Starting phenix.real_space_refine on Sat Feb 17 16:34:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vgk_21197/02_2024/6vgk_21197.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vgk_21197/02_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_21197/02_2024/6vgk_21197.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vgk_21197/02_2024/6vgk_21197.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vgk_21197/02_2024/6vgk_21197.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vgk_21197/02_2024/6vgk_21197.pdb" } 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-5238/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: 10.03, per 1000 atoms: 0.52 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: 7.32 Conformation dependent library (CDL) restraints added in 3.9 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: 2.38 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: 6.90 Time building geometry restraints manager: 7.75 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 2.520 nonbonded pdb=" OE2 GLU F 151 " pdb=" NZ LYS M 147 " model vdw 2.394 2.520 nonbonded pdb=" OE2 GLU B 151 " pdb=" NZ LYS I 147 " model vdw 2.395 2.520 nonbonded pdb=" OE2 GLU D 151 " pdb=" NZ LYS K 147 " model vdw 2.395 2.520 nonbonded pdb=" OE2 GLU A 151 " pdb=" NZ LYS H 147 " model vdw 2.395 2.520 ... (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 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.540 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 51.690 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.140 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.540 ------------------------------------------------------------------------------- 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 : 1.940 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: 0.3062 time to fit residues: 186.3556 Evaluate side-chains 277 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 1.880 ------------------------------------------------------------------------------- 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: 6.9990 chunk 185 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 222 optimal weight: 20.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 F 101 GLN 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19495 Z= 0.236 Angle : 0.609 7.794 26362 Z= 0.324 Chirality : 0.043 0.141 3066 Planarity : 0.004 0.057 3430 Dihedral : 4.825 26.672 2730 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.24 % Allowed : 4.37 % Favored : 94.39 % 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: 1.42 (0.14), residues: 1358 sheet: 1.96 (0.33), residues: 231 loop : -0.71 (0.18), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 174 HIS 0.005 0.001 HIS H 117 PHE 0.013 0.002 PHE L 185 TYR 0.014 0.002 TYR C 197 ARG 0.004 0.000 ARG E 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 329 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 304 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 160 MET cc_start: 0.6338 (mtt) cc_final: 0.6135 (mtp) REVERT: D 110 SER cc_start: 0.7751 (t) cc_final: 0.7499 (p) REVERT: F 110 SER cc_start: 0.7603 (t) cc_final: 0.7367 (p) REVERT: F 160 MET cc_start: 0.6409 (mtt) cc_final: 0.6206 (mtp) REVERT: G 110 SER cc_start: 0.7827 (t) cc_final: 0.7597 (p) REVERT: H 75 MET cc_start: 0.7923 (mmt) cc_final: 0.7562 (tpp) REVERT: J 75 MET cc_start: 0.8294 (mmt) cc_final: 0.7914 (mmm) REVERT: K 75 MET cc_start: 0.7671 (mmt) cc_final: 0.7417 (tpp) REVERT: L 75 MET cc_start: 0.7964 (mmt) cc_final: 0.7527 (mmt) REVERT: L 109 LYS cc_start: 0.8167 (mttt) cc_final: 0.7958 (mmtm) REVERT: L 150 MET cc_start: 0.6635 (ttt) cc_final: 0.6415 (ttt) REVERT: M 75 MET cc_start: 0.7994 (mmt) cc_final: 0.7715 (mmm) outliers start: 25 outliers final: 14 residues processed: 318 average time/residue: 0.3275 time to fit residues: 154.4712 Evaluate side-chains 286 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 272 time to evaluate : 1.771 ------------------------------------------------------------------------------- 