Starting phenix.real_space_refine on Fri Jun 27 23:35:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqx_37757/06_2025/8wqx_37757.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqx_37757/06_2025/8wqx_37757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wqx_37757/06_2025/8wqx_37757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqx_37757/06_2025/8wqx_37757.map" model { file = "/net/cci-nas-00/data/ceres_data/8wqx_37757/06_2025/8wqx_37757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqx_37757/06_2025/8wqx_37757.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.082 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 Fe 24 7.16 5 S 72 5.16 5 C 20922 2.51 5 N 5325 2.21 5 O 6383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 286 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32726 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "B" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "C" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "D" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "E" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "F" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "G" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "H" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "I" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "J" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "K" Number of atoms: 1353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 1 bond proxies already assigned to first conformer: 1341 Chain: "L" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "M" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "N" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "O" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "P" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "Q" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "R" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "S" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "T" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "U" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "V" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "W" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "X" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 48 residue: pdb=" N AGLU A 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU A 44 " occ=0.52 residue: pdb=" N AGLU A 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU A 108 " occ=0.54 residue: pdb=" N AGLU B 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU B 44 " occ=0.52 residue: pdb=" N AGLU B 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU B 108 " occ=0.54 residue: pdb=" N AGLU C 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU C 44 " occ=0.52 residue: pdb=" N AGLU C 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU C 108 " occ=0.54 residue: pdb=" N AGLU D 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU D 44 " occ=0.52 residue: pdb=" N AGLU D 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU D 108 " occ=0.54 residue: pdb=" N AGLU E 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU E 44 " occ=0.52 residue: pdb=" N AGLU E 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU E 108 " occ=0.54 residue: pdb=" N AGLU F 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU F 44 " occ=0.52 residue: pdb=" N AGLU F 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU F 108 " occ=0.54 ... (remaining 36 not shown) Time building chain proxies: 33.28, per 1000 atoms: 1.02 Number of scatterers: 32726 At special positions: 0 Unit cell: (132.956, 132.956, 132.956, 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) Fe 24 26.01 S 72 16.00 O 6383 8.00 N 5325 7.00 C 20922 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 8.43 Conformation dependent library (CDL) restraints added in 7.8 seconds 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7678 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 12 sheets defined 84.2% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'A' and resid 13 through 44 removed outlier: 3.915A pdb=" N ASN A 17 " --> pdb=" O SER A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 63 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.581A pdb=" N ILE A 69 " --> pdb=" O HIS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 123 removed outlier: 3.727A pdb=" N ASP A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 151 removed outlier: 4.624A pdb=" N TRP A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 155 Processing helix chain 'A' and resid 158 through 171 removed outlier: 3.600A pdb=" N ILE A 162 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 44 Processing helix chain 'B' and resid 47 through 63 Processing helix chain 'B' and resid 63 through 77 removed outlier: 4.599A pdb=" N ILE B 69 " --> pdb=" O HIS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 123 removed outlier: 3.730A pdb=" N ASP B 111 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 151 removed outlier: 4.627A pdb=" N TRP B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 155 Processing helix chain 'B' and resid 158 through 171 removed outlier: 3.599A pdb=" N ILE B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 44 Processing helix chain 'C' and resid 47 through 63 Processing helix chain 'C' and resid 63 through 77 removed outlier: 4.581A pdb=" N ILE C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 123 removed outlier: 3.726A pdb=" N ASP C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 151 removed outlier: 4.624A pdb=" N TRP C 134 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU C 140 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 155 Processing helix chain 'C' and resid 158 through 171 removed outlier: 3.691A pdb=" N ILE C 162 " --> pdb=" O ASP C 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 44 Processing helix chain 'D' and resid 47 through 63 Processing helix chain 'D' and resid 63 through 77 removed outlier: 4.581A pdb=" N ILE D 69 " --> pdb=" O HIS D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 123 removed outlier: 3.727A pdb=" N ASP D 111 " --> pdb=" O ASN D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 151 removed outlier: 4.626A pdb=" N TRP D 134 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR D 135 " --> pdb=" O PHE D 131 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU D 140 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 155 Processing helix chain 'D' and resid 158 through 171 removed outlier: 3.654A pdb=" N ILE D 162 " --> pdb=" O ASP D 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 44 Processing helix chain 'E' and resid 47 through 63 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.581A pdb=" N ILE E 69 " --> pdb=" O HIS E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 123 removed outlier: 3.726A pdb=" N ASP E 111 " --> pdb=" O ASN E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 151 removed outlier: 4.624A pdb=" N TRP E 134 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR E 135 " --> pdb=" O PHE E 131 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL E 149 " --> pdb=" O GLU E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 155 Processing helix chain 'E' and resid 158 through 171 removed outlier: 3.703A pdb=" N ILE E 162 " --> pdb=" O ASP E 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 44 Processing helix chain 'F' and resid 47 through 63 Processing helix chain 'F' and resid 63 through 77 removed outlier: 4.582A pdb=" N ILE F 69 " --> pdb=" O HIS F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 123 removed outlier: 3.727A pdb=" N ASP F 111 " --> pdb=" O ASN F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 151 removed outlier: 4.624A pdb=" N TRP F 134 " --> pdb=" O TYR F 130 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR F 135 " --> pdb=" O PHE F 131 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU F 140 " --> pdb=" O VAL F 136 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL F 149 " --> pdb=" O GLU F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 155 Processing helix chain 'F' and resid 158 through 171 removed outlier: 3.687A pdb=" N ILE F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 44 Processing helix chain 'G' and resid 47 through 63 Processing helix chain 'G' and resid 63 through 77 removed outlier: 4.581A pdb=" N ILE G 69 " --> pdb=" O HIS G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 123 removed outlier: 3.728A pdb=" N ASP G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 151 removed outlier: 4.623A pdb=" N TRP G 134 " --> pdb=" O TYR G 130 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR G 135 " --> pdb=" O PHE G 131 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU G 140 " --> pdb=" O VAL G 136 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL G 149 " --> pdb=" O GLU G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 155 Processing helix chain 'G' and resid 158 through 171 removed outlier: 3.600A pdb=" N ILE G 162 " --> pdb=" O ASP G 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 44 Processing helix chain 'H' and resid 47 through 63 Processing helix chain 'H' and resid 63 through 77 removed outlier: 4.599A pdb=" N ILE H 69 " --> pdb=" O HIS H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 123 removed outlier: 3.729A pdb=" N ASP H 111 " --> pdb=" O ASN H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 151 removed outlier: 4.625A pdb=" N TRP H 134 " --> pdb=" O TYR H 130 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR H 135 " --> pdb=" O PHE H 131 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU H 140 " --> pdb=" O VAL H 136 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL H 149 " --> pdb=" O GLU H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 155 Processing helix chain 'H' and resid 158 through 171 removed outlier: 3.600A pdb=" N ILE H 162 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 44 Processing helix chain 'I' and resid 47 through 63 Processing helix chain 'I' and resid 63 through 77 removed outlier: 4.582A pdb=" N ILE I 69 " --> pdb=" O HIS I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 123 removed outlier: 3.728A pdb=" N ASP I 111 " --> pdb=" O ASN I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 151 removed outlier: 3.521A pdb=" N PHE I 129 " --> pdb=" O ASP I 125 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TRP I 134 " --> pdb=" O TYR I 130 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR I 135 " --> pdb=" O PHE I 131 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU I 140 " --> pdb=" O VAL I 136 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 155 Processing helix chain 'I' and resid 158 through 171 removed outlier: 3.650A pdb=" N ILE I 162 " --> pdb=" O ASP I 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 44 Processing helix chain 'J' and resid 47 through 63 Processing helix chain 'J' and resid 63 through 77 removed outlier: 4.583A pdb=" N ILE J 69 " --> pdb=" O HIS J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 123 removed outlier: 3.727A pdb=" N ASP J 111 " --> pdb=" O ASN J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 151 removed outlier: 4.626A pdb=" N TRP J 134 " --> pdb=" O TYR J 130 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR J 135 " --> pdb=" O PHE J 131 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU J 140 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL J 149 " --> pdb=" O GLU J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 155 Processing helix chain 'J' and resid 158 through 171 removed outlier: 3.600A pdb=" N ILE J 162 " --> pdb=" O ASP J 158 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 44 Processing helix chain 'K' and resid 47 through 63 Processing helix chain 'K' and resid 63 through 77 removed outlier: 4.582A pdb=" N ILE K 69 " --> pdb=" O HIS K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 123 removed outlier: 3.727A pdb=" N ASP K 111 " --> pdb=" O ASN K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 151 removed outlier: 4.626A pdb=" N TRP K 134 " --> pdb=" O TYR K 130 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR K 135 " --> pdb=" O PHE K 131 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU K 140 " --> pdb=" O VAL K 136 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL K 149 " --> pdb=" O GLU K 145 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 155 Processing helix chain 'K' and resid 158 through 171 removed outlier: 3.602A pdb=" N ILE K 162 " --> pdb=" O ASP K 158 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 44 Processing helix chain 'L' and resid 47 through 63 Processing helix chain 'L' and resid 63 through 77 removed outlier: 4.581A pdb=" N ILE L 69 " --> pdb=" O HIS L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 123 removed outlier: 3.724A pdb=" N ASP L 111 " --> pdb=" O ASN L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 151 removed outlier: 3.518A pdb=" N PHE L 129 " --> pdb=" O ASP L 125 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TRP L 134 " --> pdb=" O TYR L 130 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR L 135 " --> pdb=" O PHE L 131 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU L 140 " --> pdb=" O VAL L 136 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL L 149 " --> pdb=" O GLU L 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 155 Processing helix chain 'L' and resid 158 through 171 removed outlier: 3.635A pdb=" N ILE L 162 " --> pdb=" O ASP L 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 44 Processing helix chain 'M' and resid 47 through 63 Processing helix chain 'M' and resid 63 through 77 removed outlier: 4.581A pdb=" N ILE M 69 " --> pdb=" O HIS M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 94 through 123 removed outlier: 3.729A pdb=" N ASP M 111 " --> pdb=" O ASN M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 151 removed outlier: 3.522A pdb=" N PHE M 129 " --> pdb=" O ASP M 125 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TRP M 134 " --> pdb=" O TYR M 130 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR M 135 " --> pdb=" O PHE M 131 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU M 140 " --> pdb=" O VAL M 136 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL M 149 " --> pdb=" O GLU M 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 155 Processing helix chain 'M' and resid 158 through 171 removed outlier: 3.615A pdb=" N ILE M 162 " --> pdb=" O ASP M 158 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 44 Processing helix chain 'N' and resid 47 through 63 Processing helix chain 'N' and resid 63 through 77 removed outlier: 4.581A pdb=" N ILE N 69 " --> pdb=" O HIS N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 123 removed outlier: 3.728A pdb=" N ASP N 111 " --> pdb=" O ASN N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 125 through 151 removed outlier: 4.627A pdb=" N TRP N 134 " --> pdb=" O TYR N 130 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR N 135 " --> pdb=" O PHE N 131 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU N 140 " --> pdb=" O VAL N 136 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL N 149 " --> pdb=" O GLU N 145 " (cutoff:3.500A) Processing helix chain 'N' and resid 152 through 155 Processing helix chain 'N' and resid 158 through 171 removed outlier: 3.615A pdb=" N ILE N 162 " --> pdb=" O ASP N 158 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 44 Processing helix chain 'O' and resid 47 through 63 Processing helix chain 'O' and resid 63 through 77 removed outlier: 