Starting phenix.real_space_refine on Thu Feb 22 00:41:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhq_9116/02_2024/6mhq_9116.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhq_9116/02_2024/6mhq_9116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhq_9116/02_2024/6mhq_9116.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhq_9116/02_2024/6mhq_9116.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhq_9116/02_2024/6mhq_9116.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhq_9116/02_2024/6mhq_9116.pdb" } resolution = 3.4 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= 0.001 sd= 0.006 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 96 5.16 5 C 11568 2.51 5 N 2772 2.21 5 O 2940 1.98 5 H 15264 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32640 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 2720 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain breaks: 1 Chain: "B" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 2720 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain breaks: 1 Chain: "C" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 2720 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain breaks: 1 Chain: "D" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 2720 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain breaks: 1 Chain: "E" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 2720 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain breaks: 1 Chain: "F" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 2720 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain breaks: 1 Chain: "G" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 2720 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain breaks: 1 Chain: "H" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 2720 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain breaks: 1 Chain: "I" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 2720 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain breaks: 1 Chain: "J" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 2720 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain breaks: 1 Chain: "K" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 2720 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain breaks: 1 Chain: "L" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 2720 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain breaks: 1 Time building chain proxies: 13.99, per 1000 atoms: 0.43 Number of scatterers: 32640 At special positions: 0 Unit cell: (95.095, 92.435, 134.995, 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 96 16.00 O 2940 8.00 N 2772 7.00 C 11568 6.00 H 15264 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 189 " distance=2.02 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 178 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 189 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 178 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 189 " distance=2.02 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 178 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 189 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 183 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 178 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 189 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 183 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 178 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 189 " distance=2.02 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 183 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 178 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 189 " distance=2.02 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 183 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 178 " distance=2.03 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 189 " distance=2.02 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 183 " distance=2.03 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 178 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 189 " distance=2.02 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 183 " distance=2.03 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 178 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 189 " distance=2.03 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 183 " distance=2.03 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 178 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 189 " distance=2.02 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 183 " distance=2.03 Simple disulfide: pdb=" SG CYS K 65 " - pdb=" SG CYS K 178 " distance=2.03 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 189 " distance=2.02 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS L 183 " distance=2.03 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 178 " distance=2.03 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: 25.22 Conformation dependent library (CDL) restraints added in 3.3 seconds 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4008 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 12 sheets defined 77.4% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 4 through 16 removed outlier: 3.879A pdb=" N GLU A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 32 Processing helix chain 'A' and resid 32 through 40 Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 73 through 97 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 143 through 168 Processing helix chain 'A' and resid 193 through 222 removed outlier: 3.763A pdb=" N TYR A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 16 removed outlier: 3.878A pdb=" N GLU B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 32 Processing helix chain 'B' and resid 32 through 40 Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 73 through 97 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 143 through 168 Processing