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 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 J residue 87 ASP Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 87 ASP 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: 3.9990 chunk 69 optimal weight: 6.9990 chunk 185 optimal weight: 8.9990 chunk 151 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 222 optimal weight: 4.9990 chunk 240 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 221 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 178 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 GLN F 136 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 19495 Z= 0.373 Angle : 0.653 7.270 26362 Z= 0.338 Chirality : 0.046 0.153 3066 Planarity : 0.005 0.056 3430 Dihedral : 5.126 29.487 2730 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.94 % Favored : 95.98 % Rotamer: Outliers : 1.59 % Allowed : 6.60 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.16), residues: 2485 helix: 1.76 (0.14), residues: 1351 sheet: 1.56 (0.34), residues: 196 loop : -0.89 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 174 HIS 0.006 0.002 HIS K 117 PHE 0.017 0.002 PHE J 102 TYR 0.016 0.002 TYR B 206 ARG 0.003 0.000 ARG E 40 *********************** 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 336 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 304 time to evaluate : 2.211 Fit side-chains REVERT: B 207 ARG cc_start: 0.7092 (mtt90) cc_final: 0.6744 (mtt180) REVERT: C 70 ARG cc_start: 0.7952 (mtp180) cc_final: 0.7531 (mtp180) REVERT: D 110 SER cc_start: 0.8031 (t) cc_final: 0.7762 (m) REVERT: E 182 ASP cc_start: 0.8592 (m-30) cc_final: 0.8325 (m-30) REVERT: E 207 ARG cc_start: 0.6991 (mtt90) cc_final: 0.6781 (mtt-85) REVERT: F 87 MET cc_start: 0.7165 (tpt) cc_final: 0.6735 (tpt) REVERT: G 110 SER cc_start: 0.8006 (t) cc_final: 0.7707 (m) REVERT: G 136 GLN cc_start: 0.8361 (mt0) cc_final: 0.7823 (mt0) REVERT: H 79 ASP cc_start: 0.8036 (m-30) cc_final: 0.7824 (m-30) REVERT: I 95 MET cc_start: 0.7852 (ttm) cc_final: 0.7527 (ttt) REVERT: M 187 ASP cc_start: 0.8096 (m-30) cc_final: 0.7637 (m-30) outliers start: 32 outliers final: 21 residues processed: 316 average time/residue: 0.3444 time to fit residues: 160.6377 Evaluate side-chains 292 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 271 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain H residue 83 LEU 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 J residue 83 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 87 ASP 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 190 ILE Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 87 ASP Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 190 ILE 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: 5.9990 chunk 167 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 chunk 223 optimal weight: 9.9990 chunk 236 optimal weight: 2.9990 chunk 116 optimal weight: 0.0970 chunk 212 optimal weight: 0.5980 chunk 63 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 GLN F 136 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19495 Z= 0.130 Angle : 0.491 6.499 26362 Z= 0.255 Chirality : 0.040 0.132 3066 Planarity : 0.004 0.047 3430 Dihedral : 4.495 29.647 2730 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.21 % Favored : 97.67 % Rotamer: Outliers : 1.19 % Allowed : 8.13 % Favored : 90.67 % 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: 1.59 (0.17), residues: 2485 helix: 2.19 (0.14), residues: 1365 sheet: 1.30 (0.35), residues: 196 loop : -0.78 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 174 HIS 0.004 0.001 HIS H 117 PHE 0.008 0.001 PHE D 83 TYR 0.007 0.001 TYR G 95 ARG 0.005 0.000 ARG K 119 *********************** 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 313 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 289 time to evaluate : 3.330 Fit side-chains REVERT: B 207 ARG cc_start: 0.7001 (mtt90) cc_final: 0.6765 (mtm-85) REVERT: C 70 ARG cc_start: 0.7858 (mtp180) cc_final: 0.7531 (mtp180) REVERT: C 131 ARG cc_start: 0.6849 (mtp85) cc_final: 0.6640 (mtp180) REVERT: D 91 ASP cc_start: 0.8198 (m-30) cc_final: 0.7987 (m-30) REVERT: D 110 SER cc_start: 0.8081 (t) cc_final: 0.7808 (m) REVERT: F 74 MET cc_start: 0.8195 (ttm) cc_final: 0.7585 (ttt) REVERT: G 87 MET cc_start: 0.6743 (tpt) cc_final: 0.6527 (tpt) REVERT: G 110 SER cc_start: 0.8114 (t) cc_final: 0.7774 (m) REVERT: H 75 MET cc_start: 0.7853 (mmt) cc_final: 0.7526 (tpp) REVERT: M 166 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7221 (mt-10) REVERT: M 187 ASP cc_start: 0.7980 (m-30) cc_final: 0.7567 (m-30) outliers start: 24 outliers final: 10 residues processed: 296 average time/residue: 0.3514 time to fit residues: 154.9682 Evaluate side-chains 282 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 272 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 101 GLN Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 87 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 197 optimal weight: 2.9990 chunk 134 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 202 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 212 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 129 ASN E 136 GLN K 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19495 Z= 0.235 Angle : 0.529 6.208 26362 Z= 0.271 Chirality : 0.042 0.140 3066 Planarity : 0.004 0.046 3430 Dihedral : 4.562 28.262 2730 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.74 % Favored : 96.18 % Rotamer: Outliers : 1.29 % Allowed : 8.13 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.17), residues: 2485 helix: 2.29 (0.14), residues: 1365 sheet: 1.24 (0.35), residues: 196 loop : -0.79 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 174 HIS 0.004 0.001 HIS L 117 PHE 0.012 0.001 PHE G 83 TYR 0.013 0.002 TYR L 91 ARG 0.004 0.000 ARG K 119 *********************** 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 307 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 281 time to evaluate : 2.106 Fit side-chains REVERT: B 207 ARG cc_start: 0.7058 (mtt90) cc_final: 0.6813 (mtm-85) REVERT: C 70 ARG cc_start: 0.7841 (mtp180) cc_final: 0.7529 (mtp180) REVERT: C 101 GLN cc_start: 0.7607 (pt0) cc_final: 0.7368 (pt0) REVERT: C 131 ARG cc_start: 0.6961 (mtp85) cc_final: 0.6670 (mtp180) REVERT: D 110 SER cc_start: 0.8024 (t) cc_final: 0.7751 (m) REVERT: F 87 MET cc_start: 0.6509 (tpt) cc_final: 0.6239 (tpt) REVERT: G 110 SER cc_start: 0.8149 (t) cc_final: 0.7879 (m) REVERT: H 93 MET cc_start: 0.7757 (ptt) cc_final: 0.7551 (ptt) REVERT: I 95 MET cc_start: 0.7629 (ttt) cc_final: 0.7406 (ttp) REVERT: L 187 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7576 (m-30) REVERT: M 75 MET cc_start: 0.7653 (mmm) cc_final: 0.6847 (mmm) REVERT: M 187 ASP cc_start: 0.8136 (m-30) cc_final: 0.7779 (m-30) REVERT: N 79 ASP cc_start: 0.7975 (m-30) cc_final: 0.7546 (m-30) outliers start: 26 outliers final: 15 residues processed: 292 average time/residue: 0.3421 time to fit residues: 147.4680 Evaluate side-chains 289 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 273 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain E residue 101 GLN 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 87 ASP Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 150 MET Chi-restraints excluded: chain L residue 187 ASP Chi-restraints excluded: chain L residue 190 ILE Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 87 ASP 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: 1.9990 chunk 213 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 237 optimal weight: 8.9990 chunk 196 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 19495 Z= 0.306 Angle : 0.572 6.797 26362 Z= 0.293 Chirality : 0.043 0.144 3066 Planarity : 0.004 0.049 3430 Dihedral : 4.809 30.048 2730 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.50 % Favored : 96.22 % Rotamer: Outliers : 1.19 % Allowed : 8.38 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.54 (0.17), residues: 2485 helix: 2.22 (0.14), residues: 1365 sheet: 1.15 (0.35), residues: 196 loop : -0.90 