Starting phenix.real_space_refine on Thu Mar 14 18:42:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kod_22972/03_2024/7kod_22972.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kod_22972/03_2024/7kod_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_22972/03_2024/7kod_22972.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kod_22972/03_2024/7kod_22972.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kod_22972/03_2024/7kod_22972.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kod_22972/03_2024/7kod_22972.pdb" } resolution = 1.655 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= -0.000 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 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. 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 21.72, per 1000 atoms: 0.32 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: 45.79 Conformation dependent library (CDL) restraints added in 4.9 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: 3.07 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: 21.43 Time building geometry restraints manager: 47.95 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: 29855 13.79 - 27.58: 1224 27.58 - 41.38: 253 41.38 - 55.17: 193 55.17 - 68.96: 46 Dihedral angle restraints: 31571 sinusoidal: 16936 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 31568 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 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: 5.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.960 Extract box with map and model: 27.660 Check model and map are aligned: 0.910 Set scattering table: 0.490 Process input model: 166.720 Find NCS groups from input model: 3.200 Set up NCS constraints: 0.180 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:10.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 216.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 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 % Allowed : 2.06 % Favored : 97.94 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 93 HIS 0.002 0.000 HIS E 128 PHE 0.005 0.001 PHE F 41 TYR 0.008 0.001 TYR H 137 ARG 0.002 0.000 ARG S 43 *********************** 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 : 4.717 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 717 average time/residue: 4.1445 time to fit residues: 3361.9355 Evaluate side-chains 299 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 4.309 ------------------------------------------------------------------------------- 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: 5.9990 chunk 319 optimal weight: 0.9990 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: 5.7990 ------------------------------------------------------------------------------- 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 J 112 GLN L 112 GLN M 112 GLN N 112 GLN P 112 GLN R 112 GLN T 112 GLN X 112 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 34512 Z= 0.331 Angle : 0.516 5.718 46416 Z= 0.295 Chirality : 0.037 0.130 4848 Planarity : 0.004 0.029 6096 Dihedral : 3.925 20.855 4512 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.71 % Allowed : 5.59 % Favored : 93.70 % 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 : 0.94 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.005 TRP W 93 HIS 0.005 0.001 HIS A 128 PHE 0.015 0.002 PHE C 41 TYR 0.017 0.002 TYR L 137 ARG 0.004 0.001 ARG E 9 *********************** 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 306 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 280 time to evaluate : 4.367 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 2 residues processed: 288 average time/residue: 3.7566 time to fit residues: 1242.8550 Evaluate side-chains 274 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 272 time to evaluate : 4.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 157 LYS Chi-restraints excluded: chain V residue 157 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 8.9990 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: 4.9990 chunk 330 optimal weight: 5.9990 chunk 368 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 297 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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: 0.8855 moved from start: 0.2067 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= 0.309 Angle : 0.490 5.258 46416 Z= 0.282 Chirality : 0.036 0.122 4848 Planarity : 0.003 0.032 6096 Dihedral : 4.010 22.300 4512 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.55 % Allowed : 4.96 % Favored : 94.49 % 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: 5.17 (0.13), residues: 4080 helix: 4.00 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.81 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.005 TRP Q 93 HIS 0.004 0.001 HIS A 128 PHE 0.016 0.002 PHE C 41 TYR 0.017 0.002 TYR S 137 ARG 0.003 0.001 ARG Q 9 *********************** 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 301 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 281 time to evaluate : 4.401 Fit side-chains outliers start: 20 outliers final: 0 residues processed: 284 average time/residue: 3.6676 time to fit residues: 1200.1233 Evaluate side-chains 274 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 4.313 ------------------------------------------------------------------------------- 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: 5.9990 chunk 279 optimal weight: 2.9990 chunk 192 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 chunk 249 optimal weight: 7.9990 chunk 372 optimal weight: 1.9990 chunk 394 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 353 