cc_final: 0.6631 (mm-40) REVERT: Q 80 SER cc_start: 0.8261 (m) cc_final: 0.7711 (p) REVERT: Q 110 ARG cc_start: 0.8227 (ttp80) cc_final: 0.7273 (ttp80) REVERT: R 36 GLN cc_start: 0.6838 (tp40) cc_final: 0.6470 (tp40) REVERT: R 43 LEU cc_start: 0.8206 (tp) cc_final: 0.7667 (tp) REVERT: R 60 GLN cc_start: 0.7639 (mm-40) cc_final: 0.7397 (mt0) outliers start: 81 outliers final: 53 residues processed: 642 average time/residue: 0.1674 time to fit residues: 173.3748 Evaluate side-chains 642 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 583 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 TRP Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain A residue 15 TRP Chi-restraints excluded: chain D residue 15 TRP Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 29 GLN Chi-restraints excluded: chain E residue 63 CYS Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain F residue 15 TRP Chi-restraints excluded: chain G residue 15 TRP Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain H residue 29 GLN Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 193 SER Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 15 TRP Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 193 SER Chi-restraints excluded: chain L residue 15 TRP Chi-restraints excluded: chain L residue 73 GLN Chi-restraints excluded: chain M residue 15 TRP Chi-restraints excluded: chain M residue 169 LEU Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 193 SER Chi-restraints excluded: chain O residue 25 GLN Chi-restraints excluded: chain O residue 100 GLN Chi-restraints excluded: chain O residue 169 LEU Chi-restraints excluded: chain P residue 15 TRP Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain Q residue 105 GLN Chi-restraints excluded: chain Q residue 193 SER Chi-restraints excluded: chain R residue 15 TRP Chi-restraints excluded: chain R residue 151 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 251 optimal weight: 0.5980 chunk 245 optimal weight: 9.9990 chunk 190 optimal weight: 3.9990 chunk 289 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 277 optimal weight: 0.3980 chunk 16 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 285 optimal weight: 0.9980 chunk 252 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 114 GLN K 107 GLN K 115 GLN M 56 GLN ** P 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 115 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.186456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.159748 restraints weight = 32625.703| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.51 r_work: 0.3704 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27744 Z= 0.117 Angle : 0.569 9.316 37746 Z= 0.270 Chirality : 0.035 0.193 4122 Planarity : 0.005 0.064 5040 Dihedral : 3.680 17.609 3708 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.35 % Allowed : 18.43 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.15), residues: 3438 helix: 1.96 (0.11), residues: 2448 sheet: None (None), residues: 0 loop : 0.77 (0.22), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 111 TYR 0.015 0.001 TYR G 113 PHE 0.015 0.001 PHE L 37 TRP 0.028 0.002 TRP L 133 HIS 0.004 0.001 HIS O 72 Details of bonding type rmsd covalent geometry : bond 0.00284 (27738) covalent geometry : angle 0.56867 (37746) hydrogen bonds : bond 0.03152 ( 1722) hydrogen bonds : angle 3.97337 ( 5022) Misc. bond : bond 0.00017 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 586 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 GLN cc_start: 0.7929 (tp-100) cc_final: 0.7412 (tp-100) REVERT: B 91 ASN cc_start: 0.8460 (p0) cc_final: 0.8062 (p0) REVERT: B 107 GLN cc_start: 0.8006 (tp40) cc_final: 0.7027 (tp40) REVERT: B 111 ARG cc_start: 0.7709 (tpp-160) cc_final: 0.7388 (tpp-160) REVERT: B 174 TYR cc_start: 0.8057 (t80) cc_final: 0.7566 (t80) REVERT: C 36 GLN cc_start: 0.6354 (tp-100) cc_final: 0.5912 (tp-100) REVERT: C 56 GLN cc_start: 0.7055 (tp-100) cc_final: 0.6640 (tp-100) REVERT: C 175 SER cc_start: 0.7510 (m) cc_final: 0.7183 (t) REVERT: A 17 MET cc_start: 0.7900 (tpt) cc_final: 0.7128 (tpt) REVERT: A 61 TYR cc_start: 0.7991 (t80) cc_final: 0.7606 (t80) REVERT: A 174 TYR cc_start: 0.7668 (t80) cc_final: 0.7196 (t80) REVERT: D 136 ILE cc_start: 0.6949 (mt) cc_final: 0.6620 (mp) REVERT: D 150 ARG cc_start: 0.7655 (mtt-85) cc_final: 0.7417 (mtt-85) REVERT: D 159 LEU cc_start: 0.7086 (mt) cc_final: 0.6844 (mt) REVERT: E 39 GLN cc_start: 0.8509 (mt0) cc_final: 0.8187 (mt0) REVERT: E 61 TYR cc_start: 0.8100 (t80) cc_final: 0.7848 (t80) REVERT: E 67 VAL cc_start: 0.8270 (OUTLIER) cc_final: 0.7871 (t) REVERT: E 69 SER cc_start: 0.7636 (p) cc_final: 0.7277 (t) REVERT: E 110 ARG cc_start: 0.8277 (ttp80) cc_final: 0.7857 (ttp80) REVERT: E 198 MET cc_start: 0.5825 (mmt) cc_final: 0.5507 (mmt) REVERT: F 17 MET cc_start: 0.7727 (tpp) cc_final: 0.7506 (tpt) REVERT: F 36 GLN cc_start: 0.7495 (tp40) cc_final: 0.6993 (tp40) REVERT: F 39 GLN cc_start: 0.8091 (mt0) cc_final: 0.7779 (mt0) REVERT: F 67 VAL cc_start: 0.8136 (p) cc_final: 0.7754 (t) REVERT: F 107 GLN cc_start: 0.7738 (tt0) cc_final: 0.7514 (tt0) REVERT: F 151 LEU cc_start: 0.7699 (tp) cc_final: 0.7400 (tp) REVERT: F 174 TYR cc_start: 0.7271 (t80) cc_final: 0.6878 (t80) REVERT: G 114 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7557 (tt0) REVERT: H 34 SER cc_start: 0.7970 (t) cc_final: 0.7652 (t) REVERT: H 60 GLN cc_start: 0.8012 (mt0) cc_final: 0.7738 (mt0) REVERT: H 64 SER cc_start: 0.8204 (p) cc_final: 0.7943 (p) REVERT: H 77 SER cc_start: 0.8160 (t) cc_final: 0.7388 (m) REVERT: H 80 SER cc_start: 0.8066 (m) cc_final: 0.7509 (p) REVERT: H 110 ARG cc_start: 0.7909 (ttp80) cc_final: 0.7060 (ttp80) REVERT: H 175 SER cc_start: 0.7299 (m) cc_final: 0.6950 (t) REVERT: I 36 GLN cc_start: 0.6841 (tp40) cc_final: 0.6339 (tp40) REVERT: I 43 LEU cc_start: 0.7943 (tp) cc_final: 0.7570 (tp) REVERT: I 170 ARG cc_start: 0.7697 (mtp180) cc_final: 0.7273 (mtp180) REVERT: I 174 TYR cc_start: 0.7513 (t80) cc_final: 0.6606 (t80) REVERT: J 56 GLN cc_start: 0.8031 (tp-100) cc_final: 0.7270 (tp-100) REVERT: J 110 ARG cc_start: 0.8051 (ttp80) cc_final: 0.7773 (ttp80) REVERT: J 174 TYR cc_start: 0.7899 (t80) cc_final: 0.7059 (t80) REVERT: K 54 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7180 (t0) REVERT: K 56 GLN cc_start: 0.7068 (tp-100) cc_final: 0.6661 (tp-100) REVERT: K 77 SER cc_start: 0.8102 (t) cc_final: 0.7409 (m) REVERT: K 175 SER cc_start: 0.7449 (m) cc_final: 0.7053 (t) REVERT: L 61 TYR cc_start: 0.7985 (t80) cc_final: 0.7583 (t80) REVERT: L 105 GLN cc_start: 0.6977 (mp10) cc_final: 0.6600 (mp10) REVERT: L 167 PRO cc_start: 0.7763 (Cg_exo) cc_final: 0.7436 (Cg_endo) REVERT: L 174 TYR cc_start: 0.7712 (t80) cc_final: 0.7082 (t80) REVERT: M 39 GLN cc_start: 0.8087 (mt0) cc_final: 0.7837 (mt0) REVERT: M 174 TYR cc_start: 0.7816 (t80) cc_final: 0.7379 (t80) REVERT: M 193 SER cc_start: 0.6829 (p) cc_final: 0.6619 (p) REVERT: N 29 GLN cc_start: 0.7312 (mm-40) cc_final: 0.7008 (mm-40) REVERT: N 39 GLN cc_start: 0.8380 (mt0) cc_final: 0.8038 (mt0) REVERT: N 67 VAL cc_start: 0.8210 (OUTLIER) cc_final: 0.7789 (t) REVERT: N 70 LEU cc_start: 0.7693 (mt) cc_final: 0.7454 (mp) REVERT: N 75 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7586 (tt) REVERT: N 110 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7801 (ttp80) REVERT: N 121 PHE cc_start: 0.8245 (m-80) cc_final: 0.8001 (m-80) REVERT: O 36 GLN cc_start: 0.7328 (tp40) cc_final: 0.6934 (tp40) REVERT: O 67 VAL cc_start: 0.7977 (p) cc_final: 0.7555 (t) REVERT: O 105 GLN cc_start: 0.7096 (mp10) cc_final: 0.6762 (mp10) REVERT: O 138 GLN cc_start: 0.4935 (tt0) cc_final: 0.4723 (tt0) REVERT: O 170 ARG cc_start: 0.7841 (mtp180) cc_final: 0.7632 (mtp180) REVERT: P 15 TRP cc_start: 0.7770 (OUTLIER) cc_final: 0.7441 (m100) REVERT: P 24 LYS cc_start: 0.8356 (tptm) cc_final: 0.8087 (tptm) REVERT: P 26 GLU cc_start: 0.7194 (tp30) cc_final: 0.6938 (tp30) REVERT: P 106 GLN cc_start: 0.7037 (mm-40) cc_final: 0.6618 (mm-40) REVERT: Q 34 SER cc_start: 0.8206 (t) cc_final: 0.7944 (t) REVERT: Q 80 SER cc_start: 0.8267 (m) cc_final: 0.7702 (p) REVERT: Q 100 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7834 (mt0) REVERT: Q 110 ARG cc_start: 0.8222 (ttp80) cc_final: 0.7252 (ttp80) REVERT: R 36 GLN cc_start: 0.6779 (tp40) cc_final: 0.6391 (tp40) REVERT: R 43 LEU cc_start: 0.8225 (tp) cc_final: 0.7668 (tp) REVERT: R 60 GLN cc_start: 0.7587 (mm-40) cc_final: 0.7340 (mt0) outliers start: 68 outliers final: 50 residues processed: 628 average time/residue: 0.1655 time to fit residues: 167.5130 Evaluate side-chains 640 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 583 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 TRP Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain A residue 15 TRP Chi-restraints excluded: chain D residue 15 TRP Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 29 GLN Chi-restraints excluded: chain E residue 63 CYS Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain F residue 15 TRP Chi-restraints excluded: chain G residue 15 TRP Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 193 SER Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 15 TRP Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 107 GLN Chi-restraints excluded: chain K residue 193 SER Chi-restraints excluded: chain L residue 15 TRP Chi-restraints excluded: chain M residue 15 TRP Chi-restraints excluded: chain M residue 169 LEU Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 193 SER Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 100 GLN Chi-restraints excluded: chain O residue 169 LEU Chi-restraints excluded: chain P residue 15 TRP Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain Q residue 100 GLN Chi-restraints excluded: chain Q residue 105 GLN Chi-restraints excluded: chain Q residue 193 SER Chi-restraints excluded: chain R residue 15 TRP Chi-restraints excluded: chain R residue 151 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 249 optimal weight: 0.6980 chunk 94 optimal weight: 20.0000 chunk 305 optimal weight: 0.0070 chunk 105 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 277 optimal weight: 0.9980 chunk 225 optimal weight: 10.0000 chunk 196 optimal weight: 0.8980 chunk 263 optimal weight: 4.9990 chunk 310 optimal weight: 0.7980 chunk 152 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 GLN ** F 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 GLN H 29 GLN J 73 GLN K 107 GLN K 115 GLN Q 115 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.187829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.161064 restraints weight = 32622.274| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.53 r_work: 0.3722 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27744 Z= 0.113 Angle : 0.572 8.796 37746 Z= 0.270 Chirality : 0.035 0.236 4122 Planarity : 0.005 0.066 5040 Dihedral : 3.647 17.266 3708 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.38 % Allowed : 18.43 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.15), residues: 3438 helix: 2.05 (0.11), residues: 2430 sheet: None (None), residues: 0 loop : 0.70 (0.22), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 111 TYR 0.016 0.001 TYR G 113 PHE 0.014 0.001 PHE L 37 TRP 0.030 0.002 TRP L 133 HIS 0.004 0.001 HIS O 72 Details of bonding type rmsd covalent geometry : bond 0.00276 (27738) covalent geometry : angle 0.57192 (37746) hydrogen bonds : bond 0.03108 ( 1722) hydrogen bonds : angle 3.95208 ( 5022) Misc. bond : bond 0.00015 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 586 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 GLN cc_start: 0.7935 (tp-100) cc_final: 0.7404 (tp-100) REVERT: B 91 ASN cc_start: 0.8455 (p0) cc_final: 0.8037 (p0) REVERT: B 107 GLN cc_start: 0.8031 (tp40) cc_final: 0.7139 (tp40) REVERT: B 111 ARG cc_start: 0.7727 (tpp-160) cc_final: 0.7455 (tpp-160) REVERT: B 174 TYR cc_start: 0.8079 (t80) cc_final: 0.7599 (t80) REVERT: C 36 GLN cc_start: 0.6372 (tp-100) cc_final: 0.5925 (tp-100) REVERT: C 56 GLN cc_start: 0.7041 (tp-100) cc_final: 0.6649 (tp-100) REVERT: C 175 SER cc_start: 0.7513 (m) cc_final: 0.7179 (t) REVERT: A 17 MET cc_start: 0.7870 (tpt) cc_final: 0.6994 (tpt) REVERT: A 61 TYR cc_start: 0.7980 (t80) cc_final: 0.7593 (t80) REVERT: A 174 TYR cc_start: 0.7712 (t80) cc_final: 0.7253 (t80) REVERT: D 107 GLN cc_start: 0.7653 (tp40) cc_final: 0.7314 (tp40) REVERT: D 136 ILE cc_start: 0.6942 (mt) cc_final: 0.6592 (mp) REVERT: D 150 ARG cc_start: 0.7754 (mtt-85) cc_final: 0.7535 (mtt-85) REVERT: E 39 GLN cc_start: 0.8500 (mt0) cc_final: 0.8178 (mt0) REVERT: E 61 TYR cc_start: 0.8091 (t80) cc_final: 0.7860 (t80) REVERT: E 67 VAL cc_start: 0.8257 (OUTLIER) cc_final: 0.7863 (t) REVERT: E 69 SER cc_start: 0.7631 (p) cc_final: 0.7268 (t) REVERT: E 110 ARG cc_start: 0.8281 (ttp80) cc_final: 0.7863 (ttp80) REVERT: E 198 MET cc_start: 0.5835 (mmt) cc_final: 0.5515 (mmt) REVERT: F 17 MET cc_start: 0.7723 (tpp) cc_final: 0.7502 (tpt) REVERT: F 36 GLN cc_start: 0.7460 (tp40) cc_final: 0.6974 (tp40) REVERT: F 39 GLN cc_start: 0.8098 (mt0) cc_final: 0.7751 (mt0) REVERT: F 67 VAL cc_start: 0.8105 (p) cc_final: 0.7729 (t) REVERT: F 151 LEU cc_start: 0.7710 (tp) cc_final: 0.7407 (tp) REVERT: F 174 TYR cc_start: 0.7328 (t80) cc_final: 0.6924 (t80) REVERT: G 57 ASP cc_start: 0.7176 (m-30) cc_final: 0.6963 (m-30) REVERT: H 34 SER cc_start: 0.7985 (t) cc_final: 0.7667 (t) REVERT: H 60 GLN cc_start: 0.8022 (mt0) cc_final: 0.7748 (mt0) REVERT: H 64 SER cc_start: 0.8217 (p) cc_final: 0.7961 (p) REVERT: H 77 SER cc_start: 0.8131 (t) cc_final: 0.7302 (m) REVERT: H 80 SER cc_start: 0.8006 (m) cc_final: 0.7476 (p) REVERT: H 110 ARG cc_start: 0.7924 (ttp80) cc_final: 0.7118 (ttp80) REVERT: H 175 SER cc_start: 0.7332 (m) cc_final: 0.6984 (t) REVERT: I 36 GLN cc_start: 0.6797 (tp40) cc_final: 0.6322 (tp40) REVERT: I 43 LEU cc_start: 0.7945 (tp) cc_final: 0.7560 (tp) REVERT: I 170 ARG cc_start: 0.7825 (mtp180) cc_final: 0.7396 (mtp180) REVERT: I 174 TYR cc_start: 0.7572 (t80) cc_final: 0.6669 (t80) REVERT: J 56 GLN cc_start: 0.8010 (tp-100) cc_final: 0.7272 (tp-100) REVERT: J 110 ARG cc_start: 0.8017 (ttp80) cc_final: 0.7757 (ttp80) REVERT: J 174 TYR cc_start: 0.7912 (t80) cc_final: 0.7101 (t80) REVERT: K 54 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7212 (t0) REVERT: K 56 GLN cc_start: 0.7116 (tp-100) cc_final: 0.6680 (tp-100) REVERT: K 61 TYR cc_start: 0.8033 (t80) cc_final: 0.7765 (t80) REVERT: K 77 SER cc_start: 0.8106 (t) cc_final: 0.7403 (m) REVERT: K 175 SER cc_start: 0.7457 (m) cc_final: 0.7057 (t) REVERT: L 61 TYR cc_start: 0.7973 (t80) cc_final: 0.7549 (t80) REVERT: L 105 GLN cc_start: 0.7049 (mp10) cc_final: 0.6641 (mp10) REVERT: L 138 GLN cc_start: 0.5072 (tt0) cc_final: 0.4647 (tm-30) REVERT: L 167 PRO cc_start: 0.7786 (Cg_exo) cc_final: 0.7458 (Cg_endo) REVERT: L 174 TYR cc_start: 0.7750 (t80) cc_final: 0.7101 (t80) REVERT: M 39 GLN cc_start: 0.8085 (mt0) cc_final: 0.7857 (mt0) REVERT: M 174 TYR cc_start: 0.7830 (t80) cc_final: 0.7420 (t80) REVERT: M 193 SER cc_start: 0.6880 (p) cc_final: 0.6667 (p) REVERT: N 29 GLN cc_start: 0.7339 (mm-40) cc_final: 0.7052 (mm-40) REVERT: N 39 GLN cc_start: 0.8459 (mt0) cc_final: 0.8131 (mt0) REVERT: N 67 VAL cc_start: 0.8185 (OUTLIER) cc_final: 0.7754 (t) REVERT: N 70 LEU cc_start: 0.7673 (mt) cc_final: 0.7433 (mp) REVERT: N 75 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7583 (tt) REVERT: N 110 ARG cc_start: 0.8182 (ttp80) cc_final: 0.7804 (ttp80) REVERT: N 121 PHE cc_start: 0.8249 (m-80) cc_final: 0.8000 (m-80) REVERT: O 36 GLN cc_start: 0.7332 (tp40) cc_final: 0.6950 (tp40) REVERT: O 67 VAL cc_start: 0.7954 (p) cc_final: 0.7531 (t) REVERT: O 105 GLN cc_start: 0.7148 (mp10) cc_final: 0.6789 (mp10) REVERT: O 170 ARG cc_start: 0.7833 (mtp180) cc_final: 0.7602 (mtp180) REVERT: P 15 TRP cc_start: 0.7759 (OUTLIER) cc_final: 0.7391 (m100) REVERT: P 24 LYS cc_start: 0.8348 (tptm) cc_final: 0.8078 (tptm) REVERT: P 26 GLU cc_start: 0.7261 (tp30) cc_final: 0.7007 (tp30) REVERT: P 106 GLN cc_start: 0.7090 (mm-40) cc_final: 0.6659 (mm-40) REVERT: Q 34 SER cc_start: 0.8186 (t) cc_final: 0.7931 (t) REVERT: Q 36 GLN cc_start: 0.6475 (tp-100) cc_final: 0.6105 (tp-100) REVERT: Q 80 SER cc_start: 0.8266 (m) cc_final: 0.7810 (p) REVERT: Q 100 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7840 (mt0) REVERT: Q 110 ARG cc_start: 0.8231 (ttp80) cc_final: 0.7242 (ttp80) REVERT: R 17 MET cc_start: 0.7983 (tpt) cc_final: 0.7779 (tpp) REVERT: R 36 GLN cc_start: 0.6779 (tp40) cc_final: 0.6397 (tp40) REVERT: R 43 LEU cc_start: 0.8101 (tp) cc_final: 0.7606 (tp) REVERT: R 60 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7389 (mt0) outliers start: 69 outliers final: 52 residues processed: 627 average time/residue: 0.1576 time to fit residues: 159.0678 Evaluate side-chains 637 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 579 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 TRP Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain A residue 15 TRP Chi-restraints excluded: chain D residue 15 TRP Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 29 GLN Chi-restraints excluded: chain E residue 63 CYS Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain F residue 15 TRP Chi-restraints excluded: chain G residue 15 TRP Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain H residue 29 GLN Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 193 SER Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 15 TRP Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 107 GLN Chi-restraints excluded: chain K residue 193 SER Chi-restraints excluded: chain L residue 15 TRP Chi-restraints excluded: chain M residue 15 TRP Chi-restraints excluded: chain M residue 169 LEU Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 193 SER Chi-restraints excluded: chain O residue 25 GLN Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 100 GLN Chi-restraints excluded: chain P residue 15 TRP Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain Q residue 100 GLN Chi-restraints excluded: chain Q residue 193 SER Chi-restraints excluded: chain R residue 15 TRP Chi-restraints excluded: chain R residue 151 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 64 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 331 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 195 optimal weight: 0.8980 chunk 263 optimal weight: 0.0370 chunk 75 optimal weight: 10.0000 chunk 339 optimal weight: 3.9990 chunk 221 optimal weight: 10.0000 chunk 242 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 overall best weight: 2.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 107 GLN K 115 GLN M 36 GLN ** P 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 GLN Q 114 GLN Q 115 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.180751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.152712 restraints weight = 32389.854| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.51 r_work: 0.3667 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 27744 Z= 0.241 Angle : 0.645 9.485 37746 Z= 0.311 Chirality : 0.040 0.258 4122 Planarity : 0.006 0.067 5040 Dihedral : 3.838 19.388 3708 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.10 % Allowed : 19.12 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.15), residues: 3438 helix: 1.76 (0.10), residues: 2430 sheet: None (None), residues: 0 loop : 0.82 (0.22), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 110 TYR 0.019 0.002 TYR E 61 PHE 0.023 0.002 PHE H 37 TRP 0.033 0.003 TRP L 133 HIS 0.009 0.001 HIS F 72 Details of bonding type rmsd covalent geometry : bond 0.00567 (27738) covalent geometry : angle 0.64497 (37746) hydrogen bonds : bond 0.03697 ( 1722) hydrogen bonds : angle 4.08327 ( 5022) Misc. bond : bond 0.00024 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 620 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 GLN cc_start: 0.7937 (tp-100) cc_final: 0.7431 (tp-100) REVERT: B 91 ASN cc_start: 0.8475 (p0) cc_final: 0.8072 (p0) REVERT: B 107 GLN cc_start: 0.7992 (tp40) cc_final: 0.7177 (tp40) REVERT: B 174 TYR cc_start: 0.8185 (t80) cc_final: 0.7712 (t80) REVERT: C 36 GLN cc_start: 0.6547 (tp-100) cc_final: 0.6040 (tp-100) REVERT: C 56 GLN cc_start: 0.7026 (tp-100) cc_final: 0.6566 (tp-100) REVERT: C 175 SER cc_start: 0.7567 (m) cc_final: 0.7256 (t) REVERT: A 61 TYR cc_start: 0.8065 (t80) cc_final: 0.7687 (t80) REVERT: A 174 TYR cc_start: 0.7598 (t80) cc_final: 0.7176 (t80) REVERT: D 36 GLN cc_start: 0.6455 (tp-100) cc_final: 0.5876 (tp-100) REVERT: D 39 GLN cc_start: 0.8181 (mt0) cc_final: 0.7824 (mt0) REVERT: D 107 GLN cc_start: 0.7712 (tp40) cc_final: 0.7419 (tp40) REVERT: D 110 ARG cc_start: 0.8031 (ttp80) cc_final: 0.7716 (ttp80) REVERT: D 136 ILE cc_start: 0.7047 (mt) cc_final: 0.6772 (mp) REVERT: D 150 ARG cc_start: 0.7863 (mtt-85) cc_final: 0.7639 (mtt-85) REVERT: D 159 LEU cc_start: 0.7154 (mt) cc_final: 0.6945 (mt) REVERT: E 39 GLN cc_start: 0.8542 (mt0) cc_final: 0.8219 (mt0) REVERT: E 67 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.8168 (t) REVERT: E 69 SER cc_start: 0.7712 (p) cc_final: 0.7383 (t) REVERT: E 198 MET cc_start: 0.5821 (mmt) cc_final: 0.5533 (mmt) REVERT: F 17 MET cc_start: 0.7736 (tpp) cc_final: 0.7415 (tpp) REVERT: F 36 GLN cc_start: 0.7569 (tp40) cc_final: 0.7116 (tp40) REVERT: F 67 VAL cc_start: 0.8323 (p) cc_final: 0.8075 (t) REVERT: F 151 LEU cc_start: 0.7908 (tp) cc_final: 0.7555 (tp) REVERT: F 174 TYR cc_start: 0.7285 (t80) cc_final: 0.6893 (t80) REVERT: G 36 GLN cc_start: 0.6453 (tp40) cc_final: 0.6192 (tp40) REVERT: G 57 ASP cc_start: 0.7397 (m-30) cc_final: 0.7049 (m-30) REVERT: G 114 GLN cc_start: 0.7946 (tt0) cc_final: 0.7685 (tt0) REVERT: H 34 SER cc_start: 0.8070 (t) cc_final: 0.7832 (t) REVERT: H 60 GLN cc_start: 0.8027 (mt0) cc_final: 0.7819 (mt0) REVERT: H 64 SER cc_start: 0.8250 (p) cc_final: 0.8002 (p) REVERT: H 77 SER cc_start: 0.8210 (t) cc_final: 0.7471 (m) REVERT: H 80 SER cc_start: 0.8030 (m) cc_final: 0.7536 (p) REVERT: H 110 ARG cc_start: 0.8030 (ttp80) cc_final: 0.7153 (ttp80) REVERT: H 115 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7742 (mm110) REVERT: H 175 SER cc_start: 0.7550 (m) cc_final: 0.7175 (t) REVERT: I 36 GLN cc_start: 0.6917 (tp40) cc_final: 0.6400 (tp40) REVERT: I 43 LEU cc_start: 0.7915 (tp) cc_final: 0.7631 (tp) REVERT: I 170 ARG cc_start: 0.7880 (mtp180) cc_final: 0.7466 (mtp180) REVERT: I 174 TYR cc_start: 0.7435 (t80) cc_final: 0.6503 (t80) REVERT: J 56 GLN cc_start: 0.8004 (tp-100) cc_final: 0.7264 (tp-100) REVERT: J 73 GLN cc_start: 0.7111 (mt0) cc_final: 0.6877 (mt0) REVERT: J 110 ARG cc_start: 0.8113 (ttp80) cc_final: 0.7721 (ttp80) REVERT: J 174 TYR cc_start: 0.7955 (t80) cc_final: 0.7033 (t80) REVERT: K 54 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7229 (t0) REVERT: K 56 GLN cc_start: 0.6990 (tp-100) cc_final: 0.6568 (tp-100) REVERT: K 77 SER cc_start: 0.8097 (t) cc_final: 0.7444 (m) REVERT: K 160 PRO cc_start: 0.6999 (Cg_exo) cc_final: 0.6789 (Cg_endo) REVERT: K 175 SER cc_start: 0.7503 (m) cc_final: 0.7111 (t) REVERT: L 61 TYR cc_start: 0.8053 (t80) cc_final: 0.7542 (t80) REVERT: L 105 GLN cc_start: 0.7040 (mp10) cc_final: 0.6665 (mp10) REVERT: L 138 GLN cc_start: 0.5265 (tt0) cc_final: 0.4580 (tm-30) REVERT: L 174 TYR cc_start: 0.7674 (t80) cc_final: 0.7176 (t80) REVERT: L 180 GLU cc_start: 0.6724 (mm-30) cc_final: 0.6415 (mm-30) REVERT: M 39 GLN cc_start: 0.8167 (mt0) cc_final: 0.7673 (mt0) REVERT: M 78 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8106 (mt) REVERT: M 107 GLN cc_start: 0.7787 (tp40) cc_final: 0.7428 (tp40) REVERT: N 39 GLN cc_start: 0.8549 (mt0) cc_final: 0.8208 (mt0) REVERT: N 67 VAL cc_start: 0.8338 (OUTLIER) cc_final: 0.7983 (t) REVERT: N 70 LEU cc_start: 0.7787 (mt) cc_final: 0.7525 (mp) REVERT: N 75 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7636 (tt) REVERT: N 110 ARG cc_start: 0.8301 (ttp80) cc_final: 0.7879 (ttp80) REVERT: N 145 HIS cc_start: 0.6944 (p90) cc_final: 0.6737 (p90) REVERT: O 36 GLN cc_start: 0.7454 (tp40) cc_final: 0.7076 (tp40) REVERT: O 67 VAL cc_start: 0.8206 (p) cc_final: 0.7838 (t) REVERT: O 90 TYR cc_start: 0.7628 (t80) cc_final: 0.6929 (t80) REVERT: O 105 GLN cc_start: 0.7182 (mp10) cc_final: 0.6742 (mp10) REVERT: O 138 GLN cc_start: 0.5014 (OUTLIER) cc_final: 0.4696 (tm-30) REVERT: O 151 LEU cc_start: 0.7987 (tp) cc_final: 0.7684 (tp) REVERT: P 24 LYS cc_start: 0.8360 (tptm) cc_final: 0.8084 (tptm) REVERT: P 26 GLU cc_start: 0.7316 (tp30) cc_final: 0.6945 (tp30) REVERT: P 69 SER cc_start: 0.7597 (m) cc_final: 0.7294 (p) REVERT: P 80 SER cc_start: 0.7927 (t) cc_final: 0.7537 (m) REVERT: P 169 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7312 (mm) REVERT: Q 34 SER cc_start: 0.8244 (t) cc_final: 0.7968 (t) REVERT: Q 36 GLN cc_start: 0.6700 (tp-100) cc_final: 0.6269 (tp-100) REVERT: Q 80 SER cc_start: 0.8110 (m) cc_final: 0.7546 (p) REVERT: Q 110 ARG cc_start: 0.8234 (ttp80) cc_final: 0.7387 (ttp80) REVERT: Q 198 MET cc_start: 0.6235 (mmt) cc_final: 0.5738 (mmt) REVERT: R 36 GLN cc_start: 0.6769 (tp40) cc_final: 0.6405 (tp40) REVERT: R 43 LEU cc_start: 0.8308 (tp) cc_final: 0.7793 (tp) REVERT: R 60 GLN cc_start: 0.7584 (mm-40) cc_final: 0.7340 (mt0) REVERT: R 67 VAL cc_start: 0.8349 (p) cc_final: 0.8058 (t) outliers start: 61 outliers final: 48 residues processed: 653 average time/residue: 0.1595 time to fit residues: 168.7843 Evaluate side-chains 671 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 616 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 TRP Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain A residue 15 TRP Chi-restraints excluded: chain D residue 15 TRP Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 63 CYS Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain F residue 15 TRP Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 193 SER Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 15 TRP Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 107 GLN Chi-restraints excluded: chain K residue 193 SER Chi-restraints excluded: chain L residue 15 TRP Chi-restraints excluded: chain M residue 15 TRP Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 169 LEU Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 193 SER Chi-restraints excluded: chain O residue 25 GLN Chi-restraints excluded: chain O residue 100 GLN Chi-restraints excluded: chain O residue 138 GLN Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain Q residue 193 SER Chi-restraints excluded: chain R residue 15 TRP Chi-restraints excluded: chain R residue 151 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 319 optimal weight: 2.9990 chunk 64 optimal weight: 0.0870 chunk 19 optimal weight: 1.9990 chunk 197 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 290 optimal weight: 0.9980 chunk 338 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 229 optimal weight: 0.8980 chunk 203 optimal weight: 6.9990 chunk 216 optimal weight: 3.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 GLN A 36 GLN D 73 GLN ** F 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 GLN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN K 107 GLN K 115 GLN ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 47 GLN M 56 GLN M 60 GLN ** P 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 16 GLN Q 39 GLN Q 115 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.182929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.155258 restraints weight = 32117.622| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.52 r_work: 0.3694 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27744 Z= 0.123 Angle : 0.591 9.808 37746 Z= 0.280 Chirality : 0.036 0.225 4122 Planarity : 0.006 0.067 5040 Dihedral : 3.752 18.235 3708 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.04 % Allowed : 19.57 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.15), residues: 3438 helix: 2.00 (0.11), residues: 2394 sheet: None (None), residues: 0 loop : 0.74 (0.22), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 110 TYR 0.013 0.001 TYR R 61 PHE 0.017 0.002 PHE H 37 TRP 0.032 0.002 TRP F 133 HIS 0.005 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00301 (27738) covalent geometry : angle 0.59104 (37746) hydrogen bonds : bond 0.03249 ( 1722) hydrogen bonds : angle 4.02036 ( 5022) Misc. bond : bond 0.00013 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6751.49 seconds wall clock time: 116 minutes 36.48 seconds (6996.48 seconds total)