Starting phenix.real_space_refine on Wed Aug 7 04:19:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vgk_21197/08_2024/6vgk_21197.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vgk_21197/08_2024/6vgk_21197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vgk_21197/08_2024/6vgk_21197.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vgk_21197/08_2024/6vgk_21197.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vgk_21197/08_2024/6vgk_21197.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vgk_21197/08_2024/6vgk_21197.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.498 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 119 5.16 5 C 12089 2.51 5 N 3276 2.21 5 O 3738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 18": "OD1" <-> "OD2" Residue "H TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 18": "OD1" <-> "OD2" Residue "I TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 18": "OD1" <-> "OD2" Residue "J TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 18": "OD1" <-> "OD2" Residue "K TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 18": "OD1" <-> "OD2" Residue "L TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 18": "OD1" <-> "OD2" Residue "M TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 18": "OD1" <-> "OD2" Residue "N TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 19222 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1389 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain: "B" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1389 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain: "C" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1389 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain: "D" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1389 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain: "E" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1389 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain: "F" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1389 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain: "G" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1389 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain: "H" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "I" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "J" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "K" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "L" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "M" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "N" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Time building chain proxies: 10.52, per 1000 atoms: 0.55 Number of scatterers: 19222 At special positions: 0 Unit cell: (117.66, 117.66, 104.94, 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 119 16.00 O 3738 8.00 N 3276 7.00 C 12089 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.31 Conformation dependent library (CDL) restraints added in 3.7 seconds 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4676 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 28 sheets defined 52.9% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 49 through 67 removed outlier: 4.170A pdb=" N ASP A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 96 Processing helix chain 'A' and resid 111 through 118 removed outlier: 3.565A pdb=" N LEU A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 173 Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'B' and resid 33 through 39 Processing helix chain 'B' and resid 49 through 67 removed outlier: 4.169A pdb=" N ASP B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 96 Processing helix chain 'B' and resid 111 through 118 removed outlier: 3.565A pdb=" N LEU B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 173 Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'C' and resid 33 through 39 Processing helix chain 'C' and resid 49 through 67 removed outlier: 4.168A pdb=" N ASP C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 96 Processing helix chain 'C' and resid 111 through 118 removed outlier: 3.565A pdb=" N LEU C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 173 Processing helix chain 'C' and resid 175 through 184 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'D' and resid 33 through 39 Processing helix chain 'D' and resid 49 through 67 removed outlier: 4.169A pdb=" N ASP D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 96 Processing helix chain 'D' and resid 111 through 118 removed outlier: 3.565A pdb=" N LEU D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 173 Processing helix chain 'D' and resid 175 through 184 Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'E' and resid 33 through 39 Processing helix chain 'E' and resid 