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 174 HIS 0.004 0.001 HIS D 135 PHE 0.012 0.002 PHE F 83 TYR 0.013 0.002 TYR L 91 ARG 0.003 0.000 ARG K 119 *********************** REFINEMENT MACRO_CYCLE 6 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 294 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 270 time to evaluate : 2.262 Fit side-chains REVERT: B 207 ARG cc_start: 0.7112 (mtt90) cc_final: 0.6854 (mtm-85) REVERT: C 101 GLN cc_start: 0.7611 (pt0) cc_final: 0.7342 (pt0) REVERT: C 131 ARG cc_start: 0.6981 (mtp85) cc_final: 0.6685 (mtp180) REVERT: F 87 MET cc_start: 0.6650 (tpt) cc_final: 0.6332 (tpt) REVERT: F 125 MET cc_start: 0.8378 (mtt) cc_final: 0.7977 (mtt) REVERT: G 110 SER cc_start: 0.8100 (t) cc_final: 0.7843 (m) REVERT: H 93 MET cc_start: 0.7779 (ptt) cc_final: 0.7551 (ptt) REVERT: I 95 MET cc_start: 0.7656 (ttt) cc_final: 0.7444 (ttp) REVERT: M 75 MET cc_start: 0.7642 (mmm) cc_final: 0.6745 (mmm) REVERT: M 187 ASP cc_start: 0.8142 (m-30) cc_final: 0.7787 (m-30) outliers start: 24 outliers final: 20 residues processed: 278 average time/residue: 0.3361 time to fit residues: 138.0955 Evaluate side-chains 282 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 262 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain F residue 101 GLN Chi-restraints excluded: chain F residue 200 ILE 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 J residue 190 ILE Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain K residue 190 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 87 ASP Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 190 ILE Chi-restraints excluded: chain M residue 191 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 228 optimal weight: 0.0270 chunk 26 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 199 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 236 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 109 optimal weight: 0.4980 overall best weight: 1.7044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 19495 Z= 0.197 Angle : 0.506 7.080 26362 Z= 0.261 Chirality : 0.041 0.138 3066 Planarity : 0.004 0.047 3430 Dihedral : 4.538 29.733 2730 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.02 % Favored : 96.82 % Rotamer: Outliers : 1.34 % Allowed : 8.28 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.17), residues: 2485 helix: 2.39 (0.14), residues: 1365 sheet: 1.14 (0.35), residues: 196 loop : -0.84 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 174 HIS 0.003 0.001 HIS D 135 PHE 0.010 0.001 PHE H 175 TYR 0.010 0.001 TYR L 91 ARG 0.004 0.000 ARG K 119 *********************** REFINEMENT MACRO_CYCLE 7 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 292 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 265 time to evaluate : 2.226 Fit side-chains REVERT: B 207 ARG cc_start: 0.7034 (mtt90) cc_final: 0.6796 (mtm-85) REVERT: C 101 GLN cc_start: 0.7569 (pt0) cc_final: 0.7348 (pt0) REVERT: C 131 ARG cc_start: 0.6938 (mtp85) cc_final: 0.6688 (mtp180) REVERT: F 74 MET cc_start: 0.8239 (ttm) cc_final: 0.7645 (ttt) REVERT: F 87 MET cc_start: 0.6416 (tpt) cc_final: 0.6194 (tpt) REVERT: G 110 SER cc_start: 0.8129 (t) cc_final: 0.7909 (m) REVERT: H 93 MET cc_start: 0.7811 (ptt) cc_final: 0.7568 (ptt) REVERT: H 109 LYS cc_start: 0.8777 (mttp) cc_final: 0.8524 (mmtt) REVERT: M 187 ASP cc_start: 0.8123 (m-30) cc_final: 0.7721 (m-30) outliers start: 27 outliers final: 22 residues processed: 272 average time/residue: 0.3345 time to fit residues: 134.8951 Evaluate side-chains 277 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 255 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain F residue 200 ILE 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 190 ILE Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 150 MET Chi-restraints excluded: chain L residue 190 ILE Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 87 ASP Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 190 ILE Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain N residue 150 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 146 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 chunk 45 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 160 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 185 optimal weight: 10.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19495 Z= 0.213 Angle : 0.519 7.428 26362 Z= 0.267 Chirality : 0.041 0.137 3066 Planarity : 0.004 0.047 3430 Dihedral : 4.545 31.305 2730 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.34 % Favored : 96.46 % Rotamer: Outliers : 1.44 % Allowed : 8.13 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.71 (0.17), residues: 2485 helix: 2.39 (0.14), residues: 1365 sheet: 0.47 (0.34), residues: 238 loop : -0.73 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 174 HIS 0.003 0.001 HIS D 135 PHE 0.010 0.001 PHE F 83 TYR 0.010 0.001 TYR L 91 ARG 0.004 0.000 ARG K 119 *********************** REFINEMENT MACRO_CYCLE 8 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 288 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 259 time to evaluate : 2.164 Fit side-chains REVERT: B 207 ARG cc_start: 0.7018 (mtt90) cc_final: 0.6793 (mtm-85) REVERT: C 101 GLN cc_start: 0.7590 (pt0) cc_final: 0.7360 (pt0) REVERT: C 131 ARG cc_start: 0.6952 (mtp85) cc_final: 0.6693 (mtp180) REVERT: F 74 MET cc_start: 0.8234 (ttm) cc_final: 0.7630 (ttt) REVERT: F 87 MET cc_start: 0.6506 (tpt) cc_final: 0.6242 (tpt) REVERT: G 110 SER cc_start: 0.8097 (t) cc_final: 0.7897 (m) REVERT: H 93 MET cc_start: 0.7810 (ptt) cc_final: 0.7571 (ptt) REVERT: H 109 LYS cc_start: 0.8777 (mttp) cc_final: 0.8537 (mmtt) REVERT: M 187 ASP cc_start: 0.8124 (m-30) cc_final: 0.7721 (m-30) outliers start: 29 outliers final: 25 residues processed: 269 average time/residue: 0.3296 time to fit residues: 131.3874 Evaluate side-chains 284 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 259 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain F residue 200 ILE 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 H residue 191 THR Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 150 MET Chi-restraints excluded: chain L residue 190 ILE Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 87 ASP Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 190 ILE Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain N residue 150 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 214 optimal weight: 1.9990 chunk 226 optimal weight: 9.9990 chunk 206 optimal weight: 10.0000 chunk 220 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 172 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 198 optimal weight: 2.9990 chunk 208 optimal weight: 9.9990 chunk 219 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19495 Z= 0.272 Angle : 0.553 7.355 26362 Z= 0.282 Chirality : 0.042 0.139 3066 Planarity : 0.004 0.048 3430 Dihedral : 4.683 31.364 2730 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.78 % Favored : 96.02 % Rotamer: Outliers : 1.19 % Allowed : 8.38 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.17), residues: 2485 helix: 2.29 (0.14), residues: 1365 sheet: 1.19 (0.36), residues: 196 loop : -0.85 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 174 HIS 0.003 0.001 HIS A 135 PHE 0.011 0.001 PHE F 83 TYR 0.011 0.002 TYR N 91 ARG 0.003 0.000 ARG K 119 *********************** REFINEMENT MACRO_CYCLE 9 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 281 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 257 time to evaluate : 2.057 Fit side-chains REVERT: B 207 ARG cc_start: 0.7103 (mtt90) cc_final: 0.6881 (mtm-85) REVERT: C 101 GLN cc_start: 0.7597 (pt0) cc_final: 0.7327 (pt0) REVERT: C 131 ARG cc_start: 0.6934 (mtp85) cc_final: 0.6637 (mtp180) REVERT: F 87 MET cc_start: 0.6602 (tpt) cc_final: 0.6331 (tpt) REVERT: G 110 SER cc_start: 0.8061 (t) cc_final: 0.7854 (m) REVERT: H 93 MET cc_start: 0.7857 (ptt) cc_final: 0.7622 (ptt) REVERT: H 109 LYS cc_start: 0.8769 (mttp) cc_final: 0.8511 (mmtt) REVERT: M 187 ASP cc_start: 0.8209 (m-30) cc_final: 0.7810 (m-30) outliers start: 24 outliers final: 24 residues processed: 267 average time/residue: 0.3405 time to fit residues: 134.9803 Evaluate side-chains 279 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 255 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain F residue 200 ILE 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 H residue 191 THR Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 150 MET Chi-restraints excluded: chain L residue 190 ILE Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 87 ASP Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 190 ILE Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain N residue 150 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 144 optimal weight: 0.6980 chunk 232 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 244 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 chunk 194 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 150 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 19495 Z= 0.133 Angle : 0.477 6.629 26362 Z= 0.248 Chirality : 0.039 0.133 3066 Planarity : 0.003 0.047 3430 Dihedral : 4.336 31.169 2730 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.62 % Favored : 97.18 % Rotamer: Outliers : 1.04 % Allowed : 8.58 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.17), residues: 2485 helix: 2.52 (0.14), residues: 1365 sheet: 0.47 (0.34), residues: 238 loop : -0.67 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 174 HIS 0.002 0.001 HIS D 135 PHE 0.008 0.001 PHE F 83 TYR 0.011 0.001 TYR A 95 ARG 0.003 0.000 ARG K 119 ********************** REFINEMENT MACRO_CYCLE 10 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 282 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 261 time to evaluate : 2.056 Fit side-chains REVERT: C 101 GLN cc_start: 0.7653 (pt0) cc_final: 0.7428 (pt0) REVERT: C 131 ARG cc_start: 0.6902 (mtp85) cc_final: 0.6680 (mtp180) REVERT: F 74 MET cc_start: 0.8216 (ttm) cc_final: 0.7661 (ttt) REVERT: G 87 MET cc_start: 0.6803 (tpt) cc_final: 0.6540 (tpt) REVERT: H 109 LYS cc_start: 0.8777 (mttp) cc_final: 0.8519 (mmtt) REVERT: K 95 MET cc_start: 0.8143 (ttm) cc_final: 0.7720 (ttt) REVERT: L 162 ILE cc_start: 0.6943 (mp) cc_final: 0.6721 (mp) REVERT: M 187 ASP cc_start: 0.8051 (m-30) cc_final: 0.7597 (m-30) REVERT: N 79 ASP cc_start: 0.7943 (m-30) cc_final: 0.7451 (m-30) outliers start: 21 outliers final: 18 residues processed: 270 average time/residue: 0.3607 time to fit residues: 145.3943 Evaluate side-chains 272 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 254 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 150 MET Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 87 ASP Chi-restraints excluded: chain M residue 190 ILE Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain N residue 150 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 154 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 59 optimal weight: 0.0370 chunk 179 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 54 optimal weight: 0.2980 chunk 194 optimal weight: 8.9990 chunk 81 optimal weight: 0.5980 chunk 199 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.168787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.139879 restraints weight = 19821.201| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.75 r_work: 0.3290 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 19495 Z= 0.113 Angle : 0.458 6.387 26362 Z= 0.239 Chirality : 0.039 0.131 3066 Planarity : 0.003 0.046 3430 Dihedral : 4.114 29.517 2730 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.82 % Favored : 96.98 % Rotamer: Outliers : 0.69 % Allowed : 9.18 % Favored : 90.13 % 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: 1.93 (0.17), residues: 2485 helix: 2.51 (0.14), residues: 1386 sheet: 0.55 (0.34), residues: 238 loop : -0.58 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 174 HIS 0.002 0.001 HIS B 171 PHE 0.011 0.001 PHE J 102 TYR 0.015 0.001 TYR A 95 ARG 0.004 0.000 ARG K 119 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3984.88 seconds wall clock time: 72 minutes 54.57 seconds (4374.57 seconds total)