helix chain 'B' and resid 193 through 222 removed outlier: 3.763A pdb=" N TYR B 220 " --> pdb=" O VAL B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 16 removed outlier: 3.878A pdb=" N GLU C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 32 Processing helix chain 'C' and resid 32 through 40 Processing helix chain 'C' and resid 40 through 45 Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 73 through 97 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 143 through 168 Processing helix chain 'C' and resid 193 through 222 removed outlier: 3.763A pdb=" N TYR C 220 " --> pdb=" O VAL C 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 16 removed outlier: 3.879A pdb=" N GLU D 16 " --> pdb=" O GLU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 32 Processing helix chain 'D' and resid 32 through 40 Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 73 through 97 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 143 through 168 Processing helix chain 'D' and resid 193 through 222 removed outlier: 3.764A pdb=" N TYR D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 16 removed outlier: 3.878A pdb=" N GLU E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 Processing helix chain 'E' and resid 32 through 40 Processing helix chain 'E' and resid 40 through 45 Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 73 through 97 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 143 through 168 Processing helix chain 'E' and resid 193 through 222 removed outlier: 3.763A pdb=" N TYR E 220 " --> pdb=" O VAL E 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 16 removed outlier: 3.879A pdb=" N GLU F 16 " --> pdb=" O GLU F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 32 Processing helix chain 'F' and resid 32 through 40 Processing helix chain 'F' and resid 40 through 45 Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 73 through 97 Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 143 through 168 Processing helix chain 'F' and resid 193 through 222 removed outlier: 3.763A pdb=" N TYR F 220 " --> pdb=" O VAL F 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 16 removed outlier: 3.879A pdb=" N GLU G 16 " --> pdb=" O GLU G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 32 Processing helix chain 'G' and resid 32 through 40 Processing helix chain 'G' and resid 40 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 60 through 70 Processing helix chain 'G' and resid 73 through 97 Proline residue: G 88 - end of helix Processing helix chain 'G' and resid 143 through 168 Processing helix chain 'G' and resid 193 through 222 removed outlier: 3.763A pdb=" N TYR G 220 " --> pdb=" O VAL G 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 16 removed outlier: 3.879A pdb=" N GLU H 16 " --> pdb=" O GLU H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 32 Processing helix chain 'H' and resid 32 through 40 Processing helix chain 'H' and resid 40 through 45 Processing helix chain 'H' and resid 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 60 through 70 Processing helix chain 'H' and resid 73 through 97 Proline residue: H 88 - end of helix Processing helix chain 'H' and resid 143 through 168 Processing helix chain 'H' and resid 193 through 222 removed outlier: 3.764A pdb=" N TYR H 220 " --> pdb=" O VAL H 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 16 removed outlier: 3.879A pdb=" N GLU I 16 " --> pdb=" O GLU I 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 32 Processing helix chain 'I' and resid 32 through 40 Processing helix chain 'I' and resid 40 through 45 Processing helix chain 'I' and resid 46 through 48 No H-bonds generated for 'chain 'I' and resid 46 through 48' Processing helix chain 'I' and resid 60 through 70 Processing helix chain 'I' and resid 73 through 97 Proline residue: I 88 - end of helix Processing helix chain 'I' and resid 143 through 168 Processing helix chain 'I' and resid 193 through 222 removed outlier: 3.764A pdb=" N TYR I 220 " --> pdb=" O VAL I 216 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 16 removed outlier: 3.879A pdb=" N GLU J 16 " --> pdb=" O GLU J 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 32 Processing helix chain 'J' and resid 32 through 40 Processing helix chain 'J' and resid 40 through 45 Processing helix chain 'J' and resid 46 through 48 No H-bonds generated for 'chain 'J' and resid 46 through 48' Processing helix chain 'J' and resid 60 through 70 Processing helix chain 'J' and resid 73 through 97 Proline residue: J 88 - end of helix Processing helix chain 'J' and resid 143 through 168 Processing helix chain 'J' and resid 193 through 222 removed outlier: 3.764A pdb=" N TYR J 220 " --> pdb=" O VAL J 216 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 16 removed outlier: 3.877A pdb=" N GLU K 16 " --> pdb=" O GLU K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 32 Processing helix chain 'K' and resid 32 through 40 Processing helix chain 'K' and resid 40 through 45 Processing helix chain 'K' and resid 46 through 48 No H-bonds generated for 'chain 'K' and resid 46 through 48' Processing helix chain 'K' and resid 60 through 70 Processing helix chain 'K' and resid 73 through 97 Proline residue: K 88 - end of helix Processing helix chain 'K' and resid 143 through 168 Processing helix chain 'K' and resid 193 through 222 removed outlier: 3.763A pdb=" N TYR K 220 " --> pdb=" O VAL K 216 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 16 removed outlier: 3.878A pdb=" N GLU L 16 " --> pdb=" O GLU L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 32 Processing helix chain 'L' and resid 32 through 40 Processing helix chain 'L' and resid 40 through 45 Processing helix chain 'L' and resid 46 through 48 No H-bonds generated for 'chain 'L' and resid 46 through 48' Processing helix chain 'L' and resid 60 through 70 Processing helix chain 'L' and resid 73 through 97 Proline residue: L 88 - end of helix Processing helix chain 'L' and resid 143 through 168 Processing helix chain 'L' and resid 193 through 222 removed outlier: 3.764A pdb=" N TYR L 220 " --> pdb=" O VAL L 216 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 178 Processing sheet with id=AA2, first strand: chain 'B' and resid 175 through 178 Processing sheet with id=AA3, first strand: chain 'C' and resid 175 through 178 Processing sheet with id=AA4, first strand: chain 'D' and resid 175 through 178 Processing sheet with id=AA5, first strand: chain 'E' and resid 175 through 178 Processing sheet with id=AA6, first strand: chain 'F' and resid 175 through 178 Processing sheet with id=AA7, first strand: chain 'G' and resid 175 through 178 Processing sheet with id=AA8, first strand: chain 'H' and resid 175 through 178 Processing sheet with id=AA9, first strand: chain 'I' and resid 175 through 178 Processing sheet with id=AB1, first strand: chain 'J' and resid 175 through 178 Processing sheet with id=AB2, first strand: chain 'K' and resid 175 through 178 Processing sheet with id=AB3, first strand: chain 'L' and resid 175 through 178 1212 hydrogen bonds defined for protein. 3600 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: 11.60 Time building geometry restraints manager: 26.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 15252 1.02 - 1.22: 12 1.22 - 1.41: 7824 1.41 - 1.61: 9948 1.61 - 1.80: 108 Bond restraints: 33144 Sorted by residual: bond pdb=" CB VAL G 187 " pdb=" CG1 VAL G 187 " ideal model delta sigma weight residual 1.521 1.423 0.098 3.30e-02 9.18e+02 8.77e+00 bond pdb=" CB VAL A 187 " pdb=" CG1 VAL A 187 " ideal model delta sigma weight residual 1.521 1.423 0.098 3.30e-02 9.18e+02 8.77e+00 bond pdb=" CB VAL B 187 " pdb=" CG1 VAL B 187 " ideal model delta sigma weight residual 1.521 1.423 0.098 3.30e-02 9.18e+02 8.76e+00 bond pdb=" CB VAL H 187 " pdb=" CG1 VAL H 187 " ideal model delta sigma weight residual 1.521 1.424 0.097 3.30e-02 9.18e+02 8.71e+00 bond pdb=" CB VAL L 187 " pdb=" CG1 VAL L 187 " ideal model delta sigma weight residual 1.521 1.424 0.097 3.30e-02 9.18e+02 8.70e+00 ... (remaining 33139 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.05: 459 106.05 - 113.06: 36858 113.06 - 120.08: 10112 120.08 - 127.09: 11482 127.09 - 134.10: 297 Bond angle restraints: 59208 Sorted by residual: angle pdb=" C GLY I 169 " pdb=" N PHE I 170 " pdb=" CA PHE I 170 " ideal model delta sigma weight residual 121.54 125.90 -4.36 1.91e+00 2.74e-01 5.22e+00 angle pdb=" C GLY H 169 " pdb=" N PHE H 170 " pdb=" CA PHE H 170 " ideal model delta sigma weight residual 121.54 125.90 -4.36 1.91e+00 2.74e-01 5.21e+00 angle pdb=" C GLY D 169 " pdb=" N PHE D 170 " pdb=" CA PHE D 170 " ideal model delta sigma weight residual 121.54 125.87 -4.33 1.91e+00 2.74e-01 5.15e+00 angle pdb=" C GLY B 169 " pdb=" N PHE B 170 " pdb=" CA PHE B 170 " ideal model delta sigma weight residual 121.54 125.87 -4.33 1.91e+00 2.74e-01 5.14e+00 angle pdb=" C GLY C 169 " pdb=" N PHE C 170 " pdb=" CA PHE C 170 " ideal model delta sigma weight residual 121.54 125.87 -4.33 1.91e+00 2.74e-01 5.13e+00 ... (remaining 59203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.43: 14030 15.43 - 30.85: 1509 30.85 - 46.28: 351 46.28 - 61.70: 190 61.70 - 77.13: 36 Dihedral angle restraints: 16116 sinusoidal: 8292 harmonic: 7824 Sorted by residual: dihedral pdb=" CA ASN C 185 " pdb=" C ASN C 185 " pdb=" N THR C 186 " pdb=" CA THR C 186 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ASN E 185 " pdb=" C ASN E 185 " pdb=" N THR E 186 " pdb=" CA THR E 186 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ASN H 185 " pdb=" C ASN H 185 " pdb=" N THR H 186 " pdb=" CA THR H 186 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 16113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1665 0.057 - 0.113: 710 0.113 - 0.170: 304 0.170 - 0.226: 93 0.226 - 0.283: 12 Chirality restraints: 2784 Sorted by residual: chirality pdb=" CB VAL B 187 " pdb=" CA VAL B 187 " pdb=" CG1 VAL B 187 " pdb=" CG2 VAL B 187 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB VAL F 187 " pdb=" CA VAL F 187 " pdb=" CG1 VAL F 187 " pdb=" CG2 VAL F 187 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB VAL L 187 " pdb=" CA VAL L 187 " pdb=" CG1 VAL L 187 " pdb=" CG2 VAL L 187 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 2781 not shown) Planarity restraints: 5016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 170 " 0.013 2.00e-02 2.50e+03 1.10e-02 2.11e+00 pdb=" CG PHE H 170 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE H 170 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE H 170 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE H 170 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE H 170 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE H 170 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE J 170 " 0.012 2.00e-02 2.50e+03 1.09e-02 2.06e+00 pdb=" CG PHE J 170 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE J 170 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE J 170 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE J 170 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE J 170 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE J 170 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 170 " 0.013 2.00e-02 2.50e+03 1.09e-02 2.06e+00 pdb=" CG PHE K 170 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE K 170 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE K 170 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE K 170 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE K 170 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE K 170 " 0.002 2.00e-02 2.50e+03 ... (remaining 5013 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.41: 13829 2.41 - 2.96: 71702 2.96 - 3.51: 84948 3.51 - 4.05: 106798 4.05 - 4.60: 169481 Nonbonded interactions: 446758 Sorted by model distance: nonbonded pdb=" OD1 ASP G 67 " pdb=" HG1 THR H 195 " model vdw 1.867 1.850 nonbonded pdb=" HG1 THR A 195 " pdb=" OD1 ASP F 67 " model vdw 1.872 1.850 nonbonded pdb=" OD1 ASP I 67 " pdb=" HG1 THR J 195 " model vdw 1.873 1.850 nonbonded pdb=" OD1 ASP E 67 " pdb=" HG1 THR F 195 " model vdw 1.874 1.850 nonbonded pdb=" OD1 ASP B 67 " pdb=" HG1 THR C 195 " model vdw 1.875 1.850 ... (remaining 446753 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 1.730 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: 0.490 Extract box with map and model: 8.580 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 97.270 Find NCS groups from input model: 1.530 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: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 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 : 0.018 0.107 17880 Z= 1.139 Angle : 0.800 6.363 24372 Z= 0.431 Chirality : 0.076 0.283 2784 Planarity : 0.004 0.027 3000 Dihedral : 12.179 69.979 6180 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.14 % Allowed : 3.14 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.17), residues: 2076 helix: -0.23 (0.12), residues: 1536 sheet: -2.44 (0.30), residues: 132 loop : -3.66 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP G 45 HIS 0.003 0.001 HIS F 17 PHE 0.025 0.003 PHE H 170 TYR 0.010 0.002 TYR B 146 ARG 0.003 0.001 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Evaluate side-chains 459 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 399 time to evaluate : 2.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7679 (mmt90) REVERT: A 158 VAL cc_start: 0.8841 (t) cc_final: 0.8564 (m) REVERT: B 76 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7788 (mmt90) REVERT: B 158 VAL cc_start: 0.8876 (t) cc_final: 0.8555 (m) REVERT: C 76 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7596 (mmt90) REVERT: C 158 VAL cc_start: 0.8799 (t) cc_final: 0.8546 (m) REVERT: D 76 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7714 (mmt90) REVERT: D 158 VAL cc_start: 0.8842 (t) cc_final: 0.8564 (m) REVERT: E 76 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7801 (mmt90) REVERT: E 158 VAL cc_start: 0.8868 (t) cc_final: 0.8554 (m) REVERT: F 76 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7570 (mmt90) REVERT: F 158 VAL cc_start: 0.8803 (t) cc_final: 0.8563 (m) REVERT: G 76 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7637 (mmt90) REVERT: G 158 VAL cc_start: 0.8863 (t) cc_final: 0.8569 (m) REVERT: H 76 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7771 (mmt90) REVERT: H 158 VAL cc_start: 0.8890 (t) cc_final: 0.8557 (m) REVERT: I 76 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7496 (mmt90) REVERT: I 158 VAL cc_start: 0.8810 (t) cc_final: 0.8558 (m) REVERT: J 76 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7644 (mmt90) REVERT: J 158 VAL cc_start: 0.8856 (t) cc_final: 0.8557 (m) REVERT: K 76 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7758 (mmt90) REVERT: K 158 VAL cc_start: 0.8888 (t) cc_final: 0.8562 (m) REVERT: L 76 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7499 (mmt90) REVERT: L 151 ILE cc_start: 0.8841 (pt) cc_final: 0.8627 (tt) REVERT: L 158 VAL cc_start: 0.8850 (t) cc_final: 0.8582 (m) outliers start: 60 outliers final: 36 residues processed: 459 average time/residue: 0.6728 time to fit residues: 442.5663 Evaluate side-chains 334 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 286 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 168 TYR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 168 TYR Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 168 TYR Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain G residue 67 ASP Chi-restraints excluded: chain G residue 76 ARG Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 168 TYR Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 168 TYR Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 76 ARG Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain I residue 168 TYR Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 76 ARG Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 168 TYR Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 168 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 159 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 185 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 221 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17880 Z= 0.187 Angle : 0.533 4.621 24372 Z= 0.281 Chirality : 0.038 0.180 2784 Planarity : 0.004 0.027 3000 Dihedral : 7.440 44.272 2400 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.41 % Allowed : 9.01 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.18), residues: 2076 helix: 0.90 (0.12), residues: 1548 sheet: -1.76 (0.39), residues: 132 loop : -3.23 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 4 HIS 0.005 0.001 HIS I 221 PHE 0.008 0.001 PHE C 170 TYR 0.010 0.001 TYR H 66 ARG 0.003 0.000 ARG J 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Evaluate side-chains 373 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 308 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 HIS cc_start: 0.7256 (m90) cc_final: 0.7040 (m90) REVERT: A 151 ILE cc_start: 0.8948 (mt) cc_final: 0.8585 (tt) REVERT: A 158 VAL cc_start: 0.8762 (t) cc_final: 0.8498 (m) REVERT: B 17 HIS cc_start: 0.7193 (m90) cc_final: 0.6970 (m90) REVERT: B 151 ILE cc_start: 0.8924 (mt) cc_final: 0.8594 (tt) REVERT: B 158 VAL cc_start: 0.8807 (t) cc_final: 0.8495 (m) REVERT: C 17 HIS cc_start: 0.7146 (m90) cc_final: 0.6918 (m90) REVERT: C 158 VAL cc_start: 0.8779 (t) cc_final: 0.8496 (m) REVERT: C 186 THR cc_start: 0.8892 (m) cc_final: 0.8689 (t) REVERT: D 17 HIS cc_start: 0.7271 (m90) cc_final: 0.7043 (m90) REVERT: D 158 VAL cc_start: 0.8757 (t) cc_final: 0.8487 (m) REVERT: E 151 ILE cc_start: 0.8914 (mt) cc_final: 0.8544 (tt) REVERT: E 158 VAL cc_start: 0.8803 (t) cc_final: 0.8500 (m) REVERT: F 158 VAL cc_start: 0.8757 (t) cc_final: 0.8486 (m) REVERT: G 151 ILE cc_start: 0.8969 (mt) cc_final: 0.8628 (tt) REVERT: G 158 VAL cc_start: 0.8781 (t) cc_final: 0.8500 (m) REVERT: H 151 ILE cc_start: 0.8926 (mt) cc_final: 0.8595 (tt) REVERT: H 158 VAL cc_start: 0.8833 (t) cc_final: 0.8503 (m) REVERT: I 158 VAL cc_start: 0.8795 (t) cc_final: 0.8488 (m) REVERT: J 151 ILE cc_start: 0.8970 (mt) cc_final: 0.8589 (tt) REVERT: J 158 VAL cc_start: 0.8777 (t) cc_final: 0.8500 (m) REVERT: K 151 ILE cc_start: 0.8919 (mt) cc_final: 0.8605 (tt) REVERT: K 158 VAL cc_start: 0.8802 (t) cc_final: 0.8480 (m) REVERT: L 158 VAL cc_start: 0.8792 (t) cc_final: 0.8495 (m) REVERT: L 186 THR cc_start: 0.8911 (m) cc_final: 0.8659 (t) outliers start: 65 outliers final: 52 residues processed: 354 average time/residue: 0.6218 time to fit residues: 327.9362 Evaluate side-chains 349 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 297 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 168 TYR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 168 TYR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 168 TYR Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 221 HIS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain G residue 67 ASP Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 156 PHE Chi-restraints excluded: chain G residue 168 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 168 TYR Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain I residue 168 TYR Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 168 TYR Chi-restraints excluded: chain K residue 179 ASP Chi-restraints excluded: chain K residue 221 HIS Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 156 PHE Chi-restraints excluded: chain L residue 168 TYR Chi-restraints excluded: chain L residue 179 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 185 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 184 optimal weight: 0.0980 chunk 63 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- 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: 0.8113 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17880 Z= 0.242 Angle : 0.502 4.744 24372 Z= 0.262 Chirality : 0.037 0.115 2784 Planarity : 0.003 0.028 3000 Dihedral : 6.156 43.428 2352 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.73 % Allowed : 10.80 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.18), residues: 2076 helix: 1.65 (0.13), residues: 1536 sheet: -1.49 (0.40), residues: 132 loop : -3.32 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 4 HIS 0.005 0.001 HIS J 221 PHE 0.011 0.001 PHE H 30 TYR 0.009 0.001 TYR G 146 ARG 0.002 0.000 ARG G 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Evaluate side-chains 367 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 315 time to evaluate : 2.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ILE cc_start: 0.8977 (mt) cc_final: 0.8693 (tt) REVERT: A 158 VAL cc_start: 0.8807 (t) cc_final: 0.8518 (m) REVERT: B 16 GLU cc_start: 0.7116 (mp0) cc_final: 0.6863 (mp0) REVERT: B 151 ILE cc_start: 0.8956 (mt) cc_final: 0.8652 (tt) REVERT: B 158 VAL cc_start: 0.8845 (t) cc_final: 0.8489 (m) REVERT: C 158 VAL cc_start: 0.8805 (t) cc_final: 0.8500 (m) REVERT: D 17 HIS cc_start: 0.7327 (m90) cc_final: 0.7102 (m90) REVERT: D 158 VAL cc_start: 0.8799 (t) cc_final: 0.8506 (m) REVERT: E 151 ILE cc_start: 0.8933 (mt) cc_final: 0.8597 (tt) REVERT: E 158 VAL cc_start: 0.8836 (t) cc_final: 0.8508 (m) REVERT: F 158 VAL cc_start: 0.8795 (t) cc_final: 0.8492 (m) REVERT: G 151 ILE cc_start: 0.8968 (mt) cc_final: 0.8705 (tt) REVERT: G 158 VAL cc_start: 0.8817 (t) cc_final: 0.8518 (m) REVERT: H 16 GLU cc_start: 0.7135 (mp0) cc_final: 0.6912 (mp0) REVERT: H 151 ILE cc_start: 0.8954 (mt) cc_final: 0.8634 (tt) REVERT: H 158 VAL cc_start: 0.8860 (t) cc_final: 0.8512 (m) REVERT: I 158 VAL cc_start: 0.8834 (t) cc_final: 0.8510 (m) REVERT: J 151 ILE cc_start: 0.8985 (mt) cc_final: 0.8701 (tt) REVERT: J 158 VAL cc_start: 0.8801 (t) cc_final: 0.8499 (m) REVERT: K 16 GLU cc_start: 0.7152 (mp0) cc_final: 0.6905 (mp0) REVERT: K 151 ILE cc_start: 0.8958 (mt) cc_final: 0.8666 (tt) REVERT: K 158 VAL cc_start: 0.8843 (t) cc_final: 0.8484 (m) REVERT: L 158 VAL cc_start: 0.8817 (t) cc_final: 0.8507 (m) outliers start: 52 outliers final: 48 residues processed: 351 average time/residue: 0.6517 time to fit residues: 340.9035 Evaluate side-chains 349 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 301 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 168 TYR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 168 TYR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 168 TYR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 67 ASP Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 168 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 168 TYR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain I residue 168 TYR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 168 TYR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 168 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 197 optimal weight: 6.9990 chunk 97 optimal weight: 0.3980 chunk 176 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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: 0.8155 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 17880 Z= 0.236 Angle : 0.499 4.775 24372 Z= 0.260 Chirality : 0.037 0.121 2784 Planarity : 0.003 0.024 3000 Dihedral : 6.004 44.364 2352 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.67 % Allowed : 11.11 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.19), residues: 2076 helix: 2.01 (0.13), residues: 1536 sheet: -1.23 (0.41), residues: 132 loop : -3.29 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 4 HIS 0.005 0.001 HIS C 17 PHE 0.011 0.001 PHE L 200 TYR 0.009 0.001 TYR G 146 ARG 0.002 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Evaluate side-chains 412 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 361 time to evaluate : 2.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ILE cc_start: 0.9002 (mt) cc_final: 0.8759 (tt) REVERT: B 151 ILE cc_start: 0.8978 (mt) cc_final: 0.8673 (tt) REVERT: B 158 VAL cc_start: 0.8829 (t) cc_final: 0.8483 (m) REVERT: C 151 ILE cc_start: 0.8971 (mt) cc_final: 0.8723 (tt) REVERT: C 158 VAL cc_start: 0.8835 (t) cc_final: 0.8526 (m) REVERT: D 158 VAL cc_start: 0.8832 (t) cc_final: 0.8523 (m) REVERT: E 151 ILE cc_start: 0.8977 (mt) cc_final: 0.8689 (tt) REVERT: E 158 VAL cc_start: 0.8861 (t) cc_final: 0.8517 (m) REVERT: F 151 ILE cc_start: 0.8968 (mt) cc_final: 0.8704 (tt) REVERT: F 158 VAL cc_start: 0.8828 (t) cc_final: 0.8525 (m) REVERT: G 151 ILE cc_start: 0.8997 (mt) cc_final: 0.8763 (tt) REVERT: H 151 ILE cc_start: 0.8975 (mt) cc_final: 0.8704 (tt) REVERT: H 158 VAL cc_start: 0.8874 (t) cc_final: 0.8509 (m) REVERT: I 158 VAL cc_start: 0.8840 (t) cc_final: 0.8517 (m) REVERT: J 151 ILE cc_start: 0.9002 (mt) cc_final: 0.8763 (tt) REVERT: K 151 ILE cc_start: 0.8978 (mt) cc_final: 0.8684 (tt) REVERT: K 158 VAL cc_start: 0.8825 (t) cc_final: 0.8478 (m) REVERT: L 158 VAL cc_start: 0.8841 (t) cc_final: 0.8518 (m) outliers start: 51 outliers final: 48 residues processed: 397 average time/residue: 0.6075 time to fit residues: 361.4300 Evaluate side-chains 383 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 335 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 168 TYR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 168 TYR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 168 TYR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 67 ASP Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 168 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 168 TYR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain I residue 168 TYR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 168 TYR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 168 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 168 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 176 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 221 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17880 Z= 0.264 Angle : 0.505 4.770 24372 Z= 0.264 Chirality : 0.038 0.120 2784 Planarity : 0.003 0.024 3000 Dihedral : 5.939 45.062 2352 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.67 % Allowed : 12.26 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.19), residues: 2076 helix: 2.21 (0.13), residues: 1536 sheet: -0.91 (0.44), residues: 132 loop : -3.19 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 45 HIS 0.006 0.001 HIS J 221 PHE 0.012 0.001 PHE J 200 TYR 0.007 0.001 TYR E 146 ARG 0.002 0.000 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Evaluate side-chains 446 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 395 time to evaluate : 2.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8493 (m) REVERT: B 151 ILE cc_start: 0.8985 (mt) cc_final: 0.8738 (tt) REVERT: B 158 VAL cc_start: 0.8865 (t) cc_final: 0.8517 (m) REVERT: C 151 ILE cc_start: 0.8985 (mt) cc_final: 0.8754 (tt) REVERT: C 158 VAL cc_start: 0.8845 (t) cc_final: 0.8524 (m) REVERT: D 151 ILE cc_start: 0.9009 (mt) cc_final: 0.8679 (tt) REVERT: E 151 ILE cc_start: 0.8984 (mt) cc_final: 0.8757 (tt) REVERT: E 158 VAL cc_start: 0.8879 (t) cc_final: 0.8506 (m) REVERT: F 151 ILE cc_start: 0.8986 (mt) cc_final: 0.8744 (tt) REVERT: F 158 VAL cc_start: 0.8838 (t) cc_final: 0.8526 (m) REVERT: G 158 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.8484 (m) REVERT: H 151 ILE cc_start: 0.8982 (mt) cc_final: 0.8772 (tt) REVERT: H 158 VAL cc_start: 0.8897 (t) cc_final: 0.8502 (m) REVERT: K 151 ILE cc_start: 0.8988 (mt) cc_final: 0.8751 (tt) REVERT: K 158 VAL cc_start: 0.8870 (t) cc_final: 0.8513 (m) outliers start: 51 outliers final: 48 residues processed: 420 average time/residue: 0.6159 time to fit residues: 385.0381 Evaluate side-chains 416 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 366 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 168 TYR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 168 TYR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 168 TYR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 67 ASP Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 168 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 168 TYR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain I residue 168 TYR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 168 TYR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 168 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 38 optimal weight: 0.0770 chunk 115 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 197 optimal weight: 7.9990 chunk 163 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17880 Z= 0.145 Angle : 0.462 4.689 24372 Z= 0.237 Chirality : 0.036 0.120 2784 Planarity : 0.003 0.026 3000 Dihedral : 5.766 44.210 2352 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.73 % Allowed : 13.36 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.19), residues: 2076 helix: 2.51 (0.13), residues: 1536 sheet: -1.02 (0.44), residues: 132 loop : -3.21 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 181 HIS 0.006 0.001 HIS D 221 PHE 0.009 0.001 PHE E 200 TYR 0.010 0.001 TYR J 146 ARG 0.002 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Evaluate side-chains 433 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 381 time to evaluate : 2.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 VAL cc_start: 0.8730 (OUTLIER) cc_final: 0.8496 (m) REVERT: B 158 VAL cc_start: 0.8846 (t) cc_final: 0.8494 (m) REVERT: C 151 ILE cc_start: 0.8980 (mt) cc_final: 0.8752 (tt) REVERT: C 158 VAL cc_start: 0.8817 (t) cc_final: 0.8497 (m) REVERT: D 151 ILE cc_start: 0.9013 (mt) cc_final: 0.8715 (tt) REVERT: D 158 VAL cc_start: 0.8693 (OUTLIER) cc_final: 0.8445 (m) REVERT: E 151 ILE cc_start: 0.8968 (mt) cc_final: 0.8757 (tt) REVERT: E 158 VAL cc_start: 0.8836 (t) cc_final: 0.8474 (m) REVERT: F 151 ILE cc_start: 0.8982 (mt) cc_final: 0.8742 (tt) REVERT: F 158 VAL cc_start: 0.8827 (t) cc_final: 0.8508 (m) REVERT: G 158 VAL cc_start: 0.8736 (OUTLIER) cc_final: 0.8484 (m) REVERT: H 158 VAL cc_start: 0.8856 (t) cc_final: 0.8483 (m) REVERT: K 158 VAL cc_start: 0.8843 (t) cc_final: 0.8484 (m) REVERT: L 158 VAL cc_start: 0.8909 (OUTLIER) cc_final: 0.8651 (m) REVERT: L 220 TYR cc_start: 0.6922 (m-10) cc_final: 0.6719 (m-10) outliers start: 52 outliers final: 48 residues processed: 406 average time/residue: 0.6781 time to fit residues: 414.7028 Evaluate side-chains 416 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 364 time to evaluate : 2.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 168 TYR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 168 TYR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 168 TYR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 67 ASP Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 168 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 168 TYR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain I residue 168 TYR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 168 TYR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 158 VAL Chi-restraints excluded: chain L residue 168 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 166 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 196 optimal weight: 10.0000 chunk 123 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 HIS ** D 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 HIS ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 17880 Z= 0.270 Angle : 0.494 4.788 24372 Z= 0.260 Chirality : 0.037 0.119 2784 Planarity : 0.003 0.023 3000 Dihedral : 5.830 45.262 2352 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.09 % Allowed : 14.15 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.19), residues: 2076 helix: 2.56 (0.13), residues: 1536 sheet: -0.93 (0.45), residues: 132 loop : -3.25 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 45 HIS 0.006 0.001 HIS D 221 PHE 0.013 0.001 PHE I 200 TYR 0.008 0.001 TYR J 146 ARG 0.002 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Evaluate side-chains 445 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 386 time to evaluate : 2.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8509 (m) REVERT: B 158 VAL cc_start: 0.8898 (t) cc_final: 0.8527 (m) REVERT: C 151 ILE cc_start: 0.8995 (mt) cc_final: 0.8785 (tt) REVERT: D 151 ILE cc_start: 0.9022 (mt) cc_final: 0.8742 (tt) REVERT: D 158 VAL cc_start: 0.8757 (OUTLIER) cc_final: 0.8495 (m) REVERT: E 158 VAL cc_start: 0.8882 (t) cc_final: 0.8520 (m) REVERT: F 151 ILE cc_start: 0.8997 (mt) cc_final: 0.8775 (tt) REVERT: F 158 VAL cc_start: 0.8855 (t) cc_final: 0.8529 (m) REVERT: G 158 VAL cc_start: 0.8771 (OUTLIER) cc_final: 0.8505 (m) REVERT: H 158 VAL cc_start: 0.8907 (t) cc_final: 0.8521 (m) REVERT: I 220 TYR cc_start: 0.6973 (m-10) cc_final: 0.6750 (m-10) REVERT: K 158 VAL cc_start: 0.8888 (t) cc_final: 0.8519 (m) REVERT: L 158 VAL cc_start: 0.8942 (OUTLIER) cc_final: 0.8700 (m) outliers start: 59 outliers final: 50 residues processed: 410 average time/residue: 0.6107 time to fit residues: 373.3451 Evaluate side-chains 423 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 369 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 168 TYR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 168 TYR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 168 TYR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 67 ASP Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 168 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 168 TYR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain I residue 168 TYR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 168 TYR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 158 VAL Chi-restraints excluded: chain L residue 168 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 117 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 chunk 178 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS C 17 HIS ** D 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 17880 Z= 0.301 Angle : 0.506 5.028 24372 Z= 0.268 Chirality : 0.039 0.199 2784 Planarity : 0.003 0.025 3000 Dihedral : 5.904 45.972 2352 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.04 % Allowed : 14.15 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.19), residues: 2076 helix: 2.57 (0.13), residues: 1536 sheet: -0.88 (0.44), residues: 132 loop : -3.22 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 45 HIS 0.006 0.001 HIS A 221 PHE 0.013 0.001 PHE J 200 TYR 0.012 0.001 TYR G 146 ARG 0.002 0.000 ARG F 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Evaluate side-chains 436 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 378 time to evaluate : 2.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8519 (m) REVERT: C 151 ILE cc_start: 0.9001 (mt) cc_final: 0.8794 (tt) REVERT: C 158 VAL cc_start: 0.8773 (p) cc_final: 0.8504 (m) REVERT: D 151 ILE cc_start: 0.9025 (mt) cc_final: 0.8767 (tt) REVERT: D 158 VAL cc_start: 0.8766 (OUTLIER) cc_final: 0.8496 (m) REVERT: F 151 ILE cc_start: 0.8995 (mt) cc_final: 0.8790 (tt) REVERT: F 158 VAL cc_start: 0.8853 (t) cc_final: 0.8546 (m) REVERT: H 158 VAL cc_start: 0.8937 (t) cc_final: 0.8724 (m) REVERT: I 220 TYR cc_start: 0.6986 (m-10) cc_final: 0.6754 (m-10) REVERT: L 158 VAL cc_start: 0.8958 (OUTLIER) cc_final: 0.8718 (m) outliers start: 58 outliers final: 52 residues processed: 408 average time/residue: 0.5701 time to fit residues: 354.9590 Evaluate side-chains 397 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 342 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 168 TYR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 168 TYR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 168 TYR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 67 