49 through 67 removed outlier: 4.169A pdb=" N ASP E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 96 Processing helix chain 'E' and resid 111 through 118 removed outlier: 3.565A pdb=" N LEU E 115 " --> pdb=" O ALA E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 173 Processing helix chain 'E' and resid 175 through 184 Processing helix chain 'E' and resid 192 through 197 Processing helix chain 'F' and resid 33 through 39 Processing helix chain 'F' and resid 49 through 67 removed outlier: 4.168A pdb=" N ASP F 55 " --> pdb=" O ALA F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 96 Processing helix chain 'F' and resid 111 through 118 removed outlier: 3.565A pdb=" N LEU F 115 " --> pdb=" O ALA F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 173 Processing helix chain 'F' and resid 175 through 184 Processing helix chain 'F' and resid 192 through 197 Processing helix chain 'G' and resid 33 through 39 Processing helix chain 'G' and resid 49 through 67 removed outlier: 4.169A pdb=" N ASP G 55 " --> pdb=" O ALA G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 96 Processing helix chain 'G' and resid 111 through 118 removed outlier: 3.564A pdb=" N LEU G 115 " --> pdb=" O ALA G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 173 Processing helix chain 'G' and resid 175 through 184 Processing helix chain 'G' and resid 192 through 197 Processing helix chain 'H' and resid 16 through 26 Processing helix chain 'H' and resid 37 through 55 Processing helix chain 'H' and resid 70 through 84 Processing helix chain 'H' and resid 98 through 106 Processing helix chain 'H' and resid 132 through 159 removed outlier: 3.991A pdb=" N ILE H 138 " --> pdb=" O ALA H 134 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU H 141 " --> pdb=" O ALA H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 170 Processing helix chain 'H' and resid 177 through 183 Processing helix chain 'I' and resid 16 through 26 Processing helix chain 'I' and resid 37 through 55 Processing helix chain 'I' and resid 70 through 84 Processing helix chain 'I' and resid 98 through 106 Processing helix chain 'I' and resid 132 through 159 removed outlier: 3.991A pdb=" N ILE I 138 " --> pdb=" O ALA I 134 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU I 141 " --> pdb=" O ALA I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 170 Processing helix chain 'I' and resid 177 through 183 Processing helix chain 'J' and resid 16 through 26 Processing helix chain 'J' and resid 37 through 55 Processing helix chain 'J' and resid 70 through 84 Processing helix chain 'J' and resid 98 through 106 Processing helix chain 'J' and resid 132 through 159 removed outlier: 3.992A pdb=" N ILE J 138 " --> pdb=" O ALA J 134 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU J 141 " --> pdb=" O ALA J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 170 Processing helix chain 'J' and resid 177 through 183 Processing helix chain 'K' and resid 16 through 26 Processing helix chain 'K' and resid 37 through 55 Processing helix chain 'K' and resid 70 through 84 Processing helix chain 'K' and resid 98 through 106 Processing helix chain 'K' and resid 132 through 159 removed outlier: 3.991A pdb=" N ILE K 138 " --> pdb=" O ALA K 134 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU K 141 " --> pdb=" O ALA K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 170 Processing helix chain 'K' and resid 177 through 183 Processing helix chain 'L' and resid 16 through 26 Processing helix chain 'L' and resid 37 through 55 Processing helix chain 'L' and resid 70 through 84 Processing helix chain 'L' and resid 98 through 106 Processing helix chain 'L' and resid 132 through 159 removed outlier: 3.990A pdb=" N ILE L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU L 141 " --> pdb=" O ALA L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 170 Processing helix chain 'L' and resid 177 through 183 Processing helix chain 'M' and resid 16 through 26 Processing helix chain 'M' and resid 37 through 55 Processing helix chain 'M' and resid 70 through 84 Processing helix chain 'M' and resid 98 through 106 Processing helix chain 'M' and resid 132 through 159 removed outlier: 3.991A pdb=" N ILE M 138 " --> pdb=" O ALA M 134 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU M 141 " --> pdb=" O ALA M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 170 Processing helix chain 'M' and resid 177 through 183 Processing helix chain 'N' and resid 16 through 26 Processing helix chain 'N' and resid 37 through 55 Processing helix chain 'N' and resid 70 through 84 Processing helix chain 'N' and resid 98 through 106 Processing helix chain 'N' and resid 132 through 159 removed outlier: 3.991A pdb=" N ILE N 138 " --> pdb=" O