Starting phenix.real_space_refine on Mon Mar 18 03:27:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kr2_23000/03_2024/7kr2_23000.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kr2_23000/03_2024/7kr2_23000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kr2_23000/03_2024/7kr2_23000.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kr2_23000/03_2024/7kr2_23000.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kr2_23000/03_2024/7kr2_23000.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kr2_23000/03_2024/7kr2_23000.pdb" } resolution = 3.2 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= 0.016 sd= 0.231 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 112 5.16 5 C 12530 2.51 5 N 3318 2.21 5 O 3752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19712 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1408 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain breaks: 2 Chain: "B" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1408 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain breaks: 2 Chain: "C" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1408 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain breaks: 2 Chain: "D" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1408 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain breaks: 2 Chain: "E" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1408 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain breaks: 2 Chain: "F" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1408 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain breaks: 2 Chain: "G" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1408 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain breaks: 2 Chain: "H" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1408 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain breaks: 2 Chain: "I" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1408 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain breaks: 2 Chain: "J" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1408 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain breaks: 2 Chain: "K" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1408 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain breaks: 2 Chain: "L" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1408 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain breaks: 2 Chain: "M" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1408 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain breaks: 2 Chain: "N" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1408 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain breaks: 2 Time building chain proxies: 10.29, per 1000 atoms: 0.52 Number of scatterers: 19712 At special positions: 0 Unit cell: (115.54, 113.42, 115.54, 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 112 16.00 O 3752 8.00 N 3318 7.00 C 12530 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: 7.29 Conformation dependent library (CDL) restraints added in 3.2 seconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4732 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 42 sheets defined 48.9% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 41 through 59 Processing helix chain 'A' and resid 74 through 88 Processing helix chain 'A' and resid 102 through 110 Processing helix chain 'A' and resid 147 through 165 removed outlier: 3.545A pdb=" N ILE A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 175 Processing helix chain 'A' and resid 182 through 190 Processing helix chain 'B' and resid 24 through 30 Processing helix chain 'B' and resid 41 through 59 Processing helix chain 'B' and resid 74 through 88 Processing helix chain 'B' and resid 102 through 110 Processing helix chain 'B' and resid 147 through 165 removed outlier: 3.545A pdb=" N ILE B 152 " --> pdb=" O GLU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 175 Processing helix chain 'B' and resid 182 through 190 Processing helix chain 'C' and resid 24 through 30 Processing helix chain 'C' and resid 41 through 59 Processing helix chain 'C' and resid 74 through 88 Processing helix chain 'C' and resid 102 through 110 Processing helix chain 'C' and resid 147 through 165 removed outlier: 3.546A pdb=" N ILE C 152 " --> pdb=" O GLU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 175 Processing helix chain 'C' and resid 182 through 190 Processing helix chain 'D' and resid 24 through 30 Processing helix chain 'D' and resid 41 through 59 Processing helix chain 'D' and resid 74 through 88 Processing helix chain 'D' and resid 102 through 110 Processing helix chain 'D' and resid 147 through 165 removed outlier: 3.545A pdb=" N ILE D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 175 Processing helix chain 'D' and resid 182 through 190 Processing helix chain 'E' and resid 24 through 30 Processing helix chain 'E' and resid 41 through 59 Processing helix chain 'E' and resid 74 through 88 Processing helix chain 'E' and resid 102 through 110 Processing helix chain 'E' and resid 147 through 165 removed outlier: 3.545A pdb=" N ILE E 152 " --> pdb=" O GLU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 175 Processing helix chain 'E' and resid 182 through 190 Processing helix chain 'F' and resid 24 through 30 Processing helix chain 'F' and resid 41 through 59 Processing helix chain 'F' and resid 74 through 88 Processing helix chain 'F' and resid 102 through 110 Processing helix chain 'F' and resid 147 through 165 removed outlier: 3.545A pdb=" N ILE F 152 " --> pdb=" O GLU F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 175 Processing helix chain 'F' and resid 182 through 190 Processing helix chain 'G' and resid 24 through 30 Processing helix chain 'G' and resid 41 through 59 Processing helix chain 'G' and resid 74 through 88 Processing helix chain 'G' and resid 102 through 110 Processing helix chain 'G' and resid 147 through 165 removed outlier: 3.545A pdb=" N ILE G 152 " --> pdb=" O GLU