ASP Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 168 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 168 TYR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain I residue 168 TYR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 168 TYR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 158 VAL Chi-restraints excluded: chain L residue 168 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 183 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 HIS ** D 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 221 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17880 Z= 0.241 Angle : 0.488 4.870 24372 Z= 0.255 Chirality : 0.037 0.117 2784 Planarity : 0.003 0.024 3000 Dihedral : 5.923 45.790 2352 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.99 % Allowed : 14.26 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.19), residues: 2076 helix: 2.70 (0.13), residues: 1536 sheet: -0.98 (0.44), residues: 132 loop : -3.18 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 181 HIS 0.005 0.001 HIS H 221 PHE 0.013 0.001 PHE C 200 TYR 0.010 0.001 TYR C 146 ARG 0.002 0.000 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Evaluate side-chains 431 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 374 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8519 (m) REVERT: C 158 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8511 (m) REVERT: D 158 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8499 (m) REVERT: F 151 ILE cc_start: 0.9001 (mt) cc_final: 0.8790 (tt) REVERT: F 158 VAL cc_start: 0.8850 (t) cc_final: 0.8540 (m) REVERT: H 158 VAL cc_start: 0.9073 (t) cc_final: 0.8705 (m) REVERT: I 220 TYR cc_start: 0.6974 (m-10) cc_final: 0.6731 (m-10) REVERT: L 158 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8726 (m) outliers start: 57 outliers final: 52 residues processed: 395 average time/residue: 0.6067 time to fit residues: 357.8356 Evaluate side-chains 424 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 368 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 168 TYR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 168 TYR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 168 TYR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 67 ASP Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 168 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 168 TYR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain I residue 168 TYR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 168 TYR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 158 VAL Chi-restraints excluded: chain L residue 168 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 chunk 187 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 99 optimal weight: 0.1980 chunk 128 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17880 Z= 0.196 Angle : 0.476 5.205 24372 Z= 0.246 Chirality : 0.037 0.117 2784 Planarity : 0.003 0.023 3000 Dihedral : 5.875 45.642 2352 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.83 % Allowed : 14.41 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.19), residues: 2076 helix: 2.76 (0.13), residues: 1536 sheet: -1.12 (0.43), residues: 132 loop : -3.10 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 181 HIS 0.005 0.001 HIS K 221 PHE 0.011 0.001 PHE F 200 TYR 0.010 0.001 TYR G 146 ARG 0.002 0.000 ARG G 144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Evaluate side-chains 447 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 393 time to evaluate : 2.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 VAL cc_start: 0.8787 (OUTLIER) cc_final: 0.8513 (m) REVERT: C 158 VAL cc_start: 0.8774 (OUTLIER) cc_final: 0.8515 (m) REVERT: D 158 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8503 (m) REVERT: F 158 VAL cc_start: 0.8850 (t) cc_final: 0.8547 (m) REVERT: H 158 VAL cc_start: 0.9071 (t) cc_final: 0.8707 (m) REVERT: I 220 TYR cc_start: 0.6958 (m-10) cc_final: 0.6710 (m-10) REVERT: L 158 VAL cc_start: 0.8956 (OUTLIER) cc_final: 0.8717 (m) outliers start: 54 outliers final: 50 residues processed: 409 average time/residue: 0.6078 time to fit residues: 371.4398 Evaluate side-chains 438 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 384 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 168 TYR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 168 TYR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 168 TYR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 67 ASP Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 168 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 168 TYR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain I residue 168 TYR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 168 TYR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 158 VAL Chi-restraints excluded: chain L residue 168 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 166 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 142 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 17 HIS L 17 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.153731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.117758 restraints weight = 55022.970| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.89 r_work: 0.3134 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17880 Z= 0.172 Angle : 0.467 4.827 24372 Z= 0.240 Chirality : 0.036 0.117 2784 Planarity : 0.003 0.023 3000 Dihedral : 5.799 45.325 2352 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.78 % Allowed : 14.57 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.19), residues: 2076 helix: 2.81 (0.13), residues: 1536 sheet: -1.22 (0.42), residues: 132 loop : -3.08 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 181 HIS 0.005 0.001 HIS E 221 PHE 0.011 0.001 PHE F 200 TYR 0.009 0.001 TYR A 146 ARG 0.003 0.000 ARG A 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7842.38 seconds wall clock time: 140 minutes 11.06 seconds (8411.06 seconds total)