ALA N 134 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU N 141 " --> pdb=" O ALA N 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 170 Processing helix chain 'N' and resid 177 through 183 Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 44 removed outlier: 5.175A pdb=" N SER A 78 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLN A 107 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG A 131 " --> pdb=" O CYS A 104 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY A 106 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU A 133 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA A 108 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 44 removed outlier: 5.175A pdb=" N SER A 78 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLN A 107 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N MET A 125 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N THR A 102 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 41 through 44 removed outlier: 5.175A pdb=" N SER B 78 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLN B 107 " --> pdb=" O SER B 78 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG B 131 " --> pdb=" O CYS B 104 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY B 106 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU B 133 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA B 108 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 41 through 44 removed outlier: 5.175A pdb=" N SER B 78 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLN B 107 " --> pdb=" O SER B 78 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N MET B 125 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N THR B 102 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 41 through 44 removed outlier: 5.176A pdb=" N SER C 78 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLN C 107 " --> pdb=" O SER C 78 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG C 131 " --> pdb=" O CYS C 104 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY C 106 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU C 133 " --> pdb=" O GLY C 106 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA C 108 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 41 through 44 removed outlier: 5.176A pdb=" N SER C 78 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLN C 107 " --> pdb=" O SER C 78 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N MET C 125 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N THR C 102 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 41 through 44 removed outlier: 5.175A pdb=" N SER D 78 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLN D 107 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ARG D 131 " --> pdb=" O CYS D 104 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY D 106 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU D 133 " --> pdb=" O GLY D 106 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA D 108 " --> pdb=" O LEU D 133 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 41 through 44 removed outlier: 5.175A pdb=" N SER D 78 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLN D 107 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N MET D 125 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N THR D 102 " --> pdb=" O MET D 125 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 41 through 44 removed outlier: 5.176A pdb=" N SER E 78 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLN E 107 " --> pdb=" O SER E 78 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG E 131 " --> pdb=" O CYS E 104 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY E 106 " --> pdb=" O ARG E 131 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU E 133 " --> pdb=" O GLY E 106 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA E 108 " --> pdb=" O LEU E 133 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 41 through 44 removed outlier: 5.176A pdb=" N SER E 78 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLN E 107 " --> pdb=" O SER E 78 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N MET E 125 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N THR E 102 " --> pdb=" O MET E 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 41 through 44 removed outlier: 5.175A pdb=" N SER F 78 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLN F 107 " --> pdb=" O SER F 78 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARG F 131 " --> pdb=" O CYS F 104 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY F 106 " --> pdb=" O ARG F 131 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU F 133 " --> pdb=" O GLY F 106 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA F 108 " --> pdb=" O LEU F 133 