G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 175 Processing helix chain 'G' and resid 182 through 190 Processing helix chain 'H' and resid 24 through 30 Processing helix chain 'H' and resid 41 through 59 Processing helix chain 'H' and resid 74 through 88 Processing helix chain 'H' and resid 102 through 110 Processing helix chain 'H' and resid 147 through 165 removed outlier: 3.544A pdb=" N ILE H 152 " --> pdb=" O GLU H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 175 Processing helix chain 'H' and resid 182 through 190 Processing helix chain 'I' and resid 24 through 30 Processing helix chain 'I' and resid 41 through 59 Processing helix chain 'I' and resid 74 through 88 Processing helix chain 'I' and resid 102 through 110 Processing helix chain 'I' and resid 147 through 165 removed outlier: 3.545A pdb=" N ILE I 152 " --> pdb=" O GLU I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 175 Processing helix chain 'I' and resid 182 through 190 Processing helix chain 'J' and resid 24 through 30 Processing helix chain 'J' and resid 41 through 59 Processing helix chain 'J' and resid 74 through 88 Processing helix chain 'J' and resid 102 through 110 Processing helix chain 'J' and resid 147 through 165 removed outlier: 3.545A pdb=" N ILE J 152 " --> pdb=" O GLU J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 175 Processing helix chain 'J' and resid 182 through 190 Processing helix chain 'K' and resid 24 through 30 Processing helix chain 'K' and resid 41 through 59 Processing helix chain 'K' and resid 74 through 88 Processing helix chain 'K' and resid 102 through 110 Processing helix chain 'K' and resid 147 through 165 removed outlier: 3.545A pdb=" N ILE K 152 " --> pdb=" O GLU K 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 175 Processing helix chain 'K' and resid 182 through 190 Processing helix chain 'L' and resid 24 through 30 Processing helix chain 'L' and resid 41 through 59 Processing helix chain 'L' and resid 74 through 88 Processing helix chain 'L' and resid 102 through 110 Processing helix chain 'L' and resid 147 through 165 removed outlier: 3.545A pdb=" N ILE L 152 " --> pdb=" O GLU L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 175 Processing helix chain 'L' and resid 182 through 190 Processing helix chain 'M' and resid 24 through 30 Processing helix chain 'M' and resid 41 through 59 Processing helix chain 'M' and resid 74 through 88 Processing helix chain 'M' and resid 102 through 110 Processing helix chain 'M' and resid 147 through 165 removed outlier: 3.545A pdb=" N ILE M 152 " --> pdb=" O GLU M 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 167 through 175 Processing helix chain 'M' and resid 182 through 190 Processing helix chain 'N' and resid 24 through 30 Processing helix chain 'N' and resid 41 through 59 Processing helix chain 'N' and resid 74 through 88 Processing helix chain 'N' and resid 102 through 110 Processing helix chain 'N' and resid 147 through 165 removed outlier: 3.544A pdb=" N ILE N 152 " --> pdb=" O GLU N 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 175 Processing helix chain 'N' and resid 182 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER A 70 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN A 99 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG A 123 " --> pdb=" O CYS A 96 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY A 98 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET A 125 " --> pdb=" O GLY A 98 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA A 100 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER A 70 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN A 99 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N PHE A 117 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR A 94 " --> pdb=" O PHE A 117 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 13 Processing sheet with id=AA5, first strand: chain 'B' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER B 70 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN B 99 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG B 123 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY B 98 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET B 125 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA B 100 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER B 70 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN B 99 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N PHE B 117 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR B 94 " --> pdb=" O PHE B 117 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 13 Processing sheet with id=AA8, first strand: chain 'C' and resid 33 through 37 removed outlier: 5.192A pdb=" N SER C 70 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN C 99 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG C 123 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY C 98 " --> pdb=" O ARG C 123 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET C 125 " --> pdb=" O GLY C 98 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA C 100 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 33 through 37 removed outlier: 5.192A pdb=" N SER C 70 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN C 99 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N PHE C 117 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR C 94 " --> pdb=" O PHE C 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 13 Processing sheet with id=AB2, first strand: chain 'D' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER D 70 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN D 99 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG D 123 " --> pdb=" O CYS D 96 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY D 98 " --> pdb=" O ARG D 123 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET D 125 " --> pdb=" O GLY D 98 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA D 100 " --> pdb=" O MET D 125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER D 70 