Starting phenix.real_space_refine (version: dev) on Tue Dec 13 20:30:03 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kod_22972/12_2022/7kod_22972.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kod_22972/12_2022/7kod_22972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.655 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kod_22972/12_2022/7kod_22972.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kod_22972/12_2022/7kod_22972.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kod_22972/12_2022/7kod_22972.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kod_22972/12_2022/7kod_22972.pdb" } resolution = 1.655 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= -0.000 sd= 0.001 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 68186 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2769 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "B" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2770 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "C" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2770 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "D" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2770 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "E" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2770 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "F" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2770 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "G" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2770 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "H" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2770 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "I" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2770 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "J" Number of atoms: 2762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2762 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "K" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2769 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "L" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2770 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "M" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2770 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "N" Number of atoms: 2762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2762 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "O" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2770 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "P" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2769 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Q" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2769 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "R" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2770 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "S" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2769 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "T" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2770 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "U" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2770 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "V" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2770 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "W" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2770 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "X" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2770 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "B" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "C" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "D" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "E" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "F" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "G" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "H" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "I" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Chain: "J" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "K" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "L" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "M" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "N" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "O" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "P" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "Q" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "R" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "S" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Chain: "T" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "U" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "V" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Chain: "W" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "X" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Time building chain proxies: 23.60, per 1000 atoms: 0.35 Number of scatterers: 68186 At special positions: 0 Unit cell: (133.023, 133.023, 133.023, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 192 16.00 O 8207 8.00 N 5928 7.00 C 21216 6.00 H 32643 1.00 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: 48.37 Conformation dependent library (CDL) restraints added in 4.0 seconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 76 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 163 through 174 removed outlier: 4.044A pdb=" N GLU