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 41 through 44 removed outlier: 5.175A pdb=" N SER F 78 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLN F 107 " --> pdb=" O SER F 78 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N MET F 125 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N THR F 102 " --> pdb=" O MET F 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 41 through 44 removed outlier: 5.175A pdb=" N SER G 78 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLN G 107 " --> pdb=" O SER G 78 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG G 131 " --> pdb=" O CYS G 104 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY G 106 " --> pdb=" O ARG G 131 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU G 133 " --> pdb=" O GLY G 106 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA G 108 " --> pdb=" O LEU G 133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 41 through 44 removed outlier: 5.175A pdb=" N SER G 78 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLN G 107 " --> pdb=" O SER G 78 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N MET G 125 " --> pdb=" O ILE G 100 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N THR G 102 " --> pdb=" O MET G 125 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 29 through 32 removed outlier: 7.971A pdb=" N SER H 66 " --> pdb=" O MET H 93 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N MET H 95 " --> pdb=" O SER H 66 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ARG H 119 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY H 94 " --> pdb=" O ARG H 119 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU H 121 " --> pdb=" O GLY H 94 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA H 96 " --> pdb=" O LEU H 121 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET H 122 " --> pdb=" O ARG H 173 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG H 173 " --> pdb=" O MET H 122 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 29 through 32 removed outlier: 7.971A pdb=" N SER H 66 " --> pdb=" O MET H 93 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N MET H 95 " --> pdb=" O SER H 66 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N TYR H 113 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N THR H 90 " --> pdb=" O TYR H 113 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 29 through 32 removed outlier: 7.971A pdb=" N SER I 66 " --> pdb=" O MET I 93 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N MET I 95 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ARG I 119 " --> pdb=" O ALA I 92 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY I 94 " --> pdb=" O ARG I 119 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU I 121 " --> pdb=" O GLY I 94 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA I 96 " --> pdb=" O LEU I 121 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET I 122 " --> pdb=" O ARG I 173 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG I 173 " --> pdb=" O MET I 122 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 29 through 32 removed outlier: 7.971A pdb=" N SER I 66 " --> pdb=" O MET I 93 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N MET I 95 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N TYR I 113 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N THR I 90 " --> pdb=" O TYR I 113 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 29 through 32 removed outlier: 7.971A pdb=" N SER J 66 " --> pdb=" O MET J 93 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N MET J 95 " --> pdb=" O SER J 66 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ARG J 119 " --> pdb=" O ALA J 92 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY J 94 " --> pdb=" O ARG J 119 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU J 121 " --> pdb=" O GLY J 94 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA J 96 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET J 122 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ARG J 173 " --> pdb=" O MET J 122 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 29 through 32 removed outlier: 7.971A pdb=" N SER J 66 " --> pdb=" O MET J 93 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N MET J 95 " --> pdb=" O SER J 66 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N TYR J 113 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N THR J 90 " --> pdb=" O TYR J 113 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 29 through 32 removed outlier: 7.970A pdb=" N SER K 66 " --> pdb=" O MET K 93 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N MET K 95 " --> pdb=" O SER K 66 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ARG K 119 " --> pdb=" O ALA K 92 