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN D 99 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N PHE D 117 " --> pdb=" O VAL D 92 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR D 94 " --> pdb=" O PHE D 117 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 13 Processing sheet with id=AB5, first strand: chain 'E' and resid 33 through 37 removed outlier: 5.192A pdb=" N SER E 70 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN E 99 " --> pdb=" O SER E 70 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG E 123 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY E 98 " --> pdb=" O ARG E 123 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N MET E 125 " --> pdb=" O GLY E 98 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA E 100 " --> pdb=" O MET E 125 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 33 through 37 removed outlier: 5.192A pdb=" N SER E 70 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN E 99 " --> pdb=" O SER E 70 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N PHE E 117 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR E 94 " --> pdb=" O PHE E 117 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 10 through 13 Processing sheet with id=AB8, first strand: chain 'F' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER F 70 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN F 99 " --> pdb=" O SER F 70 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG F 123 " --> pdb=" O CYS F 96 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY F 98 " --> pdb=" O ARG F 123 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET F 125 " --> pdb=" O GLY F 98 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA F 100 " --> pdb=" O MET F 125 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER F 70 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN F 99 " --> pdb=" O SER F 70 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N PHE F 117 " --> pdb=" O VAL F 92 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR F 94 " --> pdb=" O PHE F 117 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AC2, first strand: chain 'G' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER G 70 " --> pdb=" O LEU G 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN G 99 " --> pdb=" O SER G 70 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG G 123 " --> pdb=" O CYS G 96 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY G 98 " --> pdb=" O ARG G 123 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N MET G 125 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA G 100 " --> pdb=" O MET G 125 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER G 70 " --> pdb=" O LEU G 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN G 99 " --> pdb=" O SER G 70 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N PHE G 117 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N THR G 94 " --> pdb=" O PHE G 117 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 10 through 13 Processing sheet with id=AC5, first strand: chain 'H' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER H 70 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N GLN H 99 " --> pdb=" O SER H 70 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG H 123 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY H 98 " --> pdb=" O ARG H 123 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N MET H 125 " --> pdb=" O GLY H 98 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA H 100 " --> pdb=" O MET H 125 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER H 70 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N GLN H 99 " --> pdb=" O SER H 70 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N PHE H 117 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR H 94 " --> pdb=" O PHE H 117 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 10 through 13 Processing sheet with id=AC8, first strand: chain 'I' and resid 33 through 37 removed outlier: 5.192A pdb=" N SER I 70 " --> pdb=" O LEU I 97 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLN I 99 " --> pdb=" O SER I 70 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG I 123 " --> pdb=" O CYS I 96 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY I 98 " --> pdb=" O ARG I 123 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET I 125 " --> pdb=" O GLY I 98 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA I 100 " --> pdb=" O MET I 125 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 33 through 37 removed outlier: 5.192A pdb=" N SER I 70 " --> pdb=" O LEU I 97 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLN I 99 " --> pdb=" O SER I 70 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N PHE I 117 " --> pdb=" O VAL I 92 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR I 94 " --> pdb=" O PHE I 117 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 10 through 13 Processing sheet with id=AD2, first strand: chain 'J' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER J 70 " --> pdb=" O LEU J 97 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N GLN J 99 " --> pdb=" O SER J 70 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG J 123 " --> pdb=" O CYS J 96 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY J 98 " --> pdb=" O ARG J 123 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET J 125 " --> pdb=" O GLY J 98 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA J 100 " --> pdb=" O MET J 125 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER J 70 " --> pdb=" O LEU J 97 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N GLN J 99 " --> pdb=" O SER J 70 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N PHE J 117 " --> pdb=" O VAL J 92 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR J 94 " --> pdb=" O PHE J 117 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 10 through 13 Processing sheet with id=AD5, first strand: chain 'K' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER K 70 " --> pdb=" O LEU K 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN K 99 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG K 123 " --> pdb=" O CYS K 96 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY K 98 " --> pdb=" O ARG K 123 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET K 125 " --> pdb=" O GLY K 98 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA K 100 " --> pdb=" O MET K 125 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER K 70 " --> pdb=" O LEU K 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN K 99 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N PHE K 117 " --> pdb=" O VAL K 92 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR K 94 " --> pdb=" O PHE K 117 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AD8, first strand: chain 'L' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER L 70 " --> pdb=" O LEU L 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN L 99 " --> pdb=" O SER L 70 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG L 123 " --> pdb=" O CYS L 96 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY L 98 " --> pdb=" O ARG L 123 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET L 125 " --> pdb=" O GLY L 98 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA L 100 " --> pdb=" O MET L 125 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER L 70 " --> pdb=" O LEU L 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN L 99 " --> pdb=" O SER L 70 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N PHE L 117 " --> pdb=" O VAL L 92 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR L 94 " --> pdb=" O PHE L 117 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 10 through 13 Processing sheet with id=AE2, first strand: chain 'M' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER M 70 " --> pdb=" O LEU M 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN M 99 " --> pdb=" O SER M 70 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG M 123 " --> pdb=" O CYS M 96 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY M 98 " --> pdb=" O ARG M 123 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET M 125 " --> pdb=" O GLY M 98 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA M 100 " --> pdb=" O MET M 125 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER M 70 " --> pdb=" O LEU M 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN M 99 " --> pdb=" O SER M 70 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N PHE M 117 " --> pdb=" O VAL M 92 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N THR M 94 " --> pdb=" O PHE M 117 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 10 through 13 Processing sheet with id=AE5, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.192A pdb=" N SER N 70 " --> pdb=" O LEU N 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN N 99 " --> pdb=" O SER N 70 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG N 123 " --> pdb=" O CYS N 96 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY N 98 " --> pdb=" O ARG N 123 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N MET N 125 " --> pdb=" O GLY N 98 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA N 100 " --> pdb=" O MET N 125 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.192A pdb=" N SER N 70 " --> pdb=" O LEU N 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN N 99 " --> pdb=" O SER N 70 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N PHE N 117 " --> pdb=" O VAL N 92 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR N 94 " --> pdb=" O PHE N 117 " (cutoff:3.500A) 1148 hydrogen bonds defined for protein. 3360 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.18 Time building geometry restraints manager: 7.94 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: 4640 1.32 - 1.45: 5442 1.45 - 1.58: 9728 1.58 - 1.71: 0 1.71 - 1.85: 196 Bond restraints: 20006 Sorted by residual: bond pdb=" CB ASP N 23 " pdb=" CG ASP N 23 " ideal model delta sigma weight residual 1.516 1.395 0.121 2.50e-02 1.60e+03 2.35e+01 bond pdb=" CB ASP J 23 " pdb=" CG ASP J 23 " ideal model delta sigma weight residual 1.516 1.395 0.121 2.50e-02 1.60e+03 2.34e+01 bond pdb=" CB ASP G 23 " pdb=" CG ASP G 23 " ideal model delta sigma weight residual 1.516 1.395 0.121 2.50e-02 1.60e+03 2.34e+01 bond pdb=" CB ASP C 23 " pdb=" CG ASP C 23 " ideal model delta sigma weight residual 1.516 1.395 0.121 2.50e-02 1.60e+03 2.33e+01 bond pdb=" CB ASP B 23 " pdb=" CG ASP B 23 " ideal model delta sigma weight residual 1.516 1.395 0.121 2.50e-02 1.60e+03 2.33e+01 ... (remaining 20001 not shown) Histogram of bond angle deviations from ideal: 99.04 - 105.64: 538 105.64 - 112.25: 9204 112.25 - 118.86: 6962 118.86 - 125.47: 9987 125.47 - 132.08: 245 Bond angle restraints: 26936 Sorted by residual: angle pdb=" C ASN J 59 " pdb=" N PRO J 60 " pdb=" CA PRO J 60 " ideal model delta sigma weight residual 119.56 127.04 -7.48 1.02e+00 9.61e-01 5.37e+01 angle pdb=" C ASN I 59 " pdb=" N PRO I 60 " pdb=" CA PRO I 60 " ideal model delta sigma weight residual 119.56 127.02 -7.46 1.02e+00 9.61e-01 5.36e+01 angle pdb=" C ASN H 59 " pdb=" N PRO H 60 " pdb=" CA PRO H 60 " ideal model delta sigma weight residual 119.56 127.02 -7.46 1.02e+00 9.61e-01 5.35e+01 angle pdb=" C ASN F 59 " pdb=" N PRO F 60 " pdb=" CA PRO F 60 " ideal model delta sigma weight residual 119.56 127.02 -7.46 1.02e+00 9.61e-01 5.35e+01 angle pdb=" C ASN C 59 " pdb=" N PRO C 60 " pdb=" CA PRO C 60 " ideal model delta sigma weight residual 119.56 126.99 -7.43 1.02e+00 9.61e-01 5.31e+01 ... (remaining 26931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.90: 11690 15.90 - 31.79: 420 31.79 - 47.69: 112 47.69 - 63.59: 84 63.59 - 79.49: 28 Dihedral angle restraints: 12334 sinusoidal: 5082 harmonic: 7252 Sorted by residual: dihedral pdb=" CA ASP N 23 " pdb=" CB ASP N 23 " pdb=" CG ASP N 23 " pdb=" OD1 ASP N 23 " ideal model delta sinusoidal sigma weight residual -30.00 -85.62 55.62 1 2.00e+01 2.50e-03 1.04e+01 dihedral pdb=" CA ASP C 23 " pdb=" CB ASP C 23 " pdb=" CG ASP C 23 " pdb=" OD1 ASP C 23 " ideal model delta sinusoidal sigma weight residual -30.00 -85.59 55.59 1 2.00e+01 2.50e-03 1.04e+01 dihedral pdb=" CA ASP I 23 " pdb=" CB ASP I 23 " pdb=" CG ASP I 23 " pdb=" OD1 ASP I 23 " ideal model delta sinusoidal sigma weight residual -30.00 -85.57 55.57 1 2.00e+01 2.50e-03 1.04e+01 ... (remaining 12331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1661 0.064 - 0.128: 1000 0.128 - 0.192: 276 0.192 - 0.256: 129 0.256 - 0.320: 14 Chirality restraints: 3080 Sorted by residual: chirality pdb=" CA LYS D 89 " pdb=" N LYS D 89 " pdb=" C LYS D 89 " pdb=" CB LYS D 89 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA LYS B 89 " pdb=" N LYS B 89 " pdb=" C LYS B 89 " pdb=" CB LYS B 89 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA LYS K 89 " pdb=" N LYS K 89 " pdb=" C LYS K 89 " pdb=" CB LYS K 89 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 3077 not shown) Planarity restraints: 3486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR N 25 " -0.037 2.00e-02 2.50e+03 2.03e-02 8.26e+00 pdb=" CG TYR N 25 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR N 25 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR N 25 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR N 25 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR N 25 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR N 25 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR N 25 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 25 " -0.037 2.00e-02 2.50e+03 2.03e-02 8.24e+00 pdb=" CG TYR B 25 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR B 25 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 25 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR B 25 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR B 25 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 25 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 25 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 25 " 0.037 2.00e-02 2.50e+03 2.03e-02 8.22e+00 pdb=" CG TYR I 25 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR I 25 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR I 25 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR I 25 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR I 25 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR I 25 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR I 25 " 0.029 2.00e-02 2.50e+03 ... (remaining 3483 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 8201 2.91 - 3.41: 19931 3.41 - 3.91: 34285 3.91 - 4.40: 40654 4.40 - 4.90: 64907 Nonbonded interactions: 167978 Sorted by model distance: nonbonded pdb=" OD1 ASP B 61 " pdb=" NZ LYS B 89 " model vdw 2.415 2.520 nonbonded pdb=" OD1 ASP L 61 " pdb=" NZ LYS L 89 " model vdw 2.416 2.520 nonbonded pdb=" OD1 ASP J 61 " pdb=" NZ LYS J 89 " model vdw 2.416 2.520 nonbonded pdb=" OD1 ASP K 61 " pdb=" NZ LYS K 89 " model vdw 2.416 2.520 nonbonded pdb=" OD1 ASP H 61 " pdb=" NZ LYS H 89 " model vdw 2.416 2.520 ... (remaining 167973 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' selection = 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: 0.830 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: 4.570 Check model and map are aligned: 0.280 Set scattering table: 0.190 Process input model: 50.650 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 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 0.121 20006 Z= 1.278 Angle : 1.650 9.125 26936 Z= 1.135 Chirality : 0.090 0.320 3080 Planarity : 0.009 0.046 3486 Dihedral : 11.595 79.487 7602 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.65 % Allowed : 0.65 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.15), residues: 2408 helix: -0.59 (0.12), residues: 1246 sheet: 1.61 (0.30), residues: 308 loop : -0.95 (0.17), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS H 127 PHE 0.026 0.008 PHE H 22 TYR 0.037 0.009 TYR I 25 ARG 0.007 0.001 ARG K 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 933 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 919 time to evaluate : 2.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 40 VAL cc_start: 0.8262 (t) cc_final: 0.7967 (p) REVERT: F 40 VAL cc_start: 0.8056 (t) cc_final: 0.7841 (p) REVERT: F 125 MET cc_start: 0.7684 (ttm) cc_final: 0.7389 (ttp) REVERT: F 145 HIS cc_start: 0.6023 (m170) cc_final: 0.5805 (m90) REVERT: N 23 ASP cc_start: 0.6637 (p0) cc_final: 0.6302 (p0) REVERT: N 125 MET cc_start: 0.7555 (ttm) cc_final: 0.7345 (ttp) outliers start: 14 outliers final: 0 residues processed: 919 average time/residue: 0.3820 time to fit residues: 493.9455 Evaluate side-chains 413 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 186 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 216 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 HIS B 46 ASN B 86 ASN B 128 GLN C 46 ASN D 46 ASN ** D 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 86 ASN E 128 GLN F 46 ASN F 128 GLN G 46 ASN G 86 ASN G 128 GLN H 46 ASN H 86 ASN H 128 GLN I 46 ASN J 46 ASN J 51 GLN J 128 GLN K 46 ASN K 86 ASN K 128 GLN K 157 ASN L 46 ASN L 128 GLN N 86 ASN N 128 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20006 Z= 0.224 Angle : 0.633 6.108 26936 Z= 0.330 Chirality : 0.046 0.151 3080 Planarity : 0.004 0.029 3486 Dihedral : 4.814 24.447 2660 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.90 % Allowed : 11.61 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.17), residues: 2408 helix: 1.05 (0.15), residues: 1260 sheet: 1.21 (0.35), residues: 196 loop : -0.11 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS D 127 PHE 0.037 0.002 PHE F 54 TYR 0.021 0.001 TYR I 82 ARG 0.006 0.001 ARG I 173 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 456 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.7475 (mmm) cc_final: 0.7213 (mmm) REVERT: C 181 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.7386 (mtp) REVERT: D 79 MET cc_start: 0.7554 (mmm) cc_final: 0.7248 (mmt) REVERT: E 181 MET cc_start: 0.7370 (mtp) cc_final: 0.7138 (mtm) REVERT: F 79 MET cc_start: 0.7561 (mmm) cc_final: 0.7248 (mmm) REVERT: F 125 MET cc_start: 0.7637 (ttm) cc_final: 0.7392 (ttp) REVERT: F 166 ARG cc_start: 0.8316 (mmt90) cc_final: 0.8080 (mmm160) REVERT: G 23 ASP cc_start: 0.6622 (OUTLIER) cc_final: 0.6318 (p0) REVERT: M 23 ASP cc_start: 0.6903 (OUTLIER) cc_final: 0.6700 (p0) outliers start: 63 outliers final: 29 residues processed: 491 average time/residue: 0.4477 time to fit residues: 307.4464 Evaluate side-chains 411 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 379 time to evaluate : 2.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 181 MET Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 42 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 216 optimal weight: 0.8980 chunk 233 optimal weight: 9.9990 chunk 192 optimal weight: 0.0170 chunk 214 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 145 HIS B 86 ASN C 128 GLN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS E 46 ASN E 86 ASN F 46 ASN F 145 HIS G 46 ASN G 86 ASN G 145 HIS H 46 ASN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 ASN I 128 GLN J 46 ASN K 46 ASN K 86 ASN L 86 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20006 Z= 0.202 Angle : 0.580 7.544 26936 Z= 0.291 Chirality : 0.044 0.146 3080 Planarity : 0.004 0.050 3486 Dihedral : 4.521 25.058 2660 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.63 % Allowed : 13.78 % Favored : 83.59 % 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: 1.08 (0.17), residues: 2408 helix: 1.43 (0.15), residues: 1260 sheet: 0.94 (0.35), residues: 196 loop : -0.22 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS D 127 PHE 0.036 0.002 PHE F 54 TYR 0.026 0.001 TYR D 82 ARG 0.007 0.000 ARG J 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 411 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.7314 (mmm) cc_final: 0.7057 (mmm) REVERT: C 23 ASP cc_start: 0.6872 (OUTLIER) cc_final: 0.6528 (p0) REVERT: F 166 ARG cc_start: 0.8345 (mmt90) cc_final: 0.8120 (mmm160) REVERT: G 23 ASP cc_start: 0.6744 (OUTLIER) cc_final: 0.6494 (p0) outliers start: 57 outliers final: 31 residues processed: 443 average time/residue: 0.4654 time to fit residues: 285.5771 Evaluate side-chains 391 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 358 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 23 ASP Chi-restraints excluded: chain N residue 42 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 0.0970 chunk 162 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 145 optimal weight: 0.9980 chunk 217 optimal weight: 5.9990 chunk 230 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 205 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 145 HIS ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 86 ASN F 145 HIS G 46 ASN G 86 ASN G 145 HIS H 46 ASN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 ASN J 145 HIS L 46 ASN L 86 ASN N 86 ASN N 128 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20006 Z= 0.201 Angle : 0.566 6.698 26936 Z= 0.283 Chirality : 0.043 0.149 3080 Planarity : 0.004 0.039 3486 Dihedral : 4.433 24.742 2660 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.86 % Allowed : 14.75 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.05 (0.17), residues: 2408 helix: 1.49 (0.15), residues: 1260 sheet: 0.81 (0.34), residues: 196 loop : -0.33 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 145 PHE 0.032 0.002 PHE N 54 TYR 0.026 0.002 TYR H 82 ARG 0.008 0.001 ARG K 173 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 396 time to evaluate : 2.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.7283 (mmm) cc_final: 0.7002 (mmm) REVERT: C 23 ASP cc_start: 0.6833 (OUTLIER) cc_final: 0.6453 (p0) REVERT: E 181 MET cc_start: 0.7469 (mtp) cc_final: 0.7143 (mtm) REVERT: G 23 ASP cc_start: 0.6807 (OUTLIER) cc_final: 0.6550 (p0) REVERT: G 46 ASN cc_start: 0.7001 (t160) cc_final: 0.6759 (t0) REVERT: K 166 ARG cc_start: 0.8475 (mmt90) cc_final: 0.8233 (mmm160) REVERT: L 177 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.6749 (ptt90) outliers start: 62 outliers final: 38 residues processed: 428 average time/residue: 0.4411 time to fit residues: 257.2221 Evaluate side-chains 403 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 362 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain H residue 46 ASN Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 145 HIS Chi-restraints excluded: chain K residue 181 MET Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 160 MET Chi-restraints excluded: chain L residue 177 ARG Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 23 ASP Chi-restraints excluded: chain N residue 42 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 171 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 196 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 206 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 86 ASN A 145 HIS B 86 ASN ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 ASN G 128 GLN G 145 HIS H 46 ASN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 ASN J 127 HIS J 145 HIS K 86 ASN K 127 HIS L 46 ASN L 86 ASN L 127 HIS M 86 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 20006 Z= 0.381 Angle : 0.643 6.405 26936 Z= 0.324 Chirality : 0.046 0.159 3080 Planarity : 0.004 0.046 3486 Dihedral : 4.607 24.487 2660 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.32 % Allowed : 14.33 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.17), residues: 2408 helix: 1.30 (0.15), residues: 1274 sheet: 0.17 (0.33), residues: 224 loop : -0.37 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 145 PHE 0.041 0.003 PHE E 54 TYR 0.027 0.002 TYR H 82 ARG 0.010 0.001 ARG N 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 372 time to evaluate : 2.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.7571 (mmm) cc_final: 0.7346 (mmm) REVERT: C 23 ASP cc_start: 0.7141 (OUTLIER) cc_final: 0.6812 (p0) REVERT: D 79 MET cc_start: 0.7310 (mmm) cc_final: 0.7075 (mmm) REVERT: G 23 ASP cc_start: 0.6868 (OUTLIER) cc_final: 0.6642 (p0) REVERT: G 181 MET cc_start: 0.7628 (mtm) cc_final: 0.7423 (mtm) REVERT: L 79 MET cc_start: 0.7501 (mmm) cc_final: 0.7285 (mmm) outliers start: 72 outliers final: 43 residues processed: 415 average time/residue: 0.4425 time to fit residues: 251.3073 Evaluate side-chains 395 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 350 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 145 HIS Chi-restraints excluded: chain L residue 160 MET Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 23 ASP Chi-restraints excluded: chain N residue 42 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 230 optimal weight: 0.8980 chunk 191 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 HIS B 86 ASN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 ASN G 86 ASN H 46 ASN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 ASN J 46 ASN J 145 HIS K 86 ASN L 86 ASN M 86 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20006 Z= 0.194 Angle : 0.570 9.188 26936 Z= 0.283 Chirality : 0.043 0.158 3080 Planarity : 0.003 0.027 3486 Dihedral : 4.447 25.035 2660 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.67 % Allowed : 15.53 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.17), residues: 2408 helix: 1.48 (0.15), residues: 1274 sheet: 0.28 (0.33), residues: 224 loop : -0.38 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 145 PHE 0.034 0.002 PHE D 54 TYR 0.029 0.001 TYR H 82 ARG 0.008 0.000 ARG I 173 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 386 time to evaluate : 2.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.7272 (mmm) cc_final: 0.6999 (mmm) REVERT: C 23 ASP cc_start: 0.6839 (OUTLIER) cc_final: 0.6473 (p0) REVERT: D 79 MET cc_start: 0.7180 (mmm) cc_final: 0.6960 (mmm) REVERT: F 40 VAL cc_start: 0.8470 (t) cc_final: 0.8236 (p) REVERT: F 166 ARG cc_start: 0.8449 (mmt90) cc_final: 0.8232 (mmm160) REVERT: G 23 ASP cc_start: 0.6693 (OUTLIER) cc_final: 0.6420 (p0) REVERT: L 79 MET cc_start: 0.7352 (mmm) cc_final: 0.7085 (mmm) outliers start: 58 outliers final: 31 residues processed: 418 average time/residue: 0.4319 time to fit residues: 247.2444 Evaluate side-chains 400 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 367 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 160 MET Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 145 HIS Chi-restraints excluded: chain L residue 160 MET Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 23 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 131 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 193 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 229 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 105 optimal weight: 0.0170 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 ASN J 145 HIS K 86 ASN L 86 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20006 Z= 0.246 Angle : 0.587 7.470 26936 Z= 0.293 Chirality : 0.044 0.172 3080 Planarity : 0.003 0.027 3486 Dihedral : 4.446 25.546 2660 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.35 % Allowed : 16.77 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.17), residues: 2408 helix: 1.49 (0.15), residues: 1274 sheet: 0.17 (0.33), residues: 224 loop : -0.41 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS M 145 PHE 0.039 0.002 PHE I 54 TYR 0.024 0.002 TYR H 82 ARG 0.009 0.000 ARG I 173 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 377 time to evaluate : 2.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.7393 (mmm) cc_final: 0.7157 (mmm) REVERT: C 23 ASP cc_start: 0.6949 (OUTLIER) cc_final: 0.6547 (p0) REVERT: D 19 GLU cc_start: 0.7098 (mp0) cc_final: 0.6700 (mp0) REVERT: F 166 ARG cc_start: 0.8484 (mmt90) cc_final: 0.8253 (mmm160) REVERT: G 23 ASP cc_start: 0.6656 (OUTLIER) cc_final: 0.6400 (p0) REVERT: G 166 ARG cc_start: 0.8535 (mmt90) cc_final: 0.8310 (mmm160) REVERT: L 79 MET cc_start: 0.7437 (mmm) cc_final: 0.7176 (mmm) outliers start: 51 outliers final: 36 residues processed: 410 average time/residue: 0.4440 time to fit residues: 249.7377 Evaluate side-chains 399 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 361 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 160 MET Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 187 LYS Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 46 ASN Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 181 MET Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 145 HIS Chi-restraints excluded: chain L residue 160 MET Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 23 ASP Chi-restraints excluded: chain N residue 42 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 ASN G 86 ASN J 145 HIS K 86 ASN L 86 ASN N 46 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20006 Z= 0.224 Angle : 0.588 7.356 26936 Z= 0.293 Chirality : 0.044 0.146 3080 Planarity : 0.003 0.031 3486 Dihedral : 4.419 25.122 2660 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.17 % Allowed : 17.00 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.17), residues: 2408 helix: 1.57 (0.15), residues: 1260 sheet: 0.14 (0.33), residues: 224 loop : -0.51 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 145 PHE 0.032 0.002 PHE D 54 TYR 0.029 0.002 TYR B 82 ARG 0.013 0.000 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 388 time to evaluate : 2.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.7315 (mmm) cc_final: 0.7026 (mmm) REVERT: B 86 ASN cc_start: 0.7800 (OUTLIER) cc_final: 0.7508 (m110) REVERT: C 23 ASP cc_start: 0.6915 (OUTLIER) cc_final: 0.6548 (p0) REVERT: E 181 MET cc_start: 0.7615 (mtm) cc_final: 0.7377 (mtm) REVERT: F 40 VAL cc_start: 0.8449 (t) cc_final: 0.8211 (p) REVERT: F 166 ARG cc_start: 0.8527 (mmt90) cc_final: 0.8311 (mmm160) REVERT: G 23 ASP cc_start: 0.6624 (OUTLIER) cc_final: 0.6346 (p0) REVERT: G 166 ARG cc_start: 0.8592 (mmt90) cc_final: 0.8334 (mmm160) REVERT: I 151 LYS cc_start: 0.6481 (ttpp) cc_final: 0.6261 (ttpp) REVERT: L 79 MET cc_start: 0.7446 (mmm) cc_final: 0.7151 (mmm) outliers start: 47 outliers final: 32 residues processed: 412 average time/residue: 0.4301 time to fit residues: 244.8496 Evaluate side-chains 404 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 369 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 86 ASN Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 160 MET Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 187 LYS Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 46 ASN Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 181 MET Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 145 HIS Chi-restraints excluded: chain L residue 160 MET Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 23 ASP Chi-restraints excluded: chain N residue 42 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 167 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 193 optimal weight: 5.9990 chunk 202 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN C 86 ASN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 ASN J 86 ASN J 145 HIS K 86 ASN L 86 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20006 Z= 0.252 Angle : 0.604 7.308 26936 Z= 0.301 Chirality : 0.044 0.156 3080 Planarity : 0.003 0.033 3486 Dihedral : 4.470 25.142 2660 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.07 % Allowed : 17.19 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.17), residues: 2408 helix: 1.54 (0.15), residues: 1260 sheet: -0.01 (0.33), residues: 224 loop : -0.57 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 145 PHE 0.036 0.002 PHE M 54 TYR 0.023 0.002 TYR B 82 ARG 0.013 0.001 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 381 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.7426 (mmm) cc_final: 0.7143 (mmm) REVERT: B 86 ASN cc_start: 0.7892 (OUTLIER) cc_final: 0.7629 (m110) REVERT: C 23 ASP cc_start: 0.6828 (OUTLIER) cc_final: 0.6434 (p0) REVERT: D 79 MET cc_start: 0.6806 (mmm) cc_final: 0.6596 (mmm) REVERT: E 181 MET cc_start: 0.7641 (mtm) cc_final: 0.7400 (mtm) REVERT: F 166 ARG cc_start: 0.8554 (mmt90) cc_final: 0.8333 (mmm160) REVERT: G 23 ASP cc_start: 0.6625 (OUTLIER) cc_final: 0.6361 (p0) REVERT: G 166 ARG cc_start: 0.8622 (mmt90) cc_final: 0.8279 (mmm160) outliers start: 45 outliers final: 34 residues processed: 409 average time/residue: 0.4326 time to fit residues: 243.8631 Evaluate side-chains 413 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 376 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 86 ASN Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 160 MET Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 187 LYS Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 46 ASN Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 181 MET Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 23 ASP Chi-restraints excluded: chain N residue 42 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 0.9980 chunk 137 optimal weight: 0.0980 chunk 107 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 237 optimal weight: 0.6980 chunk 218 optimal weight: 5.9990 chunk 188 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 145 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 ASN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 HIS K 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20006 Z= 0.193 Angle : 0.592 7.902 26936 Z= 0.294 Chirality : 0.043 0.150 3080 Planarity : 0.003 0.029 3486 Dihedral : 4.410 24.798 2660 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.84 % Allowed : 17.56 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.17), residues: 2408 helix: 1.48 (0.15), residues: 1274 sheet: 0.21 (0.34), residues: 196 loop : -0.60 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 145 PHE 0.035 0.002 PHE A 54 TYR 0.028 0.001 TYR B 82 ARG 0.013 0.001 ARG A 173 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 393 time to evaluate : 2.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 ASP cc_start: 0.6701 (OUTLIER) cc_final: 0.6308 (p0) REVERT: E 181 MET cc_start: 0.7580 (mtm) cc_final: 0.7362 (mtm) REVERT: F 40 VAL cc_start: 0.8452 (t) cc_final: 0.8234 (p) REVERT: F 166 ARG cc_start: 0.8565 (mmt90) cc_final: 0.8361 (mmm160) REVERT: G 23 ASP cc_start: 0.6455 (OUTLIER) cc_final: 0.6172 (p0) REVERT: G 166 ARG cc_start: 0.8608 (mmt90) cc_final: 0.8313 (mmm160) REVERT: K 166 ARG cc_start: 0.8665 (mmt90) cc_final: 0.8362 (mmm160) outliers start: 40 outliers final: 26 residues processed: 417 average time/residue: 0.4229 time to fit residues: 244.2994 Evaluate side-chains 407 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 379 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 187 LYS Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 46 ASN Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 160 MET Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 23 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 201 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 174 optimal weight: 0.9980 chunk 27 optimal weight: 0.0470 chunk 52 optimal weight: 0.4980 chunk 189 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 166 optimal weight: 9.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 ASN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.132520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.102997 restraints weight = 27095.072| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.64 r_work: 0.3256 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.5609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20006 Z= 0.206 Angle : 0.591 7.661 26936 Z= 0.293 Chirality : 0.044 0.230 3080 Planarity : 0.003 0.049 3486 Dihedral : 4.377 25.543 2660 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.57 % Allowed : 17.70 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.17), residues: 2408 helix: 1.50 (0.15), residues: 1274 sheet: 0.25 (0.34), residues: 196 loop : -0.61 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 145 PHE 0.035 0.002 PHE E 54 TYR 0.025 0.001 TYR C 82 ARG 0.013 0.000 ARG A 173 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5348.82 seconds wall clock time: 97 minutes 46.90 seconds (5866.90 seconds total)