4.583A pdb=" N ILE O 69 " --> pdb=" O HIS O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 94 through 123 removed outlier: 3.728A pdb=" N ASP O 111 " --> pdb=" O ASN O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 125 through 151 removed outlier: 4.624A pdb=" N TRP O 134 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR O 135 " --> pdb=" O PHE O 131 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU O 140 " --> pdb=" O VAL O 136 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL O 149 " --> pdb=" O GLU O 145 " (cutoff:3.500A) Processing helix chain 'O' and resid 152 through 155 Processing helix chain 'O' and resid 158 through 171 removed outlier: 3.688A pdb=" N ILE O 162 " --> pdb=" O ASP O 158 " (cutoff:3.500A) Processing helix chain 'P' and resid 14 through 44 Processing helix chain 'P' and resid 47 through 63 Processing helix chain 'P' and resid 63 through 77 removed outlier: 4.581A pdb=" N ILE P 69 " --> pdb=" O HIS P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 123 removed outlier: 3.728A pdb=" N ASP P 111 " --> pdb=" O ASN P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 151 removed outlier: 4.624A pdb=" N TRP P 134 " --> pdb=" O TYR P 130 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR P 135 " --> pdb=" O PHE P 131 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU P 140 " --> pdb=" O VAL P 136 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL P 149 " --> pdb=" O GLU P 145 " (cutoff:3.500A) Processing helix chain 'P' and resid 152 through 155 Processing helix chain 'P' and resid 158 through 171 removed outlier: 3.600A pdb=" N ILE P 162 " --> pdb=" O ASP P 158 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 44 Processing helix chain 'Q' and resid 47 through 63 Processing helix chain 'Q' and resid 63 through 77 removed outlier: 4.583A pdb=" N ILE Q 69 " --> pdb=" O HIS Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 94 through 123 removed outlier: 3.728A pdb=" N ASP Q 111 " --> pdb=" O ASN Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 151 removed outlier: 4.626A pdb=" N TRP Q 134 " --> pdb=" O TYR Q 130 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR Q 135 " --> pdb=" O PHE Q 131 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU Q 140 " --> pdb=" O VAL Q 136 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL Q 149 " --> pdb=" O GLU Q 145 " (cutoff:3.500A) Processing helix chain 'Q' and resid 152 through 155 Processing helix chain 'Q' and resid 158 through 171 removed outlier: 3.691A pdb=" N ILE Q 162 " --> pdb=" O ASP Q 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 44 Processing helix chain 'R' and resid 47 through 63 Processing helix chain 'R' and resid 63 through 77 removed outlier: 4.599A pdb=" N ILE R 69 " --> pdb=" O HIS R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 123 removed outlier: 3.725A pdb=" N ASP R 111 " --> pdb=" O ASN R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 151 removed outlier: 4.624A pdb=" N TRP R 134 " --> pdb=" O TYR R 130 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR R 135 " --> pdb=" O PHE R 131 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU R 140 " --> pdb=" O VAL R 136 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL R 149 " --> pdb=" O GLU R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 155 Processing helix chain 'R' and resid 158 through 171 removed outlier: 3.655A pdb=" N ILE R 162 " --> pdb=" O ASP R 158 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 44 Processing helix chain 'S' and resid 47 through 63 Processing helix chain 'S' and resid 63 through 77 removed outlier: 4.582A pdb=" N ILE S 69 " --> pdb=" O HIS S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 94 through 123 removed outlier: 3.731A pdb=" N ASP S 111 " --> pdb=" O ASN S 107 " (cutoff:3.500A) Processing helix chain 'S' and resid 125 through 151 removed outlier: 3.519A pdb=" N PHE S 129 " --> pdb=" O ASP S 125 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TRP S 134 " --> pdb=" O TYR S 130 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR S 135 " --> pdb=" O PHE S 131 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU S 140 " --> pdb=" O VAL S 136 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL S 149 " --> pdb=" O GLU S 145 " (cutoff:3.500A) Processing helix chain 'S' and resid 152 through 155 Processing helix chain 'S' and resid 158 through 171 removed outlier: 3.615A pdb=" N ILE S 162 " --> pdb=" O ASP S 158 " (cutoff:3.500A) Processing helix chain 'T' and resid 14 through 44 Processing helix chain 'T' and resid 47 through 63 Processing helix chain 'T' and resid 63 through 77 removed outlier: 4.581A pdb=" N ILE T 69 " --> pdb=" O HIS T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 94 through 123 removed outlier: 3.730A pdb=" N ASP T 111 " --> pdb=" O ASN T 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 125 through 151 removed outlier: 4.624A pdb=" N TRP T 134 " --> pdb=" O TYR T 130 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR T 135 " --> pdb=" O PHE T 131 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU T 140 " --> pdb=" O VAL T 136 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL T 149 " --> pdb=" O GLU T 145 " (cutoff:3.500A) Processing helix chain 'T' and resid 152 through 155 Processing helix chain 'T' and resid 158 through 171 removed outlier: 3.599A pdb=" N ILE T 162 " --> pdb=" O ASP T 158 " (cutoff:3.500A) Processing helix chain 'U' and resid 14 through 44 Processing helix chain 'U' and resid 47 through 63 Processing helix chain 'U' and resid 63 through 77 removed outlier: 4.599A pdb=" N ILE U 69 " --> pdb=" O HIS U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 94 through 123 removed outlier: 3.728A pdb=" N ASP U 111 " --> pdb=" O ASN U 107 " (cutoff:3.500A) Processing helix chain 'U' and resid 125 through 151 removed outlier: 4.624A pdb=" N TRP U 134 " --> pdb=" O TYR U 130 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR U 135 " --> pdb=" O PHE U 131 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU U 140 " --> pdb=" O VAL U 136 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL U 149 " --> pdb=" O GLU U 145 " (cutoff:3.500A) Processing helix chain 'U' and resid 152 through 155 Processing helix chain 'U' and resid 158 through 171 removed outlier: 3.612A pdb=" N ILE U 162 " --> pdb=" O ASP U 158 " (cutoff:3.500A) Processing helix chain 'V' and resid 14 through 44 Processing helix chain 'V' and resid 47 through 63 Processing helix chain 'V' and resid 63 through 77 removed outlier: 4.599A pdb=" N ILE V 69 " --> pdb=" O HIS V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 94 through 123 removed outlier: 3.729A pdb=" N ASP V 111 " --> pdb=" O ASN V 107 " (cutoff:3.500A) Processing helix chain 'V' and resid 125 through 151 removed outlier: 4.624A pdb=" N TRP V 134 " --> pdb=" O TYR V 130 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR V 135 " --> pdb=" O PHE V 131 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU V 140 " --> pdb=" O VAL V 136 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL V 149 " --> pdb=" O GLU V 145 " (cutoff:3.500A) Processing helix chain 'V' and resid 152 through 155 Processing helix chain 'V' and resid 158 through 171 removed outlier: 3.603A pdb=" N ILE V 162 " --> pdb=" O ASP V 158 " (cutoff:3.500A) Processing helix chain 'W' and resid 14 through 44 Processing helix chain 'W' and resid 47 through 63 Processing helix chain 'W' and resid 63 through 77 removed outlier: 4.581A pdb=" N ILE W 69 " --> pdb=" O HIS W 65 " (cutoff:3.500A) Processing helix chain 'W' and resid 94 through 123 removed outlier: 3.715A pdb=" N ASP W 111 " --> pdb=" O ASN W 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 125 through 151 removed outlier: 3.522A pdb=" N PHE W 129 " --> pdb=" O ASP W 125 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TRP W 134 " --> pdb=" O TYR W 130 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR W 135 " --> pdb=" O PHE W 131 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU W 140 " --> pdb=" O VAL W 136 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL W 149 " --> pdb=" O GLU W 145 " (cutoff:3.500A) Processing helix chain 'W' and resid 152 through 155 Processing helix chain 'W' and resid 158 through 171 removed outlier: 3.616A pdb=" N ILE W 162 " --> pdb=" O ASP W 158 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 44 Processing helix chain 'X' and resid 47 through 63 Processing helix chain 'X' and resid 63 through 77 removed outlier: 4.581A pdb=" N ILE X 69 " --> pdb=" O HIS X 65 " (cutoff:3.500A) Processing helix chain 'X' and resid 94 through 123 removed outlier: 3.727A pdb=" N ASP X 111 " --> pdb=" O ASN X 107 " (cutoff:3.500A) Processing helix chain 'X' and resid 125 through 151 removed outlier: 4.627A pdb=" N TRP X 134 " --> pdb=" O TYR X 130 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR X 135 " --> pdb=" O PHE X 131 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU X 140 " --> pdb=" O VAL X 136 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL X 149 " --> pdb=" O GLU X 145 " (cutoff:3.500A) Processing helix chain 'X' and resid 152 through 155 Processing helix chain 'X' and resid 158 through 171 removed outlier: 3.659A pdb=" N ILE X 162 " --> pdb=" O ASP X 158 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 87 Processing sheet with id=AA2, first strand: chain 'B' and resid 83 through 87 Processing sheet with id=AA3, first strand: chain 'C' and resid 83 through 87 Processing sheet with id=AA4, first strand: chain 'D' and resid 83 through 87 Processing sheet with id=AA5, first strand: chain 'I' and resid 83 through 87 Processing sheet with id=AA6, first strand: chain 'J' and resid 83 through 87 Processing sheet with id=AA7, first strand: chain 'K' and resid 83 through 87 Processing sheet with id=AA8, first strand: chain 'L' and resid 83 through 87 Processing sheet with id=AA9, first strand: chain 'M' and resid 83 through 87 Processing sheet with id=AB1, first strand: chain 'N' and resid 83 through 87 Processing sheet with id=AB2, first strand: chain 'O' and resid 83 through 87 Processing sheet with id=AB3, first strand: chain 'P' and resid 83 through 87 2611 hydrogen bonds defined for protein. 7785 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: 11.31 Time building geometry restraints manager: 9.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10748 1.34 - 1.46: 4461 1.46 - 1.57: 18044 1.57 - 1.69: 0 1.69 - 1.80: 144 Bond restraints: 33397 Sorted by residual: bond pdb=" C VAL K 28 " pdb=" O VAL K 28 " ideal model delta sigma weight residual 1.237 1.248 -0.011 1.13e-02 7.83e+03 9.69e-01 bond pdb=" C VAL J 28 " pdb=" O VAL J 28 " ideal model delta sigma weight residual 1.237 1.248 -0.011 1.13e-02 7.83e+03 9.69e-01 bond pdb=" C VAL C 28 " pdb=" O VAL C 28 " ideal model delta sigma weight residual 1.237 1.247 -0.011 1.13e-02 7.83e+03 8.72e-01 bond pdb=" C VAL H 28 " pdb=" O VAL H 28 " ideal model delta sigma weight residual 1.237 1.247 -0.011 1.13e-02 7.83e+03 8.72e-01 bond pdb=" C VAL I 28 " pdb=" O VAL I 28 " ideal model delta sigma weight residual 1.237 1.247 -0.011 1.13e-02 7.83e+03 8.72e-01 ... (remaining 33392 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.78: 40328 0.78 - 1.56: 3968 1.56 - 2.33: 534 2.33 - 3.11: 227 3.11 - 3.89: 72 Bond angle restraints: 45129 Sorted by residual: angle pdb=" N ILE K 179 " pdb=" CA ILE K 179 " pdb=" C ILE K 179 " ideal model delta sigma weight residual 110.42 108.51 1.91 9.40e-01 1.13e+00 4.13e+00 angle pdb=" C VAL F 149 " pdb=" N VAL F 150 " pdb=" CA VAL F 150 " ideal model delta sigma weight residual 120.64 117.78 2.86 1.66e+00 3.63e-01 2.98e+00 angle pdb=" C VAL W 149 " pdb=" N VAL W 150 " pdb=" CA VAL W 150 " ideal model delta sigma weight residual 120.64 117.78 2.86 1.66e+00 3.63e-01 2.96e+00 angle pdb=" C VAL A 149 " pdb=" N VAL A 150 " pdb=" CA VAL A 150 " ideal model delta sigma weight residual 120.64 117.78 2.86 1.66e+00 3.63e-01 2.96e+00 angle pdb=" C VAL I 149 " pdb=" N VAL I 150 " pdb=" CA VAL I 150 " ideal model delta sigma weight residual 120.64 117.79 2.85 1.66e+00 3.63e-01 2.95e+00 ... (remaining 45124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.96: 17374 14.96 - 29.92: 1861 29.92 - 44.88: 566 44.88 - 59.84: 186 59.84 - 74.80: 48 Dihedral angle restraints: 20035 sinusoidal: 8134 harmonic: 11901 Sorted by residual: dihedral pdb=" CA ASP P 71 " pdb=" CB ASP P 71 " pdb=" CG ASP P 71 " pdb=" OD1 ASP P 71 " ideal model delta sinusoidal sigma weight residual -30.00 -84.96 54.96 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA ASP Q 71 " pdb=" CB ASP Q 71 " pdb=" CG ASP Q 71 " pdb=" OD1 ASP Q 71 " ideal model delta sinusoidal sigma weight residual -30.00 -84.94 54.94 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA ASP U 71 " pdb=" CB ASP U 71 " pdb=" CG ASP U 71 " pdb=" OD1 ASP U 71 " ideal model delta sinusoidal sigma weight residual -30.00 -84.91 54.91 1 2.00e+01 2.50e-03 1.02e+01 ... (remaining 20032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2315 0.025 - 0.049: 1539 0.049 - 0.074: 704 0.074 - 0.099: 234 0.099 - 0.123: 103 Chirality restraints: 4895 Sorted by residual: chirality pdb=" CB VAL N 136 " pdb=" CA VAL N 136 " pdb=" CG1 VAL N 136 " pdb=" CG2 VAL N 136 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CB VAL F 136 " pdb=" CA VAL F 136 " pdb=" CG1 VAL F 136 " pdb=" CG2 VAL F 136 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CB VAL Q 136 " pdb=" CA VAL Q 136 " pdb=" CG1 VAL Q 136 " pdb=" CG2 VAL Q 136 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.66e-01 ... (remaining 4892 not shown) Planarity restraints: 5806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE T 91 " -0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO T 92 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO T 92 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO T 92 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE I 91 " -0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO I 92 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO I 92 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO I 92 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE W 91 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO W 92 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO W 92 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO W 92 " -0.017 5.00e-02 4.00e+02 ... (remaining 5803 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 161 2.59 - 3.17: 26587 3.17 - 3.74: 48316 3.74 - 4.32: 66401 4.32 - 4.90: 112581 Nonbonded interactions: 254046 Sorted by model distance: nonbonded pdb=" NE2 HIS E 65 " pdb="FE FE E 201 " model vdw 2.012 2.340 nonbonded pdb=" NE2 HIS O 65 " pdb="FE FE O 201 " model vdw 2.012 2.340 nonbonded pdb=" NE2 HIS W 65 " pdb="FE FE W 201 " model vdw 2.012 2.340 nonbonded pdb=" NE2 HIS S 65 " pdb="FE FE S 201 " model vdw 2.012 2.340 nonbonded pdb=" NE2 HIS C 65 " pdb="FE FE C 201 " model vdw 2.012 2.340 ... (remaining 254041 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 181 or resid 201)) selection = (chain 'B' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 181 or resid 201)) selection = (chain 'C' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 181 or resid 201)) selection = (chain 'D' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 181 or resid 201)) selection = (chain 'E' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 181 or resid 201)) selection = (chain 'F' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 181 or resid 201)) selection = (chain 