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY K 94 " --> pdb=" O ARG K 119 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU K 121 " --> pdb=" O GLY K 94 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA K 96 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET K 122 " --> pdb=" O ARG K 173 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ARG K 173 " --> pdb=" O MET K 122 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 29 through 32 removed outlier: 7.970A pdb=" N SER K 66 " --> pdb=" O MET K 93 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N MET K 95 " --> pdb=" O SER K 66 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N TYR K 113 " --> pdb=" O ILE K 88 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR K 90 " --> pdb=" O TYR K 113 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 29 through 32 removed outlier: 7.971A pdb=" N SER L 66 " --> pdb=" O MET L 93 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N MET L 95 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ARG L 119 " --> pdb=" O ALA L 92 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY L 94 " --> pdb=" O ARG L 119 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU L 121 " --> pdb=" O GLY L 94 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA L 96 " --> pdb=" O LEU L 121 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET L 122 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG L 173 " --> pdb=" O MET L 122 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 29 through 32 removed outlier: 7.971A pdb=" N SER L 66 " --> pdb=" O MET L 93 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N MET L 95 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N TYR L 113 " --> pdb=" O ILE L 88 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR L 90 " --> pdb=" O TYR L 113 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 29 through 32 removed outlier: 7.971A pdb=" N SER M 66 " --> pdb=" O MET M 93 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N MET M 95 " --> pdb=" O SER M 66 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ARG M 119 " --> pdb=" O ALA M 92 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY M 94 " --> pdb=" O ARG M 119 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU M 121 " --> pdb=" O GLY M 94 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA M 96 " --> pdb=" O LEU M 121 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET M 122 " --> pdb=" O ARG M 173 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ARG M 173 " --> pdb=" O MET M 122 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 29 through 32 removed outlier: 7.971A pdb=" N SER M 66 " --> pdb=" O MET M 93 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N MET M 95 " --> pdb=" O SER M 66 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N TYR M 113 " --> pdb=" O ILE M 88 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N THR M 90 " --> pdb=" O TYR M 113 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 29 through 32 removed outlier: 7.970A pdb=" N SER N 66 " --> pdb=" O MET N 93 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N MET N 95 " --> pdb=" O SER N 66 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ARG N 119 " --> pdb=" O ALA N 92 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY N 94 " --> pdb=" O ARG N 119 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU N 121 " --> pdb=" O GLY N 94 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA N 96 " --> pdb=" O LEU N 121 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET N 122 " --> pdb=" O ARG N 173 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG N 173 " --> pdb=" O MET N 122 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 29 through 32 removed outlier: 7.970A pdb=" N SER N 66 " --> pdb=" O MET N 93 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N MET N 95 " --> pdb=" O SER N 66 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N TYR N 113 " --> pdb=" O ILE N 88 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR N 90 " --> pdb=" O TYR N 113 " (cutoff:3.500A) 1218 hydrogen bonds defined for protein. 3612 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: 6.46 Time building geometry restraints manager: 9.