A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 76 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 163 through 174 removed outlier: 4.192A pdb=" N GLU B 167 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 42 Processing helix chain 'C' and resid 48 through 76 Processing helix chain 'C' and resid 95 through 124 Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 137 through 159 Processing helix chain 'C' and resid 163 through 174 removed outlier: 4.073A pdb=" N GLU C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 42 Processing helix chain 'D' and resid 48 through 76 Processing helix chain 'D' and resid 95 through 124 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 137 through 159 Processing helix chain 'D' and resid 163 through 174 removed outlier: 4.149A pdb=" N GLU D 167 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 42 Processing helix chain 'E' and resid 48 through 76 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 163 through 174 removed outlier: 4.063A pdb=" N GLU E 167 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR E 168 " --> pdb=" O GLY E 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 42 Processing helix chain 'F' and resid 48 through 76 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 163 through 174 removed outlier: 4.174A pdb=" N GLU F 167 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR F 168 " --> pdb=" O GLY F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 42 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 163 through 174 removed outlier: 4.099A pdb=" N GLU G 167 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR G 168 " --> pdb=" O GLY G 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 42 Processing helix chain 'H' and resid 48 through 76 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 163 through 174 removed outlier: 4.180A pdb=" N GLU H 167 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR H 168 " --> pdb=" O GLY H 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 42 Processing helix chain 'I' and resid 48 through 76 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 163 through 174 removed outlier: 4.159A pdb=" N GLU I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR I 168 " --> pdb=" O GLY I 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 42 Processing helix chain 'J' and resid 48 through 76 Processing helix chain 'J' and resid 95 through 124 Processing helix chain 'J' and resid 126 through 137 Processing helix chain 'J' and resid 137 through 159 Processing helix chain 'J' and resid 163 through 174 removed outlier: 4.151A pdb=" N GLU J 167 " --> pdb=" O ALA J 163 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR J 168 " --> pdb=" O GLY J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 42 Processing helix chain 'K' and resid 48 through 76 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 163 through 174 removed outlier: 4.068A pdb=" N GLU K 167 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR K 168 " --> pdb=" O GLY K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 42 Processing helix chain 'L' and resid 48 through 76 Processing helix chain 'L' and resid 95 through 124 Processing helix chain 'L' and resid 126 through 137 Processing helix chain 'L' and resid 137 through 159 Processing helix chain 'L' and resid 163 through 174 removed outlier: 4.067A pdb=" N GLU L 167 " --> pdb=" O ALA L 163 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR L 168 " --> pdb=" O GLY L 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 42 Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 163 through 174 removed outlier: 4.037A pdb=" N GLU M 167 " --> pdb=" O ALA M 163 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR M 168 " --> pdb=" O GLY M 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 42 Processing helix chain 'N' and resid 48 through 76 Processing helix chain 'N' and resid 95 through 124 Processing helix chain 'N' and resid 126 through 137 Processing helix chain 'N' and resid 137 through 159 Processing helix chain 'N' and resid 163 through 174 removed outlier: 4.070A pdb=" N GLU N 167 " --> pdb=" O ALA N 163 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR N 168 " --> pdb=" O GLY N 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 42 Processing helix chain 'O' and resid 48 through 76 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 163 through 174 removed outlier: 4.042A pdb=" N GLU O 167 " --> pdb=" O ALA O 163 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR O 168 " --> pdb=" O GLY O 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 76 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 163 through 174 removed outlier: 4.160A pdb=" N GLU P 167 " --> pdb=" O ALA P 163 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR P 168 " --> pdb=" O GLY P 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 42 Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 163 through 174 removed outlier: 4.152A pdb=" N GLU Q 167 " --> pdb=" O ALA Q 163 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR Q 168 " --> pdb=" O GLY Q 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 42 Processing helix chain 'R' and resid 48 through 76 Processing helix chain 'R' and resid 95 through 124 Processing helix chain 'R' and resid 126 through 137 Processing helix chain 'R' and resid 137 through 159 Processing helix chain 'R' and resid 163 through 174 removed outlier: 4.172A pdb=" N GLU R 