'G' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 181 or resid 201)) selection = (chain 'H' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 181 or resid 201)) selection = (chain 'I' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 181 or resid 201)) selection = (chain 'J' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 181 or resid 201)) selection = (chain 'K' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'L' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 181 or resid 201)) selection = (chain 'M' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 181 or resid 201)) selection = (chain 'N' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 181 or resid 201)) selection = (chain 'O' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 181 or resid 201)) selection = (chain 'P' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 181 or resid 201)) selection = (chain 'Q' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 181 or resid 201)) selection = (chain 'R' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 181 or resid 201)) selection = (chain 'S' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 181 or resid 201)) selection = (chain 'T' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 181 or resid 201)) selection = (chain 'U' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 181 or resid 201)) selection = (chain 'V' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 181 or resid 201)) selection = (chain 'W' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 181 or resid 201)) selection = (chain 'X' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 181 or resid 201)) } 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=0.46 max=1.00 mean=0.99 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: 1.030 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: 0.020 Extract box with map and model: 1.320 Check model and map are aligned: 0.240 Set scattering table: 0.340 Process input model: 90.840 Find NCS groups from input model: 2.540 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 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 : 0.005 0.023 33397 Z= 0.223 Angle : 0.515 3.888 45129 Z= 0.300 Chirality : 0.040 0.123 4895 Planarity : 0.003 0.030 5806 Dihedral : 14.735 74.802 12357 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.68 % Allowed : 3.80 % Favored : 95.52 % 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 (0.12), residues: 3983 helix: -0.08 (0.08), residues: 3072 sheet: None (None), residues: 0 loop : -3.17 (0.17), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 134 HIS 0.003 0.001 HIS Q 36 PHE 0.006 0.001 PHE B 129 TYR 0.015 0.002 TYR U 126 ARG 0.002 0.000 ARG H 75 Details of bonding type rmsd hydrogen bonds : bond 0.13371 ( 2611) hydrogen bonds : angle 4.38140 ( 7785) covalent geometry : bond 0.00502 (33397) covalent geometry : angle 0.51481 (45129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 467 time to evaluate : 4.080 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: A 78 MET cc_start: 0.7972 (mtt) cc_final: 0.7638 (mtt) REVERT: B 78 MET cc_start: 0.8036 (mtt) cc_final: 0.7700 (mtt) REVERT: D 78 MET cc_start: 0.8044 (mtt) cc_final: 0.7659 (mtt) REVERT: E 78 MET cc_start: 0.7960 (mtt) cc_final: 0.7624 (mtt) REVERT: F 78 MET cc_start: 0.8035 (mtt) cc_final: 0.7676 (mtt) REVERT: G 78 MET cc_start: 0.8011 (mtt) cc_final: 0.7659 (mtt) REVERT: H 78 MET cc_start: 0.7995 (mtt) cc_final: 0.7626 (mtt) REVERT: I 78 MET cc_start: 0.7950 (mtt) cc_final: 0.7624 (mtt) REVERT: J 78 MET cc_start: 0.7983 (mtt) cc_final: 0.7647 (mtt) REVERT: K 78 MET cc_start: 0.8007 (mtt) cc_final: 0.7669 (mtt) REVERT: L 78 MET cc_start: 0.8019 (mtt) cc_final: 0.7648 (mtt) REVERT: M 78 MET cc_start: 0.8036 (mtt) cc_final: 0.7672 (mtt) REVERT: N 78 MET cc_start: 0.8066 (mtt) cc_final: 0.7684 (mtt) REVERT: O 78 MET cc_start: 0.8021 (mtt) cc_final: 0.7672 (mtt) REVERT: P 78 MET cc_start: 0.8022 (mtt) cc_final: 0.7662 (mtt) REVERT: Q 78 MET cc_start: 0.7987 (mtt) cc_final: 0.7645 (mtt) REVERT: R 78 MET cc_start: 0.8050 (mtt) cc_final: 0.7652 (mtt) REVERT: S 78 MET cc_start: 0.8016 (mtt) cc_final: 0.7664 (mtt) REVERT: T 78 MET cc_start: 0.7962 (mtt) cc_final: 0.7619 (mtt) REVERT: U 78 MET cc_start: 0.8034 (mtt) cc_final: 0.7697 (mtt) REVERT: V 78 MET cc_start: 0.7987 (mtt) cc_final: 0.7652 (mtt) REVERT: W 78 MET cc_start: 0.8076 (mtt) cc_final: 0.7729 (mtt) REVERT: X 78 MET cc_start: 0.8055 (mtt) cc_final: 0.7701 (mtt) outliers start: 0 outliers final: 0 residues processed: 467 average time/residue: 0.4610 time to fit residues: 340.2653 Evaluate side-chains 255 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 4.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 2.9990 chunk 291 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 300 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 348 optimal weight: 0.5980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS B 23 HIS C 23 HIS D 23 HIS E 23 HIS F 23 HIS G 23 HIS H 23 HIS I 23 HIS J 23 HIS K 23 HIS L 23 HIS M 23 HIS N 23 HIS O 23 HIS P 23 HIS Q 23 HIS R 23 HIS S 23 HIS T 23 HIS U 23 HIS V 23 HIS W 23 HIS X 23 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.131403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.113903 restraints weight = 314069.933| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 5.45 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 33397 Z= 0.137 Angle : 0.466 4.834 45129 Z= 0.255 Chirality : 0.039 0.157 4895 Planarity : 0.003 0.033 5806 Dihedral : 3.602 11.562 4319 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 1.13 % Allowed : 8.98 % Favored : 89.89 % 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: 0.66 (0.13), residues: 3983 helix: 1.24 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -2.69 (0.18), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 134 HIS 0.003 0.001 HIS J 39 PHE 0.007 0.001 PHE P 129 TYR 0.011 0.001 TYR J 24 ARG 0.006 0.001 ARG W 105 Details of bonding type rmsd hydrogen bonds : bond 0.06142 ( 2611) hydrogen bonds : angle 3.23420 ( 7785) covalent geometry : bond 0.00271 (33397) covalent geometry : angle 0.46644 (45129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 368 time to evaluate : 3.979 Fit side-chains REVERT: A 78 MET cc_start: 0.8423 (mtt) cc_final: 0.8132 (mtt) REVERT: B 78 MET cc_start: 0.8462 (mtt) cc_final: 0.8178 (mtt) REVERT: C 78 MET cc_start: 0.8400 (mtt) cc_final: 0.8095 (mtt) REVERT: D 78 MET cc_start: 0.8458 (mtt) cc_final: 0.8163 (mtt) REVERT: E 78 MET cc_start: 0.8405 (mtt) cc_final: 0.8116 (mtt) REVERT: F 78 MET cc_start: 0.8432 (mtt) cc_final: 0.8146 (mtt) REVERT: G 78 MET cc_start: 0.8424 (mtt) cc_final: 0.8133 (mtt) REVERT: H 78 MET cc_start: 0.8447 (mtt) cc_final: 0.8165 (mtt) REVERT: I 78 MET cc_start: 0.8449 (mtt) cc_final: 0.8158 (mtt) REVERT: J 78 MET cc_start: 0.8442 (mtt) cc_final: 0.8145 (mtt) REVERT: K 78 MET cc_start: 0.8400 (mtt) cc_final: 0.8125 (mtt) REVERT: L 78 MET cc_start: 0.8454 (mtt) cc_final: 0.8163 (mtt) REVERT: M 78 MET cc_start: 0.8445 (mtt) cc_final: 0.8164 (mtt) REVERT: N 78 MET cc_start: 0.8469 (mtt) cc_final: 0.8187 (mtt) REVERT: O 47 MET cc_start: 0.8585 (mtm) cc_final: 0.8117 (mtp) REVERT: O 78 MET cc_start: 0.8453 (mtt) cc_final: 0.8155 (mtt) REVERT: P 78 MET cc_start: 0.8429 (mtt) cc_final: 0.8129 (mtt) REVERT: Q 78 MET cc_start: 0.8449 (mtt) cc_final: 0.8166 (mtt) REVERT: R 78 MET cc_start: 0.8418 (mtt) cc_final: 0.8130 (mtt) REVERT: S 78 MET cc_start: 0.8451 (mtt) cc_final: 0.8164 (mtt) REVERT: T 78 MET cc_start: 0.8447 (mtt) cc_final: 0.8160 (mtt) REVERT: U 78 MET cc_start: 0.8432 (mtt) cc_final: 0.8148 (mtt) REVERT: V 78 MET cc_start: 0.8435 (mtt) cc_final: 0.8142 (mtt) REVERT: W 78 MET cc_start: 0.8459 (mtt) cc_final: 0.8168 (mtt) REVERT: X 78 MET cc_start: 0.8458 (mtt) cc_final: 0.8164 (mtt) outliers start: 16 outliers final: 0 residues processed: 371 average time/residue: 0.3493 time to fit residues: 229.4795 Evaluate side-chains 307 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 3.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 315 optimal weight: 0.9980 chunk 373 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 chunk 256 optimal weight: 10.0000 chunk 333 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 230 optimal weight: 8.9990 chunk 252 optimal weight: 7.9990 chunk 368 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 76 ASN D 76 ASN E 76 ASN F 76 ASN G 76 ASN H 76 ASN I 76 ASN J 76 ASN K 76 ASN L 76 ASN M 76 ASN N 76 ASN O 76 ASN P 76 ASN Q 76 ASN R 76 ASN S 76 ASN T 76 ASN U 76 ASN V 76 ASN W 76 ASN X 76 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.125496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.107194 restraints weight = 332098.532| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 5.69 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 33397 Z= 0.172 Angle : 0.499 6.843 45129 Z= 0.274 Chirality : 0.039 0.128 4895 Planarity : 0.003 0.032 5806 Dihedral : 3.618 11.686 4319 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.66 % Allowed : 8.98 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.13), residues: 3983 helix: 1.57 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -2.70 (0.17), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 134 HIS 0.003 0.001 HIS F 39 PHE 0.006 0.001 PHE W 129 TYR 0.014 0.001 TYR H 24 ARG 0.005 0.001 ARG U 105 Details of bonding type rmsd hydrogen bonds : bond 0.07360 ( 2611) hydrogen bonds : angle 3.41769 ( 7785) covalent geometry : bond 0.00377 (33397) covalent geometry : angle 0.49914 (45129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 310 time to evaluate : 3.974 Fit side-chains REVERT: C 78 MET cc_start: 0.8462 (mtt) cc_final: 0.8223 (mtt) outliers start: 35 outliers final: 27 residues processed: 345 average time/residue: 0.3527 time to fit residues: 216.4753 Evaluate side-chains 297 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 270 time to evaluate : 4.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain L residue 76 ASN Chi-restraints excluded: chain M residue 76 ASN Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain P residue 76 ASN Chi-restraints excluded: chain Q residue 76 ASN Chi-restraints excluded: chain R residue 76 ASN Chi-restraints excluded: chain S residue 76 ASN Chi-restraints excluded: chain T residue 76 ASN Chi-restraints excluded: chain U residue 76 ASN Chi-restraints excluded: chain V residue 76 ASN Chi-restraints excluded: chain W residue 76 ASN Chi-restraints excluded: chain X residue 76 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 212 optimal weight: 2.9990 chunk 174 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 262 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 256 optimal weight: 7.9990 chunk 250 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 266 optimal weight: 4.9990 chunk 292 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.124827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.106896 restraints weight = 338607.894| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 5.71 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 33397 Z= 0.173 Angle : 0.489 6.090 45129 Z= 0.270 Chirality : 0.039 0.123 4895 Planarity : 0.003 0.034 5806 Dihedral : 3.595 11.125 4319 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.90 % Allowed : 9.60 % Favored : 89.50 % 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: 1.36 (0.13), residues: 3983 helix: 1.74 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -2.46 (0.17), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 134 HIS 0.003 0.001 HIS J 39 PHE 0.005 0.001 PHE S 129 TYR 0.013 0.001 TYR N 24 ARG 0.004 0.001 ARG O 105 Details of bonding type rmsd hydrogen bonds : bond 0.07399 ( 2611) hydrogen bonds : angle 3.41114 ( 7785) covalent geometry : bond 0.00378 (33397) covalent geometry : angle 0.48879 (45129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 250 time to evaluate : 3.566 Fit side-chains REVERT: C 78 MET cc_start: 0.8548 (mtt) cc_final: 0.8279 (mtt) outliers start: 8 outliers final: 4 residues processed: 257 average time/residue: 0.3646 time to fit residues: 166.5113 Evaluate side-chains 252 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 248 time to evaluate : 4.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain M residue 91 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 240 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 317 optimal weight: 6.9990 chunk 329 optimal weight: 0.9980 chunk 208 optimal weight: 10.0000 chunk 366 optimal weight: 0.0870 chunk 66 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 223 optimal weight: 0.9980 overall best weight: 2.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 ASN G 76 ASN H 76 ASN K 76 ASN L 76 ASN N 76 ASN O 76 ASN P 76 ASN Q 76 ASN R 76 ASN U 76 ASN W 76 ASN X 76 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.127323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.109116 restraints weight = 349817.787| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 5.79 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 33397 Z= 0.144 Angle : 0.446 5.693 45129 Z= 0.247 Chirality : 0.038 0.112 4895 Planarity : 0.003 0.032 5806 Dihedral : 3.513 10.720 4319 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.68 % Allowed : 10.87 % Favored : 88.45 % 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: 1.73 (0.13), residues: 3983 helix: 2.01 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -2.33 (0.17), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 134 HIS 0.003 0.001 HIS R 39 PHE 0.006 0.001 PHE L 129 TYR 0.012 0.001 TYR N 24 ARG 0.004 0.001 ARG T 105 Details of bonding type rmsd hydrogen bonds : bond 0.06570 ( 2611) hydrogen bonds : angle 3.22050 ( 7785) covalent geometry : bond 0.00296 (33397) covalent geometry : angle 0.44602 (45129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 3.576 Fit side-chains REVERT: D 47 MET cc_start: 0.8623 (mmm) cc_final: 0.8399 (mmt) REVERT: E 47 MET cc_start: 0.8609 (mmm) cc_final: 0.8402 (mmt) REVERT: F 47 MET cc_start: 0.8593 (mmm) cc_final: 0.8390 (mmt) REVERT: I 47 MET cc_start: 0.8583 (mmm) cc_final: 0.8377 (mmt) REVERT: Q 47 MET cc_start: 0.8591 (mmm) cc_final: 0.8383 (mmt) REVERT: R 47 MET cc_start: 0.8620 (mmm) cc_final: 0.8398 (mmt) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.4274 time to fit residues: 206.6663 Evaluate side-chains 264 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 3.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 66 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 227 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 239 optimal weight: 0.9990 chunk 221 optimal weight: 0.9990 chunk 229 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 chunk 371 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.133997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.116684 restraints weight = 307034.043| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 5.44 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3572 r_free = 0.3572 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 33397 Z= 0.109 Angle : 0.394 5.325 45129 Z= 0.221 Chirality : 0.036 0.113 4895 Planarity : 0.003 0.031 5806 Dihedral : 3.354 9.945 4319 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.68 % Allowed : 11.12 % Favored : 88.20 % 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: 2.35 (0.13), residues: 3983 helix: 2.45 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -2.17 (0.17), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP L 134 HIS 0.003 0.001 HIS H 39 PHE 0.006 0.001 PHE W 129 TYR 0.009 0.001 TYR Q 24 ARG 0.006 0.001 ARG U 105 Details of bonding type rmsd hydrogen bonds : bond 0.05043 ( 2611) hydrogen bonds : angle 2.91049 ( 7785) covalent geometry : bond 0.00202 (33397) covalent geometry : angle 0.39360 (45129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 3.687 Fit side-chains REVERT: A 47 MET cc_start: 0.8219 (mmt) cc_final: 0.7509 (mmt) REVERT: B 47 MET cc_start: 0.8119 (mmt) cc_final: 0.7417 (mmt) REVERT: C 78 MET cc_start: 0.8375 (mtt) cc_final: 0.8168 (mtt) REVERT: G 47 MET cc_start: 0.8127 (mmt) cc_final: 0.7412 (mmt) REVERT: H 47 MET cc_start: 0.8249 (mmt) cc_final: 0.7542 (mmt) REVERT: J 47 MET cc_start: 0.8093 (mmt) cc_final: 0.7374 (mmt) REVERT: K 47 MET cc_start: 0.8122 (mmt) cc_final: 0.7404 (mmt) REVERT: L 47 MET cc_start: 0.8086 (mmt) cc_final: 0.7387 (mmt) REVERT: M 47 MET cc_start: 0.8110 (mmt) cc_final: 0.7396 (mmt) REVERT: M 125 ASP cc_start: 0.8058 (t0) cc_final: 0.7539 (t70) REVERT: N 47 MET cc_start: 0.8146 (mmt) cc_final: 0.7439 (mmt) REVERT: P 47 MET cc_start: 0.8127 (mmt) cc_final: 0.7417 (mmt) REVERT: S 47 MET cc_start: 0.8126 (mmt) cc_final: 0.7412 (mmt) REVERT: T 47 MET cc_start: 0.8096 (mmt) cc_final: 0.7389 (mmt) REVERT: U 47 MET cc_start: 0.8137 (mmt) cc_final: 0.7428 (mmt) REVERT: V 47 MET cc_start: 0.8114 (mmt) cc_final: 0.7415 (mmt) REVERT: W 47 MET cc_start: 0.8153 (mmt) cc_final: 0.7441 (mmt) REVERT: X 47 MET cc_start: 0.8114 (mmt) cc_final: 0.7394 (mmt) outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.3606 time to fit residues: 220.9050 Evaluate side-chains 293 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 3.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 120 optimal weight: 3.9990 chunk 280 optimal weight: 0.7980 chunk 283 optimal weight: 8.9990 chunk 239 optimal weight: 8.9990 chunk 237 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 358 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 272 optimal weight: 10.0000 chunk 334 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 22 GLN B 76 ASN C 22 GLN D 22 GLN E 22 GLN F 22 GLN G 22 GLN H 22 GLN J 22 GLN K 22 GLN L 22 GLN M 22 GLN N 22 GLN O 22 GLN P 22 GLN Q 22 GLN R 22 GLN S 22 GLN T 22 GLN U 22 GLN W 22 GLN X 22 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.124704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.106794 restraints weight = 326099.580| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 5.68 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 33397 Z= 0.183 Angle : 0.479 5.173 45129 Z= 0.266 Chirality : 0.039 0.119 4895 Planarity : 0.003 0.028 5806 Dihedral : 3.529 11.048 4319 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.70 % Allowed : 11.52 % Favored : 87.78 % 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: 2.13 (0.13), residues: 3983 helix: 2.28 (0.09), residues: 3168 sheet: None (None), residues: 0 loop : -2.30 (0.17), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 134 HIS 0.003 0.001 HIS M 39 PHE 0.005 0.001 PHE L 129 TYR 0.015 0.002 TYR G 24 ARG 0.006 0.001 ARG L 105 Details of bonding type rmsd hydrogen bonds : bond 0.07515 ( 2611) hydrogen bonds : angle 3.38546 ( 7785) covalent geometry : bond 0.00408 (33397) covalent geometry : angle 0.47880 (45129) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 240 time to evaluate : 3.863 Fit side-chains REVERT: A 47 MET cc_start: 0.8569 (mmt) cc_final: 0.7666 (mmt) REVERT: C 47 MET cc_start: 0.8584 (mmt) cc_final: 0.7733 (mmt) REVERT: H 47 MET cc_start: 0.8568 (mmt) cc_final: 0.7666 (mmt) outliers start: 1 outliers final: 0 residues processed: 241 average time/residue: 0.3834 time to fit residues: 163.0921 Evaluate side-chains 234 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 4.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 259 optimal weight: 1.9990 chunk 374 optimal weight: 7.9990 chunk 136 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 chunk 355 optimal weight: 0.9990 chunk 378 optimal weight: 0.9980 chunk 358 optimal weight: 0.0770 chunk 200 optimal weight: 0.9990 chunk 383 optimal weight: 0.9990 chunk 286 optimal weight: 2.9990 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN F 17 ASN G 17 ASN H 76 ASN I 17 ASN J 17 ASN L 17 ASN N 17 ASN O 17 ASN O 76 ASN P 17 ASN Q 17 ASN R 17 ASN S 17 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.134719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.116360 restraints weight = 335371.105| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 5.87 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 33397 Z= 0.102 Angle : 0.380 4.947 45129 Z= 0.214 Chirality : 0.035 0.109 4895 Planarity : 0.003 0.026 5806 Dihedral : 3.326 9.915 4319 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.68 % Allowed : 12.17 % Favored : 87.16 % 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: 2.68 (0.13), residues: 3983 helix: 2.69 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -2.04 (0.17), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP L 134 HIS 0.003 0.001 HIS A 39 PHE 0.006 0.001 PHE I 129 TYR 0.008 0.001 TYR W 24 ARG 0.007 0.001 ARG W 105 Details of bonding type rmsd hydrogen bonds : bond 0.04711 ( 2611) hydrogen bonds : angle 2.83158 ( 7785) covalent geometry : bond 0.00179 (33397) covalent geometry : angle 0.38008 (45129) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 3.936 Fit side-chains REVERT: A 47 MET cc_start: 0.8246 (mmt) cc_final: 0.7526 (mmt) REVERT: B 47 MET cc_start: 0.8070 (mmt) cc_final: 0.7418 (mmt) REVERT: C 47 MET cc_start: 0.8240 (mmt) cc_final: 0.7522 (mmt) REVERT: D 47 MET cc_start: 0.8246 (mmt) cc_final: 0.7526 (mmt) REVERT: E 47 MET cc_start: 0.8240 (mmt) cc_final: 0.7546 (mmt) REVERT: F 47 MET cc_start: 0.8226 (mmt) cc_final: 0.7537 (mmt) REVERT: G 47 MET cc_start: 0.8040 (mmt) cc_final: 0.7364 (mmt) REVERT: H 47 MET cc_start: 0.8236 (mmt) cc_final: 0.7527 (mmt) REVERT: I 47 MET cc_start: 0.8245 (mmt) cc_final: 0.7552 (mmt) REVERT: I 125 ASP cc_start: 0.8083 (t0) cc_final: 0.7596 (t70) REVERT: J 47 MET cc_start: 0.8007 (mmt) cc_final: 0.7335 (mmt) REVERT: K 47 MET cc_start: 0.8028 (mmt) cc_final: 0.7357 (mmt) REVERT: L 47 MET cc_start: 0.8034 (mmt) cc_final: 0.7375 (mmt) REVERT: M 47 MET cc_start: 0.8033 (mmt) cc_final: 0.7368 (mmt) REVERT: M 125 ASP cc_start: 0.8101 (t0) cc_final: 0.7617 (t70) REVERT: N 47 MET cc_start: 0.8084 (mmt) cc_final: 0.7430 (mmt) REVERT: O 47 MET cc_start: 0.8177 (mmt) cc_final: 0.7458 (mmt) REVERT: P 47 MET cc_start: 0.8032 (mmt) cc_final: 0.7366 (mmt) REVERT: Q 47 MET cc_start: 0.8247 (mmt) cc_final: 0.7535 (mmt) REVERT: R 47 MET cc_start: 0.8263 (mmt) cc_final: 0.7558 (mmt) REVERT: S 47 MET cc_start: 0.8078 (mmt) cc_final: 0.7415 (mmt) REVERT: S 125 ASP cc_start: 0.8086 (t0) cc_final: 0.7591 (t70) REVERT: T 47 MET cc_start: 0.7999 (mmt) cc_final: 0.7333 (mmt) REVERT: U 47 MET cc_start: 0.8031 (mmt) cc_final: 0.7370 (mmt) REVERT: V 47 MET cc_start: 0.8035 (mmt) cc_final: 0.7375 (mmt) REVERT: W 47 MET cc_start: 0.8124 (mmt) cc_final: 0.7468 (mmt) REVERT: W 125 ASP cc_start: 0.8105 (t0) cc_final: 0.7629 (t70) REVERT: X 47 MET cc_start: 0.8046 (mmt) cc_final: 0.7378 (mmt) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.3647 time to fit residues: 191.2685 Evaluate side-chains 293 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 3.