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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: 0.8853 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 34512 Z= 0.281 Angle : 0.473 5.336 46416 Z= 0.272 Chirality : 0.035 0.120 4848 Planarity : 0.003 0.034 6096 Dihedral : 3.990 22.441 4512 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.71 % Allowed : 5.04 % Favored : 94.24 % 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: 5.20 (0.13), residues: 4080 helix: 4.02 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.80 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP D 93 HIS 0.004 0.001 HIS A 128 PHE 0.016 0.002 PHE C 41 TYR 0.017 0.002 TYR N 137 ARG 0.002 0.000 ARG M 63 *********************** 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 304 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 278 time to evaluate : 4.255 Fit side-chains outliers start: 26 outliers final: 2 residues processed: 284 average time/residue: 3.5697 time to fit residues: 1172.2901 Evaluate side-chains 282 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 280 time to evaluate : 4.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain E residue 165 MET 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: 7.9990 chunk 162 optimal weight: 6.9990 chunk 336 optimal weight: 6.9990 chunk 272 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 201 optimal weight: 8.9990 chunk 353 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- 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: 0.8860 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 34512 Z= 0.319 Angle : 0.489 5.344 46416 Z= 0.281 Chirality : 0.036 0.122 4848 Planarity : 0.003 0.036 6096 Dihedral : 4.037 22.208 4512 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.33 % Allowed : 5.59 % Favored : 94.08 % 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: 5.16 (0.13), residues: 4080 helix: 3.97 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.92 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP X 93 HIS 0.004 0.001 HIS A 128 PHE 0.018 0.002 PHE C 41 TYR 0.018 0.002 TYR B 137 ARG 0.002 0.000 ARG M 63 *********************** 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 298 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 286 time to evaluate : 4.367 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 287 average time/residue: 3.5943 time to fit residues: 1191.3777 Evaluate side-chains 290 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 285 time to evaluate : 4.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain O residue 165 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 6.9990 chunk 355 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 231 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 394 optimal weight: 6.9990 chunk 327 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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: 0.8843 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 34512 Z= 0.213 Angle : 0.444 5.167 46416 Z= 0.253 Chirality : 0.033 0.119 4848 Planarity : 0.003 0.038 6096 Dihedral : 3.897 22.145 4512 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.25 % Allowed : 5.70 % Favored : 94.05 % 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: 5.38 (0.13), residues: 4080 helix: 4.12 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 1.01 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP E 93 HIS 0.003 0.001 HIS P 128 PHE 0.014 0.002 PHE C 41 TYR 0.016 0.002 TYR M 137 ARG 0.002 0.000 ARG M 63 *********************** 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 : 4.459 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 289 average time/residue: 3.5985 time to fit residues: 1205.4936 Evaluate side-chains 289 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 282 time to evaluate : 4.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain W residue 165 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 224 optimal weight: 0.9990 chunk 288 optimal weight: 8.9990 chunk 223 optimal weight: 6.9990 chunk 332 optimal weight: 6.9990 chunk 220 optimal weight: 6.9990 chunk 393 optimal weight: 3.9990 chunk 246 optimal weight: 6.9990 chunk 239 optimal weight: 8.9990 chunk 181 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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: 0.8856 moved from start: 0.2207 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= 0.293 Angle : 0.475 5.288 46416 Z= 0.272 Chirality : 0.035 0.121 4848 Planarity : 0.003 0.039 6096 Dihedral : 3.979 22.154 4512 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.22 % Allowed : 5.78 % Favored : 94.00 % 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: 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.004 TRP J 93 HIS 0.004 0.001 HIS H 128 PHE 0.017 0.002 PHE C 41 TYR 0.017 0.002 TYR L 137 ARG 0.002 0.000 ARG M 63 *********************** 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 293 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 285 time to evaluate : 4.345 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 285 average time/residue: 3.5328 time to fit residues: 1166.1520 Evaluate side-chains 288 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 281 time to evaluate : 4.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain W residue 165 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 8.9990 chunk 157 optimal weight: 7.9990 chunk 234 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 250 optimal weight: 1.9990 chunk 267 optimal weight: 7.9990 chunk 194 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 309 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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: 0.8858 moved from start: 0.2235 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= 0.302 Angle : 0.477 5.404 46416 Z= 0.273 Chirality : 0.035 0.121 4848 Planarity : 0.003 0.040 6096 Dihedral : 3.988 22.139 4512 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.22 % Allowed : 5.78 % Favored : 94.00 % 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: 5.26 (0.13), residues: 4080 helix: 4.01 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 1.07 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP C 93 HIS 0.004 0.001 HIS D 128 PHE 0.018 0.002 PHE C 41 TYR 0.017 0.002 TYR K 137 ARG 0.002 0.000 ARG M 63 *********************** 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 291 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 283 time to evaluate : 4.427 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 283 average time/residue: 3.5458 time to fit residues: 1161.0897 Evaluate side-chains 290 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 282 time to evaluate : 4.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain W residue 165 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 0.8980 chunk 376 optimal weight: 6.9990 chunk 343 optimal weight: 4.9990 chunk 366 optimal weight: 5.9990 chunk 220 optimal weight: 0.5980 chunk 159 optimal weight: 0.8980 chunk 287 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 chunk 331 optimal weight: 6.9990 chunk 346 optimal weight: 7.9990 chunk 365 optimal weight: 6.9990 overall best weight: 2.6784 ------------------------------------------------------------------------------- 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: 0.8835 moved from start: 0.2260 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= 0.174 Angle : 0.424 5.007 46416 Z= 0.240 Chirality : 0.032 0.119 4848 Planarity : 0.003 0.041 6096 Dihedral : 3.808 21.748 4512 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.25 % Allowed : 6.06 % Favored : 93.70 % 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: 5.58 (0.13), residues: 4080 helix: 4.23 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 1.21 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 93 HIS 0.003 0.001 HIS B 128 PHE 0.012 0.002 PHE C 41 TYR 0.015 0.001 TYR M 137 ARG 0.002 0.000 ARG M 63 *********************** 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 291 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 282 time to evaluate : 4.350 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 283 average time/residue: 3.6314 time to fit residues: 1189.9842 Evaluate side-chains 287 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 281 time to evaluate : 4.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain W residue 165 MET 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: 5.9990 chunk 236 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 chunk 269 optimal weight: 7.9990 chunk 406 optimal weight: 7.9990 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: 6.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- 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: 0.8844 moved from start: 0.2272 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= 0.216 Angle : 0.442 5.045 46416 Z= 0.251 Chirality : 0.033 0.119 4848 Planarity : 0.003 0.042 6096 Dihedral : 3.849 21.977 4512 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.16 % Allowed : 6.41 % Favored : 93.42 % 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: 5.44 (0.13), residues: 4080 helix: 4.15 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 1.06 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 93 HIS 0.003 0.001 HIS N 128 PHE 0.014 0.002 PHE C 41 TYR 0.016 0.002 TYR P 137 ARG 0.002 0.000 ARG F 90 ********************** 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: 6 poor density : 284 time to evaluate : 4.854 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 284 average time/residue: 3.5086 time to fit residues: 1154.3577 Evaluate side-chains 287 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 281 time to evaluate : 4.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain W residue 165 MET 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: 5.9990 chunk 47 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 324 optimal weight: 7.9990 chunk 135 optimal weight: 8.9990 chunk 332 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 59 optimal weight: 0.0970 overall best weight: 5.6186 ------------------------------------------------------------------------------- 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 = 0.2758 r_free = 0.2758 target = 0.066177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.058143 restraints weight = 128041.878| |-----------------------------------------------------------------------------| r_work (start): 0.2551 rms_B_bonded: 1.32 r_work: 0.2400 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2259 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9281 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 34512 Z= 0.314 Angle : 0.476 5.366 46416 Z= 0.271 Chirality : 0.035 0.123 4848 Planarity : 0.003 0.042 6096 Dihedral : 3.987 22.142 4512 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.25 % Allowed : 6.30 % Favored : 93.45 % 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: 5.20 (0.13), residues: 4080 helix: 4.01 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.86 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 93 HIS 0.004 0.001 HIS M 128 PHE 0.018 0.002 PHE C 41 TYR 0.017 0.002 TYR N 137 ARG 0.003 0.000 ARG F 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21942.23 seconds wall clock time: 377 minutes 59.02 seconds (22679.02 seconds total)