167 " --> pdb=" O ALA R 163 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR R 168 " --> pdb=" O GLY R 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 42 Processing helix chain 'S' and resid 48 through 76 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 163 through 174 removed outlier: 4.100A pdb=" N GLU S 167 " --> pdb=" O ALA S 163 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR S 168 " --> pdb=" O GLY S 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 42 Processing helix chain 'T' and resid 48 through 76 Processing helix chain 'T' and resid 95 through 124 Processing helix chain 'T' and resid 126 through 137 Processing helix chain 'T' and resid 137 through 159 Processing helix chain 'T' and resid 163 through 174 removed outlier: 4.186A pdb=" N GLU T 167 " --> pdb=" O ALA T 163 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR T 168 " --> pdb=" O GLY T 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 42 Processing helix chain 'U' and resid 48 through 76 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'U' and resid 137 through 159 Processing helix chain 'U' and resid 163 through 174 removed outlier: 4.185A pdb=" N GLU U 167 " --> pdb=" O ALA U 163 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR U 168 " --> pdb=" O GLY U 164 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 42 Processing helix chain 'V' and resid 48 through 76 Processing helix chain 'V' and resid 95 through 124 Processing helix chain 'V' and resid 126 through 137 Processing helix chain 'V' and resid 137 through 159 Processing helix chain 'V' and resid 163 through 174 removed outlier: 4.163A pdb=" N GLU V 167 " --> pdb=" O ALA V 163 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR V 168 " --> pdb=" O GLY V 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 42 Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 163 through 174 removed outlier: 4.044A pdb=" N GLU W 167 " --> pdb=" O ALA W 163 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR W 168 " --> pdb=" O GLY W 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 42 Processing helix chain 'X' and resid 48 through 76 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 163 through 174 removed outlier: 4.068A pdb=" N GLU X 167 " --> pdb=" O ALA X 163 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR X 168 " --> pdb=" O GLY X 164 " (cutoff:3.500A) 2640 hydrogen bonds defined for protein. 7920 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: 22.24 Time building geometry restraints manager: 50.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 32571 1.03 - 1.23: 72 1.23 - 1.42: 14976 1.42 - 1.61: 19224 1.61 - 1.81: 312 Bond restraints: 67155 Sorted by residual: bond pdb=" CB PRO S 161 " pdb=" CG PRO S 161 " ideal model delta sigma weight residual 1.506 1.485 0.021 3.90e-02 6.57e+02 2.88e-01 bond pdb=" NE ARG A 63 " pdb=" CZ ARG A 63 " ideal model delta sigma weight residual 1.326 1.332 -0.006 1.10e-02 8.26e+03 2.80e-01 bond pdb=" NE ARG O 79 " pdb=" CZ ARG O 79 " ideal model delta sigma weight residual 1.326 1.332 -0.006 1.10e-02 8.26e+03 2.71e-01 bond pdb=" CB PRO V 161 " pdb=" CG PRO V 161 " ideal model delta sigma weight residual 1.506 1.486 0.020 3.90e-02 6.57e+02 2.71e-01 bond pdb=" CB PRO B 161 " pdb=" CG PRO B 161 " ideal model delta sigma weight residual 1.506 1.486 0.020 3.90e-02 6.57e+02 2.70e-01 ... (remaining 67150 not shown) Histogram of bond angle deviations from ideal: 100.58 - 107.26: 1422 107.26 - 113.94: 77774 113.94 - 120.62: 25862 120.62 - 127.30: 15516 127.30 - 133.99: 312 Bond angle restraints: 120886 Sorted by residual: angle pdb=" N TRP K 93 " pdb=" CA TRP K 93 " pdb=" C TRP K 93 " ideal model delta sigma weight residual 110.19 107.35 2.84 1.24e+00 6.50e-01 5.23e+00 angle pdb=" N TRP D 93 " pdb=" CA TRP D 93 " pdb=" C TRP D 93 " ideal model delta sigma weight residual 110.19 107.37 2.82 1.24e+00 6.50e-01 5.19e+00 angle pdb=" N TRP L 93 " pdb=" CA TRP L 93 " pdb=" C TRP L 93 " ideal model delta sigma weight residual 110.19 107.38 2.81 1.24e+00 6.50e-01 5.15e+00 angle pdb=" N TRP R 93 " pdb=" CA TRP R 93 " pdb=" C TRP R 93 " ideal model delta sigma weight residual 110.19 107.38 2.81 1.24e+00 6.50e-01 5.15e+00 angle pdb=" N TRP G 93 " pdb=" CA TRP G 93 " pdb=" C TRP G 93 " ideal model delta sigma weight residual 110.19 107.38 2.81 1.24e+00 6.50e-01 5.14e+00 ... (remaining 120881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.79: 25992 13.79 - 27.58: 1074 27.58 - 41.38: 143 41.38 - 55.17: 43 55.17 - 68.96: 31 Dihedral angle restraints: 27283 sinusoidal: 12648 harmonic: 14635 Sorted by residual: dihedral pdb=" CA TRP C 93 " pdb=" C TRP C 93 " pdb=" N GLU C 94 " pdb=" CA GLU C 94 " ideal model delta harmonic sigma weight residual 180.00 161.81 18.19 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ASP X 171 " pdb=" CB ASP X 171 " pdb=" CG ASP X 171 " pdb=" OD1 ASP X 171 " ideal model delta sinusoidal sigma weight residual -30.00 -89.38 59.38 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP R 171 " pdb=" CB ASP R 171 " pdb=" CG ASP R 171 " pdb=" OD1 ASP R 171 " ideal model delta sinusoidal sigma weight residual -30.00 -89.02 59.02 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 27280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 3744 0.025 - 0.051: 672 0.051 - 0.076: 308 0.076 - 0.101: 29 0.101 - 0.127: 95 Chirality restraints: 4848 Sorted by residual: chirality pdb=" CA ILE M 85 " pdb=" N ILE M 85 " pdb=" C ILE M 85 " pdb=" CB ILE M 85 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 chirality pdb=" CA ILE V 85 " pdb=" N ILE V 85 " pdb=" C ILE V 85 " pdb=" CB ILE V 85 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 chirality pdb=" CA ILE S 85 " pdb=" N ILE S 85 " pdb=" C ILE S 85 " pdb=" CB ILE S 85 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 4845 not shown) Planarity restraints: 10126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA X 160 " -0.014 5.00e-02 4.00e+02 2.07e-02 6.84e-01 pdb=" N PRO X 161 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO X 161 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO X 161 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA T 160 " -0.013 5.00e-02 4.00e+02 2.03e-02 6.62e-01 pdb=" N PRO T 161 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO T 161 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO T 161 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA S 160 " 0.013 5.00e-02 4.00e+02 2.03e-02 6.61e-01 pdb=" N PRO S 161 " -0.035 5.00e-02 4.00e+02 pdb=" CA PRO S 161 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO S 161 " 0.011 5.00e-02 4.00e+02 ... (remaining 10123 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 8660 2.27 - 2.85: 163591 2.85 - 3.44: 200686 3.44 - 4.02: 277003 4.02 - 4.60: 423272 Nonbonded interactions: 1073212 Sorted by model distance: nonbonded pdb=" HH TYR E 12 " pdb=" OE1 GLN E 73 " model vdw 1.691 1.850 nonbonded pdb=" HH TYR L 12 " pdb=" OE1 GLN L 73 " model vdw 1.692 1.850 nonbonded pdb=" HH TYR X 12 " pdb=" OE1 GLN X 73 " model vdw 1.692 1.850 nonbonded pdb=" HH TYR O 12 " pdb=" OE1 GLN O 73 " model vdw 1.692 1.850 nonbonded pdb=" HH TYR W 12 " pdb=" OE1 GLN W 73 " model vdw 1.693 1.850 ... (remaining 1073207 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' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD )) or (resid 6 and (name N or name CA or name C or name O o \ r name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 7 \ through 176)) selection = (chain 'B' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD )) or (resid 6 and (name N or name CA or name C or name O o \ r name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 7 \ through 117 or (resid 118 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 119 thro \ ugh 176)) selection = (chain 'C' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD )) or (resid 6 and (name N or name CA or name C or name O o \ r name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 7 \ through 117 or (resid 118 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 119 thro \ ugh 176)) selection = (chain 'D' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD )) or (resid 6 and (name N or name CA or name C or name O o \ r name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 7 \ through 117 or (resid 118 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 119 thro \ ugh 176)) selection = (chain 'E' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD )) or (resid 6 and (name N or name CA or name C or name O o \ r name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 7 \ through 117 or (resid 118 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 119 thro \ ugh 176)) selection = (chain 'F' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD )) or (resid 6 and (name N or name CA or name C or name O o \ r name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 7 \ through 117 or (resid 118 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 119 thro \ ugh 176)) selection = (chain 'G' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD )) or (resid 6 and (name N or name CA or name C or name O o \ r name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 7 \ through 117 or (resid 118 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 119 thro \ ugh 176)) selection = (chain 'H' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD )) or (resid 6 and (name N or name CA or name C or name O o \ r name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 7 \ through 117 or (resid 118 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 119 thro \ ugh 176)) selection = (chain 'I' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD )) or (resid 6 and (name N or name CA or name C or name O o \ r name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 7 \ through 117 or (resid 118 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 119 thro \ ugh 176)) selection = (chain 'J' and (resid 5 through 117 or (resid 118 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 119 through 176)) selection = (chain 'K' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD )) or (resid 6 and (name N or name CA or name C or name O o \ r name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 7 \ through 176)) selection = (chain 'L' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD )) or (resid 6 and (name N or name CA or name C or name O o \ r name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 7 \ through 117 or (resid 118 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 119 thro \ ugh 176)) selection = (chain 'M' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD )) or (resid 6 and (name N or name CA or name C or name O o \ r name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 7 \ through 117 or (resid 118 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 119 thro \ ugh 176)) selection = (chain 'N' and (resid 5 through 117 or (resid 118 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 119 through 176)) selection = (chain 'O' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD )) or (resid 6 and (name N or name CA or name C or name O o \ r name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 7 \ through 117 or (resid 118 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 119 thro \ ugh 176)) selection = (chain 'P' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD )) or (resid 6 and (name N or name CA or name C or name O o \ r name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 7 \ through 176)) selection = (chain 'Q' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD )) or (resid 6 and (name N or name CA or name C or name O o \ r name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 7 \ through 176)) selection = (chain 'R' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD )) or (resid 6 and (name N or name CA or name C or name O o \ r name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 7 \ through 117 or (resid 118 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 119 thro \ ugh 176)) selection = (chain 'S' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD )) or (resid 6 and (name N or name CA or name C or name O o \ r name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 7 \ through 176)) selection = (chain 'T' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD )) or (resid 6 and (name N or name CA or name C or name O o \ r name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 7 \ through 117 or (resid 118 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 119 thro \ ugh 176)) selection = (chain 'U' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD )) or (resid 6 and (name N or name CA or name C or name O o \ r name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 7 \ through 117 or (resid 118 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 119 thro \ ugh 176)) selection = (chain 'V' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD )) or (resid 6 and (name N or name CA or name C or name O o \ r name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 7 \ through 117 or (resid 118 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 119 thro \ ugh 176)) selection = (chain 'W' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD )) or (resid 6 and (name N or name CA or name C or name O o \ r name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 7 \ through 117 or (resid 118 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 119 thro \ ugh 176)) selection = (chain 'X' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD )) or (resid 6 and (name N or name CA or name C or name O o \ r name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 7 \ through 117 or (resid 118 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 119 thro \ ugh 176)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 192 5.16 5 C 21216 2.51 5 N 5928 2.21 5 O 8207 1.98 5 H 32643 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.920 Extract box with map and model: 29.140 Check model and map are aligned: 0.740 Convert atoms to be neutral: 0.440 Process input model: 169.900 Find NCS groups from input model: 2.950 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:11.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 221.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9134 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 : 0.001 0.021 34512 Z= 0.092 Angle : 0.333 4.331 46416 Z= 0.199 Chirality : 0.029 0.127 4848 Planarity : 0.002 0.021 6096 Dihedral : 8.486 68.962 13080 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 0.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 6.14 (0.13), residues: 4080 helix: 4.72 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 1.08 (0.26), residues: 864 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 717 time to evaluate : 5.206 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 717 average time/residue: 3.5540 time to fit residues: 2921.2738 Evaluate side-chains 299 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 5.388 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 6.9990 chunk 309 optimal weight: 6.9990 chunk 171 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 208 optimal weight: 7.9990 chunk 165 optimal weight: 4.9990 chunk 319 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 194 optimal weight: 7.9990 chunk 238 optimal weight: 7.9990 chunk 370 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN C 98 ASN F 112 GLN G 112 GLN H 112 GLN J 112 GLN K 112 GLN L 112 GLN M 112 GLN N 112 GLN O 112 GLN P 112 GLN R 112 GLN T 112 GLN X 112 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9210 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.027 34512 Z= 0.338 Angle : 0.521 5.712 46416 Z= 0.297 Chirality : 0.037 0.130 4848 Planarity : 0.004 0.027 6096 Dihedral : 3.940 20.912 4512 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.53 (0.13), residues: 4080 helix: 4.25 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.93 (0.24), residues: 840 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 277 time to evaluate : 5.061 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 2 residues processed: 285 average time/residue: 3.3535 time to fit residues: 1114.1654 Evaluate side-chains 274 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 272 time to evaluate : 4.371 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 5.3812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 308 optimal weight: 5.9990 chunk 252 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 371 optimal weight: 8.9990 chunk 400 optimal weight: 8.9990 chunk 330 optimal weight: 3.9990 chunk 368 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 297 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 GLN J 14 GLN K 14 GLN N 14 GLN O 14 GLN R 14 GLN S 14 GLN T 14 GLN W 14 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9218 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.024 34512 Z= 0.349 Angle : 0.509 5.338 46416 Z= 0.292 Chirality : 0.037 0.124 4848 Planarity : 0.004 0.029 6096 Dihedral : 4.068 22.268 4512 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.11 (0.13), residues: 4080 helix: 3.95 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.80 (0.24), residues: 840 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 282 time to evaluate : 4.588 Fit side-chains outliers start: 20 outliers final: 2 residues processed: 286 average time/residue: 3.2628 time to fit residues: 1088.7430 Evaluate side-chains 276 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 274 time to evaluate : 4.326 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 1.7573 time to fit residues: 9.9523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 8.9990 chunk 279 optimal weight: 8.9990 chunk 192 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 177 optimal weight: 5.9990 chunk 249 optimal weight: 7.9990 chunk 372 optimal weight: 0.0170 chunk 394 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 353 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 overall best weight: 5.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN L 14 GLN P 14 GLN Q 14 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9216 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.021 34512 Z= 0.310 Angle : 0.487 5.397 46416 Z= 0.279 Chirality : 0.036 0.121 4848 Planarity : 0.003 0.031 6096 Dihedral : 4.037 22.573 4512 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.14 (0.13), residues: 4080 helix: 3.97 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.84 (0.24), residues: 840 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 279 time to evaluate : 4.354 Fit side-chains outliers start: 26 outliers final: 6 residues processed: 284 average time/residue: 3.1431 time to fit residues: 1045.9006 Evaluate side-chains 283 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 277 time to evaluate : 4.290 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 1.7491 time to fit residues: 18.9224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 6.9990 chunk 223 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 293 optimal weight: 8.9990 chunk 162 optimal weight: 8.9990 chunk 336 optimal weight: 6.9990 chunk 272 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 201 optimal weight: 6.9990 chunk 353 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 14 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9223 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.025 34512 Z= 0.361 Angle : 0.508 5.422 46416 Z= 0.291 Chirality : 0.037 0.125 4848 Planarity : 0.003 0.032 6096 Dihedral : 4.098 22.289 4512 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.18 (0.13), residues: 4080 helix: 3.97 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 1.11 (0.24), residues: 864 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 281 time to evaluate : 4.966 Fit side-chains outliers start: 22 outliers final: 6 residues processed: 282 average time/residue: 3.2327 time to fit residues: 1068.0193 Evaluate side-chains 287 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 281 time to evaluate : 4.346 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 1 residues processed: 5 average time/residue: 1.7546 time to fit residues: 16.7500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 5.9990 chunk 355 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 394 optimal weight: 6.9990 chunk 327 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9211 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.018 34512 Z= 0.260 Angle : 0.465 5.300 46416 Z= 0.265 Chirality : 0.034 0.119 4848 Planarity : 0.003 0.033 6096 Dihedral : 3.974 22.113 4512 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.25 (0.13), residues: 4080 helix: 4.03 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.97 (0.24), residues: 840 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 288 time to evaluate : 4.400 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 289 average time/residue: 3.1982 time to fit residues: 1085.0657 Evaluate side-chains 291 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 285 time to evaluate : 4.430 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 1 residues processed: 5 average time/residue: 1.8290 time to fit residues: 17.2668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 224 optimal weight: 7.9990 chunk 288 optimal weight: 6.9990 chunk 223 optimal weight: 3.9990 chunk 332 optimal weight: 8.9990 chunk 220 optimal weight: 6.9990 chunk 393 optimal weight: 3.9990 chunk 246 optimal weight: 7.9990 chunk 239 optimal weight: 8.9990 chunk 181 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9218 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.022 34512 Z= 0.313 Angle : 0.485 5.418 46416 Z= 0.277 Chirality : 0.036 0.121 4848 Planarity : 0.003 0.036 6096 Dihedral : 4.021 21.981 4512 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.18 (0.13), residues: 4080 helix: 3.95 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 1.04 (0.24), residues: 840 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 288 time to evaluate : 4.428 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 289 average time/residue: 3.1116 time to fit residues: 1054.6787 Evaluate side-chains 296 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 288 time to evaluate : 4.372 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 1.7331 time to fit residues: 23.2835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 7.9990 chunk 157 optimal weight: 6.9990 chunk 234 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 250 optimal weight: 0.9980 chunk 267 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 309 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9199 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.015 34512 Z= 0.182 Angle : 0.431 5.103 46416 Z= 0.244 Chirality : 0.033 0.120 4848 Planarity : 0.003 0.038 6096 Dihedral : 3.846 21.880 4512 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.48 (0.13), residues: 4080 helix: 4.17 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 1.13 (0.24), residues: 840 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 289 time to evaluate : 4.388 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 290 average time/residue: 3.1724 time to fit residues: 1080.4648 Evaluate side-chains 282 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 280 time to evaluate : 4.344 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 1.8065 time to fit residues: 10.0558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 3.9990 chunk 376 optimal weight: 6.9990 chunk 343 optimal weight: 5.9990 chunk 366 optimal weight: 8.9990 chunk 220 optimal weight: 7.9990 chunk 159 optimal weight: 7.9990 chunk 287 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 331 optimal weight: 4.9990 chunk 346 optimal weight: 2.9990 chunk 365 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9200 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.017 34512 Z= 0.189 Angle : 0.433 4.928 46416 Z= 0.245 Chirality : 0.033 0.119 4848 Planarity : 0.003 0.038 6096 Dihedral : 3.814 21.925 4512 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.54 (0.13), residues: 4080 helix: 4.20 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 1.25 (0.24), residues: 840 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 285 time to evaluate : 4.465 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 285 average time/residue: 3.0961 time to fit residues: 1036.5713 Evaluate side-chains 286 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 284 time to evaluate : 4.317 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 1.7265 time to fit residues: 9.8531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 6.9990 chunk 387 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 269 optimal weight: 10.0000 chunk 406 optimal weight: 6.9990 chunk 374 optimal weight: 0.9980 chunk 323 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 250 optimal weight: 2.9990 chunk 198 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9208 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.018 34512 Z= 0.233 Angle : 0.450 5.121 46416 Z= 0.255 Chirality : 0.034 0.120 4848 Planarity : 0.003 0.038 6096 Dihedral : 3.880 22.161 4512 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.38 (0.13), residues: 4080 helix: 4.12 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 1.02 (0.24), residues: 840 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 285 time to evaluate : 4.351 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 285 average time/residue: 3.0984 time to fit residues: 1037.0422 Evaluate side-chains 293 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 288 time to evaluate : 4.413 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 1.7429 time to fit residues: 16.7334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 6.9990 chunk 344 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 298 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 324 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 chunk 332 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 59 optimal weight: 0.4980 overall best weight: 6.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 14 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.066040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.057991 restraints weight = 128530.846| |-----------------------------------------------------------------------------| r_work (start): 0.2548 rms_B_bonded: 1.32 r_work: 0.2396 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2255 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9341 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.024 34512 Z= 0.336 Angle : 0.486 5.396 46416 Z= 0.276 Chirality : 0.036 0.124 4848 Planarity : 0.003 0.038 6096 Dihedral : 4.020 22.247 4512 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.13 (0.13), residues: 4080 helix: 3.97 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.80 (0.24), residues: 840 =============================================================================== Job complete usr+sys time: 19769.92 seconds wall clock time: 340 minutes 53.61 seconds (20453.61 seconds total)