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 148 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 287 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 chunk 302 optimal weight: 0.5980 chunk 294 optimal weight: 5.9990 chunk 239 optimal weight: 2.9990 chunk 319 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 72 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 ASN A 22 GLN B 22 GLN C 22 GLN D 22 GLN E 22 GLN F 22 GLN G 22 GLN H 22 GLN I 17 ASN I 22 GLN J 17 ASN J 22 GLN K 22 GLN L 22 GLN M 22 GLN N 22 GLN O 17 ASN O 22 GLN P 22 GLN Q 22 GLN R 22 GLN S 22 GLN T 22 GLN U 22 GLN V 22 GLN W 22 GLN X 22 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.126502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.108389 restraints weight = 338123.185| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 5.90 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 33397 Z= 0.152 Angle : 0.442 4.966 45129 Z= 0.247 Chirality : 0.038 0.113 4895 Planarity : 0.003 0.027 5806 Dihedral : 3.435 10.428 4319 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.70 % Allowed : 12.22 % Favored : 87.07 % 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: 2.52 (0.13), residues: 3983 helix: 2.55 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -2.03 (0.17), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP V 134 HIS 0.003 0.001 HIS N 39 PHE 0.006 0.001 PHE L 129 TYR 0.014 0.001 TYR C 24 ARG 0.007 0.001 ARG W 105 Details of bonding type rmsd hydrogen bonds : bond 0.06842 ( 2611) hydrogen bonds : angle 3.21996 ( 7785) covalent geometry : bond 0.00319 (33397) covalent geometry : angle 0.44187 (45129) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 3.816 Fit side-chains REVERT: A 47 MET cc_start: 0.8547 (mmt) cc_final: 0.7712 (mmt) REVERT: B 47 MET cc_start: 0.8380 (mmt) cc_final: 0.7583 (mmt) REVERT: C 47 MET cc_start: 0.8474 (mmt) cc_final: 0.7596 (mmt) REVERT: D 47 MET cc_start: 0.8469 (mmt) cc_final: 0.7603 (mmt) REVERT: E 47 MET cc_start: 0.8461 (mmt) cc_final: 0.7638 (mmt) REVERT: F 47 MET cc_start: 0.8461 (mmt) cc_final: 0.7623 (mmt) REVERT: G 47 MET cc_start: 0.8386 (mmt) cc_final: 0.7565 (mmt) REVERT: H 47 MET cc_start: 0.8543 (mmt) cc_final: 0.7705 (mmt) REVERT: I 47 MET cc_start: 0.8459 (mmt) cc_final: 0.7622 (mmt) REVERT: J 47 MET cc_start: 0.8373 (mmt) cc_final: 0.7563 (mmt) REVERT: K 47 MET cc_start: 0.8377 (mmt) cc_final: 0.7572 (mmt) REVERT: L 47 MET cc_start: 0.8401 (mmt) cc_final: 0.7606 (mmt) REVERT: M 47 MET cc_start: 0.8408 (mmt) cc_final: 0.7607 (mmt) REVERT: N 47 MET cc_start: 0.8403 (mmt) cc_final: 0.7618 (mmt) REVERT: O 47 MET cc_start: 0.8527 (mmt) cc_final: 0.7711 (mmt) REVERT: P 47 MET cc_start: 0.8382 (mmt) cc_final: 0.7578 (mmt) REVERT: Q 47 MET cc_start: 0.8445 (mmt) cc_final: 0.7608 (mmt) REVERT: R 47 MET cc_start: 0.8478 (mmt) cc_final: 0.7625 (mmt) REVERT: S 47 MET cc_start: 0.8406 (mmt) cc_final: 0.7599 (mmt) REVERT: T 47 MET cc_start: 0.8392 (mmt) cc_final: 0.7588 (mmt) REVERT: U 47 MET cc_start: 0.8400 (mmt) cc_final: 0.7616 (mmt) REVERT: V 47 MET cc_start: 0.8389 (mmt) cc_final: 0.7595 (mmt) REVERT: W 47 MET cc_start: 0.8404 (mmt) cc_final: 0.7602 (mmt) REVERT: W 93 SER cc_start: 0.8461 (m) cc_final: 0.8252 (t) REVERT: X 47 MET cc_start: 0.8391 (mmt) cc_final: 0.7594 (mmt) outliers start: 1 outliers final: 1 residues processed: 241 average time/residue: 0.3802 time to fit residues: 161.7292 Evaluate side-chains 242 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 4.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 173 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 189 optimal weight: 0.0870 chunk 93 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 163 optimal weight: 0.6980 chunk 212 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 overall best weight: 2.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 76 ASN P 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.127715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.109738 restraints weight = 316916.480| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 5.67 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 33397 Z= 0.139 Angle : 0.425 4.882 45129 Z= 0.238 Chirality : 0.037 0.107 4895 Planarity : 0.003 0.026 5806 Dihedral : 3.437 10.440 4319 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.68 % Allowed : 12.22 % Favored : 87.10 % 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: 2.57 (0.13), residues: 3983 helix: 2.58 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -1.97 (0.18), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP V 134 HIS 0.003 0.001 HIS H 39 PHE 0.006 0.001 PHE L 129 TYR 0.012 0.001 TYR N 24 ARG 0.007 0.001 ARG W 105 Details of bonding type rmsd hydrogen bonds : bond 0.06409 ( 2611) hydrogen bonds : angle 3.13490 ( 7785) covalent geometry : bond 0.00283 (33397) covalent geometry : angle 0.42482 (45129) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 3.894 Fit side-chains REVERT: A 47 MET cc_start: 0.8425 (mmt) cc_final: 0.7546 (mmt) REVERT: B 47 MET cc_start: 0.8338 (mmt) cc_final: 0.7614 (mmt) REVERT: C 47 MET cc_start: 0.8419 (mmt) cc_final: 0.7636 (mmt) REVERT: D 47 MET cc_start: 0.8423 (mmt) cc_final: 0.7632 (mmt) REVERT: E 47 MET cc_start: 0.8432 (mmt) cc_final: 0.7672 (mmt) REVERT: F 47 MET cc_start: 0.8411 (mmt) cc_final: 0.7635 (mmt) REVERT: F 93 SER cc_start: 0.8537 (m) cc_final: 0.8328 (t) REVERT: G 47 MET cc_start: 0.8346 (mmt) cc_final: 0.7607 (mmt) REVERT: H 47 MET cc_start: 0.8437 (mmt) cc_final: 0.7558 (mmt) REVERT: I 47 MET cc_start: 0.8409 (mmt) cc_final: 0.7654 (mmt) REVERT: J 47 MET cc_start: 0.8337 (mmt) cc_final: 0.7604 (mmt) REVERT: K 47 MET cc_start: 0.8336 (mmt) cc_final: 0.7608 (mmt) REVERT: L 47 MET cc_start: 0.8352 (mmt) cc_final: 0.7625 (mmt) REVERT: M 47 MET cc_start: 0.8364 (mmt) cc_final: 0.7639 (mmt) REVERT: N 47 MET cc_start: 0.8351 (mmt) cc_final: 0.7636 (mmt) REVERT: O 47 MET cc_start: 0.8485 (mmt) cc_final: 0.7741 (mmt) REVERT: P 47 MET cc_start: 0.8356 (mmt) cc_final: 0.7628 (mmt) REVERT: P 93 SER cc_start: 0.8477 (m) cc_final: 0.8276 (t) REVERT: Q 47 MET cc_start: 0.8397 (mmt) cc_final: 0.7636 (mmt) REVERT: R 47 MET cc_start: 0.8434 (mmt) cc_final: 0.7650 (mmt) REVERT: S 47 MET cc_start: 0.8361 (mmt) cc_final: 0.7631 (mmt) REVERT: T 47 MET cc_start: 0.8360 (mmt) cc_final: 0.7637 (mmt) REVERT: U 47 MET cc_start: 0.8361 (mmt) cc_final: 0.7646 (mmt) REVERT: V 47 MET cc_start: 0.8339 (mmt) cc_final: 0.7631 (mmt) REVERT: W 47 MET cc_start: 0.8371 (mmt) cc_final: 0.7648 (mmt) REVERT: W 93 SER cc_start: 0.8511 (m) cc_final: 0.8295 (t) REVERT: X 47 MET cc_start: 0.8356 (mmt) cc_final: 0.7658 (mmt) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.3630 time to fit residues: 175.8645 Evaluate side-chains 267 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 3.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 260 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 277 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 285 optimal weight: 6.9990 chunk 369 optimal weight: 0.9990 chunk 333 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 111 optimal weight: 0.7980 chunk 142 optimal weight: 0.3980 chunk 243 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.134133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.115987 restraints weight = 318437.771| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 5.63 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 33397 Z= 0.104 Angle : 0.378 4.741 45129 Z= 0.214 Chirality : 0.035 0.108 4895 Planarity : 0.003 0.028 5806 Dihedral : 3.317 9.706 4319 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.68 % Allowed : 12.42 % Favored : 86.91 % 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: 2.90 (0.13), residues: 3983 helix: 2.83 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -1.91 (0.18), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP W 180 HIS 0.003 0.001 HIS H 39 PHE 0.006 0.001 PHE M 129 TYR 0.008 0.001 TYR F 24 ARG 0.007 0.001 ARG W 105 Details of bonding type rmsd hydrogen bonds : bond 0.04801 ( 2611) hydrogen bonds : angle 2.82207 ( 7785) covalent geometry : bond 0.00190 (33397) covalent geometry : angle 0.37840 (45129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12013.47 seconds wall clock time: 213 minutes 1.04 seconds (12781.04 seconds total)