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4094 1.32 - 1.45: 5222 1.45 - 1.58: 9934 1.58 - 1.71: 28 1.71 - 1.84: 217 Bond restraints: 19495 Sorted by residual: bond pdb=" CB LEU F 86 " pdb=" CG LEU F 86 " ideal model delta sigma weight residual 1.530 1.635 -0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" CB LEU C 86 " pdb=" CG LEU C 86 " ideal model delta sigma weight residual 1.530 1.634 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" CB LEU B 86 " pdb=" CG LEU B 86 " ideal model delta sigma weight residual 1.530 1.634 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" CB LEU A 86 " pdb=" CG LEU A 86 " ideal model delta sigma weight residual 1.530 1.634 -0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" CB LEU D 86 " pdb=" CG LEU D 86 " ideal model delta sigma weight residual 1.530 1.634 -0.104 2.00e-02 2.50e+03 2.70e+01 ... (remaining 19490 not shown) Histogram of bond angle deviations from ideal: 99.38 - 109.43: 3539 109.43 - 119.48: 13596 119.48 - 129.53: 9171 129.53 - 139.58: 49 139.58 - 149.63: 7 Bond angle restraints: 26362 Sorted by residual: angle pdb=" C MET H 93 " pdb=" N GLY H 94 " pdb=" CA GLY H 94 " ideal model delta sigma weight residual 121.41 149.63 -28.22 1.96e+00 2.60e-01 2.07e+02 angle pdb=" C MET K 93 " pdb=" N GLY K 94 " pdb=" CA GLY K 94 " ideal model delta sigma weight residual 121.41 149.62 -28.21 1.96e+00 2.60e-01 2.07e+02 angle pdb=" C MET M 93 " pdb=" N GLY M 94 " pdb=" CA GLY M 94 " ideal model delta sigma weight residual 121.41 149.61 -28.20 1.96e+00 2.60e-01 2.07e+02 angle pdb=" C MET J 93 " pdb=" N GLY J 94 " pdb=" CA GLY J 94 " ideal model delta sigma weight residual 121.41 149.60 -28.19 1.96e+00 2.60e-01 2.07e+02 angle pdb=" C MET L 93 " pdb=" N GLY L 94 " pdb=" CA GLY L 94 " ideal model delta sigma weight residual 121.41 149.59 -28.18 1.96e+00 2.60e-01 2.07e+02 ... (remaining 26357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.31: 11156 13.31 - 26.63: 541 26.63 - 39.94: 140 39.94 - 53.25: 28 53.25 - 66.56: 42 Dihedral angle restraints: 11907 sinusoidal: 4648 harmonic: 7259 Sorted by residual: dihedral pdb=" CA PRO D 32 " pdb=" C PRO D 32 " pdb=" N TYR D 33 " pdb=" CA TYR D 33 " ideal model delta harmonic sigma weight residual -180.00 -149.78 -30.22 0 5.00e+00 4.00e-02 3.65e+01 dihedral pdb=" CA PRO E 32 " pdb=" C PRO E 32 " pdb=" N TYR E 33 " pdb=" CA TYR E 33 " ideal model delta harmonic sigma weight residual -180.00 -149.80 -30.20 0 5.00e+00 4.00e-02 3.65e+01 dihedral pdb=" CA PRO G 32 " pdb=" C PRO G 32 " pdb=" N TYR G 33 " pdb=" CA TYR G 33 " ideal model delta harmonic sigma weight residual 180.00 -149.81 -30.19 0 5.00e+00 4.00e-02 3.64e+01 ... (remaining 11904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1881 0.068 - 0.136: 830 0.136 - 0.204: 264 0.204 - 0.272: 74 0.272 - 0.341: 17 Chirality restraints: 3066 Sorted by residual: chirality pdb=" CA GLU K 35 " pdb=" N GLU K 35 " pdb=" C GLU K 35 " pdb=" CB GLU K 35 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA GLU L 35 " pdb=" N GLU L 35 " pdb=" C GLU L 35 " pdb=" CB GLU L 35 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CA GLU I 35 " pdb=" N GLU I 35 " pdb=" C GLU I 35 " pdb=" CB GLU I 35 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 3063 not shown) Planarity restraints: 3430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 110 " 0.068 2.00e-02 2.50e+03 1.42e-01 2.02e+02 pdb=" C SER A 110 " -0.246 2.00e-02 2.50e+03 pdb=" O SER A 110 " 0.094 2.00e-02 2.50e+03 pdb=" N ALA A 111 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER G 110 " 0.068 2.00e-02 2.50e+03 1.42e-01 2.01e+02 pdb=" C SER G 110 " -0.245 2.00e-02 2.50e+03 pdb=" O SER G 110 " 0.094 2.00e-02 2.50e+03 pdb=" N ALA G 111 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 110 " -0.068 2.00e-02 2.50e+03 1.42e-01 2.01e+02 pdb=" C SER C 110 " 0.245 2.00e-02 2.50e+03 pdb=" O SER C 110 " -0.094 2.00e-02 2.50e+03 pdb=" N ALA C 111 " -0.083 2.00e-02 2.50e+03 ... (remaining 3427 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 7868 2.90 - 3.40: 19209 3.40 - 3.90: 33527 3.90 - 4.40: 40202 4.40 - 4.90: 63297 Nonbonded interactions: 164103 Sorted by model distance: nonbonded pdb=" OE2 GLU E 151 " pdb=" NZ LYS L 147 " model vdw 2.394 3.120 nonbonded pdb=" OE2 GLU F 151 " pdb=" NZ LYS M 147 " model vdw 2.394 3.120 nonbonded pdb=" OE2 GLU B 151 " pdb=" NZ LYS I 147 " model vdw 2.395 3.120 nonbonded pdb=" OE2 GLU D 151 " pdb=" NZ LYS K 147 " model vdw 2.395 3.120 nonbonded pdb=" OE2 GLU A 151 " pdb=" NZ LYS H 147 " model vdw 2.395 3.120 ... (remaining 164098 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 53.630 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 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 : 0.020 0.137 19495 Z= 1.299 Angle : 1.841 28.225 26362 Z= 1.226 Chirality : 0.088 0.341 3066 Planarity : 0.014 0.142 3430 Dihedral : 9.906 66.564 7231 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 0.31 Ramachandran Plot: Outliers : 0.85 % Allowed : 3.38 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.15), residues: 2485 helix: -0.49 (0.11), residues: 1386 sheet: 2.64 (0.30), residues: 231 loop : -0.23 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.007 TRP J 174 HIS 0.010 0.003 HIS L 123 PHE 0.019 0.004 PHE E 43 TYR 0.038 0.008 TYR K 183 ARG 0.006 0.001 ARG E 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 2.145 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.6697 (mmmt) cc_final: 0.6487 (tptp) REVERT: B 35 LYS cc_start: 0.6843 (mmmt) cc_final: 0.6364 (tptp) REVERT: C 35 LYS cc_start: 0.6600 (mmmt) cc_final: 0.5992 (tptp) REVERT: C 164 MET cc_start: 0.6174 (ttm) cc_final: 0.5939 (ttt) REVERT: D 35 LYS cc_start: 0.6727 (mmmt) cc_final: 0.5974 (tptp) REVERT: D 136 GLN cc_start: 0.8155 (mt0) cc_final: 0.7822 (mt0) REVERT: E 35 LYS cc_start: 0.6755 (mmmt) cc_final: 0.6157 (tptp) REVERT: F 125 MET cc_start: 0.7738 (mtm) cc_final: 0.7527 (mtt) REVERT: H 70 SER cc_start: 0.8558 (m) cc_final: 0.8156 (p) REVERT: H 75 MET cc_start: 0.7948 (mmt) cc_final: 0.7536 (mmm) REVERT: J 70 SER cc_start: 0.8532 (m) cc_final: 0.8250 (p) REVERT: J 75 MET cc_start: 0.8130 (mmt) cc_final: 0.7765 (mmm) REVERT: K 70 SER cc_start: 0.8507 (m) cc_final: 0.8195 (p) REVERT: K 75 MET cc_start: 0.8010 (mmt) cc_final: 0.7639 (mmt) REVERT: L 70 SER cc_start: 0.8265 (m) cc_final: 0.8003 (p) REVERT: L 75 MET cc_start: 0.8105 (mmt) cc_final: 0.7779 (mmt) REVERT: M 70 SER cc_start: 0.8367 (m) cc_final: 0.8030 (p) REVERT: M 75 MET cc_start: 0.8001 (mmt) cc_final: 0.7600 (mmm) REVERT: N 70 SER cc_start: 0.8468 (m) cc_final: 0.8129 (p) outliers start: 0 outliers final: 0 residues processed: 400 average time/residue: 0.3157 time to fit residues: 191.7875 Evaluate side-chains 277 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 206 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 142 optimal weight: 4.9990 chunk 222 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 59 GLN C 59 GLN D 59 GLN D 77 ASN H 123 HIS I 123 HIS J 123 HIS K 123 HIS L 123 HIS M 123 HIS N 123 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19495 Z= 0.233 Angle : 0.615 7.682 26362 Z= 0.327 Chirality : 0.044 0.144 3066 Planarity : 0.005 0.056 3430 Dihedral : 4.852 26.473 2730 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.99 % Allowed : 4.56 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.16), residues: 2485 helix: 1.41 (0.14), residues: 1358 sheet: 1.91 (0.33), residues: 231 loop : -0.67 (0.18), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 174 HIS 0.004 0.001 HIS H 117 PHE 0.015 0.002 PHE L 185 TYR 0.014 0.002 TYR C 197 ARG 0.003 0.000 ARG G 207 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 301 time to evaluate : 3.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 GLN cc_start: 0.7247 (pt0) cc_final: 0.7046 (pt0) REVERT: B 136 GLN cc_start: 0.8402 (mt0) cc_final: 0.7971 (mm-40) REVERT: D 110 SER cc_start: 0.7921 (t) cc_final: 0.7565 (p) REVERT: D 125 MET cc_start: 0.8116 (mtt) cc_final: 0.7900 (mtt) REVERT: E 123 LYS cc_start: 0.7687 (mttt) cc_final: 0.7461 (mttp) REVERT: F 110 SER cc_start: 0.7756 (t) cc_final: 0.7382 (m) REVERT: G 110 SER cc_start: 0.8078 (t) cc_final: 0.7764 (m) REVERT: H 75 MET cc_start: 0.7954 (mmt) cc_final: 0.7647 (tpp) REVERT: I 75 MET cc_start: 0.7573 (mmm) cc_final: 0.7369 (mmm) REVERT: J 75 MET cc_start: 0.8287 (mmt) cc_final: 0.7918 (mmm) REVERT: K 75 MET cc_start: 0.7654 (mmt) cc_final: 0.7315 (tpp) REVERT: M 75 MET cc_start: 0.7981 (mmt) cc_final: 0.7715 (mmm) outliers start: 20 outliers final: 10 residues processed: 311 average time/residue: 0.3618 time to fit residues: 168.7986 Evaluate side-chains 281 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 271 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain N residue 36 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 123 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 222 optimal weight: 30.0000 chunk 240 optimal weight: 9.9990 chunk 198 optimal weight: 0.0060 chunk 221 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 178 optimal weight: 0.6980 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 GLN E 136 GLN F 136 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19495 Z= 0.184 Angle : 0.534 8.301 26362 Z= 0.277 Chirality : 0.041 0.139 3066 Planarity : 0.004 0.047 3430 Dihedral : 4.590 26.909 2730 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.24 % Allowed : 5.95 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.16), residues: 2485 helix: 1.91 (0.14), residues: 1365 sheet: 1.39 (0.33), residues: 231 loop : -0.70 (0.18), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 174 HIS 0.004 0.001 HIS E 135 PHE 0.010 0.001 PHE M 175 TYR 0.011 0.001 TYR C 197 ARG 0.003 0.000 ARG E 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 270 time to evaluate : 1.973 Fit side-chains REVERT: B 101 GLN cc_start: 0.7313 (pt0) cc_final: 0.7093 (pt0) REVERT: B 136 GLN cc_start: 0.8431 (mt0) cc_final: 0.8195 (mt0) REVERT: D 37 PHE cc_start: 0.7806 (t80) cc_final: 0.7549 (t80) REVERT: D 110 SER cc_start: 0.7966 (t) cc_final: 0.7594 (m) REVERT: D 125 MET cc_start: 0.8208 (mtt) cc_final: 0.7991 (mtt) REVERT: E 37 PHE cc_start: 0.7756 (t80) cc_final: 0.7485 (t80) REVERT: H 75 MET cc_start: 0.7927 (mmt) cc_final: 0.7603 (tpp) REVERT: I 95 MET cc_start: 0.8087 (ttm) cc_final: 0.7803 (ttt) REVERT: J 75 MET cc_start: 0.8255 (mmt) cc_final: 0.7766 (mmm) REVERT: K 75 MET cc_start: 0.7754 (mmt) cc_final: 0.7468 (tpp) REVERT: K 79 ASP cc_start: 0.7741 (m-30) cc_final: 0.7500 (m-30) REVERT: M 75 MET cc_start: 0.7939 (mmt) cc_final: 0.7701 (mmm) outliers start: 25 outliers final: 15 residues processed: 279 average time/residue: 0.3292 time to fit residues: 138.3908 Evaluate side-chains 269 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 254 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 190 ILE Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 83 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 220 optimal weight: 0.7980 chunk 167 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 223 optimal weight: 7.9990 chunk 236 optimal weight: 8.9990 chunk 116 optimal weight: 0.9980 chunk 212 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19495 Z= 0.192 Angle : 0.522 6.802 26362 Z= 0.269 Chirality : 0.041 0.145 3066 Planarity : 0.004 0.044 3430 Dihedral : 4.578 27.117 2730 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.49 % Allowed : 6.85 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.17), residues: 2485 helix: 2.13 (0.14), residues: 1365 sheet: 1.08 (0.34), residues: 231 loop : -0.60 (0.19), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 174 HIS 0.004 0.001 HIS H 117 PHE 0.010 0.001 PHE F 83 TYR 0.010 0.001 TYR K 91 ARG 0.003 0.000 ARG D 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 266 time to evaluate : 1.965 Fit side-chains REVERT: B 101 GLN cc_start: 0.7413 (pt0) cc_final: 0.7201 (pt0) REVERT: D 110 SER cc_start: 0.7989 (t) cc_final: 0.7676 (m) REVERT: E 37 PHE cc_start: 0.7831 (t80) cc_final: 0.7611 (t80) REVERT: E 101 GLN cc_start: 0.7155 (pt0) cc_final: 0.6912 (pt0) REVERT: F 123 LYS cc_start: 0.8366 (mtmm) cc_final: 0.8154 (mttp) REVERT: I 95 MET cc_start: 0.7971 (ttm) cc_final: 0.7671 (ttt) REVERT: M 166 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7283 (mt-10) REVERT: N 79 ASP cc_start: 0.7992 (m-30) cc_final: 0.7580 (m-30) outliers start: 30 outliers final: 15 residues processed: 274 average time/residue: 0.3017 time to fit residues: 126.5397 Evaluate side-chains 270 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 255 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 190 ILE Chi-restraints excluded: chain N residue 36 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 197 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 176 optimal weight: 0.6980 chunk 97 optimal weight: 8.9990 chunk 202 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 212 optimal weight: 0.5980 chunk 59 optimal weight: 9.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19495 Z= 0.283 Angle : 0.574 6.638 26362 Z= 0.296 Chirality : 0.043 0.152 3066 Planarity : 0.004 0.047 3430 Dihedral : 4.802 28.644 2730 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.90 % Favored : 96.06 % Rotamer: Outliers : 1.49 % Allowed : 7.29 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.17), residues: 2485 helix: 2.15 (0.14), residues: 1365 sheet: 1.22 (0.35), residues: 196 loop : -0.67 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 174 HIS 0.004 0.001 HIS K 117 PHE 0.013 0.002 PHE G 83 TYR 0.015 0.002 TYR N 91 ARG 0.002 0.000 ARG B 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 266 time to evaluate : 2.413 Fit side-chains REVERT: F 87 MET cc_start: 0.6572 (tpt) cc_final: 0.6281 (tpt) REVERT: H 93 MET cc_start: 0.7866 (ptt) cc_final: 0.7645 (ptt) REVERT: H 156 GLU cc_start: 0.7867 (tt0) cc_final: 0.7666 (tt0) REVERT: I 95 MET cc_start: 0.8111 (ttm) cc_final: 0.7781 (ttt) REVERT: N 79 ASP cc_start: 0.8038 (m-30) cc_final: 0.7544 (m-30) outliers start: 30 outliers final: 20 residues processed: 276 average time/residue: 0.3308 time to fit residues: 139.7743 Evaluate side-chains 272 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 252 time to evaluate : 2.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain F residue 101 GLN Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 150 MET Chi-restraints excluded: chain L residue 190 ILE Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 190 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 79 optimal weight: 6.9990 chunk 213 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 237 optimal weight: 0.8980 chunk 196 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.4240 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: