Starting phenix.real_space_refine on Wed Feb 21 18:48:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7k_28906/02_2024/8f7k_28906_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7k_28906/02_2024/8f7k_28906.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7k_28906/02_2024/8f7k_28906_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7k_28906/02_2024/8f7k_28906_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7k_28906/02_2024/8f7k_28906_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7k_28906/02_2024/8f7k_28906.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7k_28906/02_2024/8f7k_28906.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7k_28906/02_2024/8f7k_28906_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7k_28906/02_2024/8f7k_28906_neut_trim_updated.pdb" } resolution = 1.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 210 5.16 5 C 29946 2.51 5 N 7980 2.21 5 O 9128 1.98 5 H 47978 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 23": "OE1" <-> "OE2" Residue "I GLU 23": "OE1" <-> "OE2" Residue "J GLU 23": "OE1" <-> "OE2" Residue "K GLU 23": "OE1" <-> "OE2" Residue "L GLU 23": "OE1" <-> "OE2" Residue "M GLU 23": "OE1" <-> "OE2" Residue "N GLU 23": "OE1" <-> "OE2" Residue "V GLU 23": "OE1" <-> "OE2" Residue "W GLU 23": "OE1" <-> "OE2" Residue "X GLU 23": "OE1" <-> "OE2" Residue "Y GLU 23": "OE1" <-> "OE2" Residue "Z GLU 23": "OE1" <-> "OE2" Residue "a GLU 23": "OE1" <-> "OE2" Residue "b GLU 23": "OE1" <-> "OE2" Residue "B PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 95242 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3610 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain: "H" Number of atoms: 3165 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 202, 3147 Classifications: {'peptide': 202} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Conformer: "B" Number of residues, atoms: 202, 3147 Classifications: {'peptide': 202} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} bond proxies already assigned to first conformer: 3147 Chain: "I" Number of atoms: 3165 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 202, 3147 Classifications: {'peptide': 202} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Conformer: "B" Number of residues, atoms: 202, 3147 Classifications: {'peptide': 202} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} bond proxies already assigned to first conformer: 3147 Chain: "J" Number of atoms: 3165 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 202, 3147 Classifications: {'peptide': 202} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Conformer: "B" Number of residues, atoms: 202, 3147 Classifications: {'peptide': 202} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} bond proxies already assigned to first conformer: 3147 Chain: "K" Number of atoms: 3165 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 202, 3147 Classifications: {'peptide': 202} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Conformer: "B" Number of residues, atoms: 202, 3147 Classifications: {'peptide': 202} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} bond proxies already assigned to first conformer: 3147 Chain: "L" Number of atoms: 3165 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 202, 3147 Classifications: {'peptide': 202} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Conformer: "B" Number of residues, atoms: 202, 3147 Classifications: {'peptide': 202} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} bond proxies already assigned to first conformer: 3147 Chain: "M" Number of atoms: 3165 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 202, 3147 Classifications: {'peptide': 202} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Conformer: "B" Number of residues, atoms: 202, 3147 Classifications: {'peptide': 202} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} bond proxies already assigned to first conformer: 3147 Chain: "N" Number of atoms: 3165 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 202, 3147 Classifications: {'peptide': 202} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Conformer: "B" Number of residues, atoms: 202, 3147 Classifications: {'peptide': 202} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} bond proxies already assigned to first conformer: 3147 Chain: "V" Number of atoms: 3165 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 202, 3147 Classifications: {'peptide': 202} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Conformer: "B" Number of residues, atoms: 202, 3147 Classifications: {'peptide': 202} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} bond proxies already assigned to first conformer: 3147 Chain: "W" Number of atoms: 3165 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 202, 3147 Classifications: {'peptide': 202} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Conformer: "B" Number of residues, atoms: 202, 3147 Classifications: {'peptide': 202} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} bond proxies already assigned to first conformer: 3147 Chain: "X" Number of atoms: 3165 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 202, 3147 Classifications: {'peptide': 202} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Conformer: "B" Number of residues, atoms: 202, 3147 Classifications: {'peptide': 202} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} bond proxies already assigned to first conformer: 3147 Chain: "Y" Number of atoms: 3165 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 202, 3147 Classifications: {'peptide': 202} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Conformer: "B" Number of residues, atoms: 202, 3147 Classifications: {'peptide': 202} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} bond proxies already assigned to first conformer: 3147 Chain: "Z" Number of atoms: 3165 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 202, 3147 Classifications: {'peptide': 202} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Conformer: "B" Number of residues, atoms: 202, 3147 Classifications: {'peptide': 202} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} bond proxies already assigned to first conformer: 3147 Chain: "a" Number of atoms: 3165 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 202, 3147 Classifications: {'peptide': 202} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Conformer: "B" Number of residues, atoms: 202, 3147 Classifications: {'peptide': 202} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} bond proxies already assigned to first conformer: 3147 Chain: "b" Number of atoms: 3165 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 202, 3147 Classifications: {'peptide': 202} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Conformer: "B" Number of residues, atoms: 202, 3147 Classifications: {'peptide': 202} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} bond proxies already assigned to first conformer: 3147 Chain: "B" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3610 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain: "C" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3610 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain: "D" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3610 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain: "E" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3610 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain: "F" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3610 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain: "G" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3610 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain: "O" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3610 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain: "P" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3610 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain: "Q" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3610 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain: "R" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3610 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain: "S" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3610 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain: "T" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3610 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain: "U" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3610 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'XIB': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'XIB': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'XIB': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'XIB': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'XIB': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'XIB': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'XIB': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'XIB': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'XIB': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'XIB': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'XIB': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'XIB': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'XIB': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'XIB': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 14 residue: pdb=" N AGLN H 89 " occ=0.50 ... (32 atoms not shown) pdb="HE22BGLN H 89 " occ=0.50 residue: pdb=" N AGLN I 89 " occ=0.50 ... (32 atoms not shown) pdb="HE22BGLN I 89 " occ=0.50 residue: pdb=" N AGLN J 89 " occ=0.50 ... (32 atoms not shown) pdb="HE22BGLN J 89 " occ=0.50 residue: pdb=" N AGLN K 89 " occ=0.50 ... (32 atoms not shown) pdb="HE22BGLN K 89 " occ=0.50 residue: pdb=" N AGLN L 89 " occ=0.50 ... (32 atoms not shown) pdb="HE22BGLN L 89 " occ=0.50 residue: pdb=" N AGLN M 89 " occ=0.50 ... (32 atoms not shown) pdb="HE22BGLN M 89 " occ=0.50 residue: pdb=" N AGLN N 89 " occ=0.50 ... (32 atoms not shown) pdb="HE22BGLN N 89 " occ=0.50 residue: pdb=" N AGLN V 89 " occ=0.50 ... (32 atoms not shown) pdb="HE22BGLN V 89 " occ=0.50 residue: pdb=" N AGLN W 89 " occ=0.50 ... (32 atoms not shown) pdb="HE22BGLN W 89 " occ=0.50 residue: pdb=" N AGLN X 89 " occ=0.50 ... (32 atoms not shown) pdb="HE22BGLN X 89 " occ=0.50 residue: pdb=" N AGLN Y 89 " occ=0.50 ... (32 atoms not shown) pdb="HE22BGLN Y 89 " occ=0.50 residue: pdb=" N AGLN Z 89 " occ=0.50 ... (32 atoms not shown) pdb="HE22BGLN Z 89 " occ=0.50 ... (remaining 2 not shown) Time building chain proxies: 42.76, per 1000 atoms: 0.45 Number of scatterers: 95242 At special positions: 0 Unit cell: (134.754, 133.281, 174.517, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 210 16.00 O 9128 8.00 N 7980 7.00 C 29946 6.00 H 47978 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 60.43 Conformation dependent library (CDL) restraints added in 11.3 seconds 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11144 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 168 helices and 56 sheets defined 37.3% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.58 Creating SS restraints... Processing helix chain 'A' and resid 5 through 7 No H-bonds generated for 'chain 'A' and resid 5 through 7' Processing helix chain 'A' and resid 22 through 33 removed outlier: 3.556A pdb=" N ALA A 30 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 103 Processing helix chain 'A' and resid 109 through 124 removed outlier: 3.624A pdb=" N TYR A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 179 Processing helix chain 'A' and resid 186 through 200 removed outlier: 3.630A pdb=" N SER A 200 " --> pdb=" O ALA A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'H' and resid 49 through 70 Processing helix chain 'H' and resid 76 through 93 removed outlier: 3.971A pdb=" N VAL H 90 " --> pdb=" O MET H 86 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TYR H 92 " --> pdb=" O ASN H 88 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N MET H 93 " --> pdb=" O AGLN H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 141 Processing helix chain 'H' and resid 148 through 163 Processing helix chain 'H' and resid 189 through 198 Processing helix chain 'I' and resid 49 through 70 Processing helix chain 'I' and resid 76 through 93 removed outlier: 3.970A pdb=" N VAL I 90 " --> pdb=" O MET I 86 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TYR I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N MET I 93 " --> pdb=" O AGLN I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 141 Processing helix chain 'I' and resid 148 through 163 Processing helix chain 'I' and resid 189 through 198 Processing helix chain 'J' and resid 49 through 70 Processing helix chain 'J' and resid 76 through 93 removed outlier: 3.970A pdb=" N VAL J 90 " --> pdb=" O MET J 86 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TYR J 92 " --> pdb=" O ASN J 88 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N MET J 93 " --> pdb=" O AGLN J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 141 Processing helix chain 'J' and resid 148 through 163 Processing helix chain 'J' and resid 189 through 199 Processing helix chain 'K' and resid 49 through 70 Processing helix chain 'K' and resid 76 through 93 removed outlier: 3.971A pdb=" N VAL K 90 " --> pdb=" O MET K 86 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TYR K 92 " --> pdb=" O ASN K 88 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N MET K 93 " --> pdb=" O AGLN K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 141 Processing helix chain 'K' and resid 148 through 163 Processing helix chain 'K' and resid 189 through 198 Processing helix chain 'L' and resid 49 through 70 Processing helix chain 'L' and resid 76 through 93 removed outlier: 3.971A pdb=" N VAL L 90 " --> pdb=" O MET L 86 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TYR L 92 " --> pdb=" O ASN L 88 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET L 93 " --> pdb=" O AGLN L 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 141 Processing helix chain 'L' and resid 148 through 163 Processing helix chain 'L' and resid 189 through 198 Processing helix chain 'M' and resid 49 through 70 Processing helix chain 'M' and resid 76 through 93 removed outlier: 3.970A pdb=" N VAL M 90 " --> pdb=" O MET M 86 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TYR M 92 " --> pdb=" O ASN M 88 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N MET M 93 " --> pdb=" O AGLN M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 141 Processing helix chain 'M' and resid 148 through 163 Processing helix chain 'M' and resid 189 through 198 Processing helix chain 'N' and resid 49 through 70 Processing helix chain 'N' and resid 76 through 93 removed outlier: 3.970A pdb=" N VAL N 90 " --> pdb=" O MET N 86 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TYR N 92 " --> pdb=" O ASN N 88 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N MET N 93 " --> pdb=" O AGLN N 89 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 141 Processing helix chain 'N' and resid 148 through 163 Processing helix chain 'N' and resid 189 through 199 Processing helix chain 'V' and resid 49 through 70 Processing helix chain 'V' and resid 76 through 93 removed outlier: 3.971A pdb=" N VAL V 90 " --> pdb=" O MET V 86 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TYR V 92 " --> pdb=" O ASN V 88 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N MET V 93 " --> pdb=" O AGLN V 89 " (cutoff:3.500A) Processing helix chain 'V' and resid 131 through 141 Processing helix chain 'V' and resid 148 through 163 Processing helix chain 'V' and resid 189 through 198 Processing helix chain 'W' and resid 49 through 70 Processing helix chain 'W' and resid 76 through 93 removed outlier: 3.970A pdb=" N VAL W 90 " --> pdb=" O MET W 86 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N TYR W 92 " --> pdb=" O ASN W 88 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N MET W 93 " --> pdb=" O AGLN W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 131 through 141 Processing helix chain 'W' and resid 148 through 163 Processing helix chain 'W' and resid 189 through 198 Processing helix chain 'X' and resid 49 through 70 Processing helix chain 'X' and resid 76 through 93 removed outlier: 3.971A pdb=" N VAL X 90 " --> pdb=" O MET X 86 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TYR X 92 " --> pdb=" O ASN X 88 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N MET X 93 " --> pdb=" O AGLN X 89 " (cutoff:3.500A) Processing helix chain 'X' and resid 131 through 141 Processing helix chain 'X' and resid 148 through 163 Processing helix chain 'X' and resid 189 through 199 Processing helix chain 'Y' and resid 49 through 70 Processing helix chain 'Y' and resid 76 through 93 removed outlier: 3.971A pdb=" N VAL Y 90 " --> pdb=" O MET Y 86 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TYR Y 92 " --> pdb=" O ASN Y 88 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N MET Y 93 " --> pdb=" O AGLN Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 131 through 141 Processing helix chain 'Y' and resid 148 through 163 Processing helix chain 'Y' and resid 189 through 198 Processing helix chain 'Z' and resid 49 through 70 Processing helix chain 'Z' and resid 76 through 93 removed outlier: 3.970A pdb=" N VAL Z 90 " --> pdb=" O MET Z 86 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TYR Z 92 " --> pdb=" O ASN Z 88 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N MET Z 93 " --> pdb=" O AGLN Z 89 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 141 Processing helix chain 'Z' and resid 148 through 163 Processing helix chain 'Z' and resid 189 through 199 Processing helix chain 'a' and resid 49 through 70 Processing helix chain 'a' and resid 76 through 93 removed outlier: 3.971A pdb=" N VAL a 90 " --> pdb=" O MET a 86 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TYR a 92 " --> pdb=" O ASN a 88 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N MET a 93 " --> pdb=" O AGLN a 89 " (cutoff:3.500A) Processing helix chain 'a' and resid 131 through 141 Processing helix chain 'a' and resid 148 through 163 Processing helix chain 'a' and resid 189 through 198 Processing helix chain 'b' and resid 49 through 70 Processing helix chain 'b' and resid 76 through 93 removed outlier: 3.971A pdb=" N VAL b 90 " --> pdb=" O MET b 86 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TYR b 92 " --> pdb=" O ASN b 88 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N MET b 93 " --> pdb=" O AGLN b 89 " (cutoff:3.500A) Processing helix chain 'b' and resid 131 through 141 Processing helix chain 'b' and resid 148 through 163 Processing helix chain 'b' and resid 189 through 198 Processing helix chain 'B' and resid 5 through 7 No H-bonds generated for 'chain 'B' and resid 5 through 7' Processing helix chain 'B' and resid 22 through 33 removed outlier: 3.556A pdb=" N ALA B 30 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 103 Processing helix chain 'B' and resid 109 through 124 removed outlier: 3.624A pdb=" N TYR B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR B 124 " --> pdb=" O MET B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 179 Processing helix chain 'B' and resid 186 through 200 removed outlier: 3.630A pdb=" N SER B 200 " --> pdb=" O ALA B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'C' and resid 5 through 7 No H-bonds generated for 'chain 'C' and resid 5 through 7' Processing helix chain 'C' and resid 22 through 33 removed outlier: 3.555A pdb=" N ALA C 30 " --> pdb=" O TYR C 26 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS C 33 " --> pdb=" O GLU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 103 Processing helix chain 'C' and resid 109 through 124 removed outlier: 3.625A pdb=" N TYR C 123 " --> pdb=" O GLN C 119 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR C 124 " --> pdb=" O MET C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 179 Processing helix chain 'C' and resid 186 through 200 removed outlier: 3.630A pdb=" N SER C 200 " --> pdb=" O ALA C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 230 Processing helix chain 'D' and resid 5 through 7 No H-bonds generated for 'chain 'D' and resid 5 through 7' Processing helix chain 'D' and resid 22 through 33 removed outlier: 3.555A pdb=" N ALA D 30 " --> pdb=" O TYR D 26 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS D 33 " --> pdb=" O GLU D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 103 Processing helix chain 'D' and resid 109 through 124 removed outlier: 3.624A pdb=" N TYR D 123 " --> pdb=" O GLN D 119 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR D 124 " --> pdb=" O MET D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 179 Processing helix chain 'D' and resid 186 through 200 removed outlier: 3.631A pdb=" N SER D 200 " --> pdb=" O ALA D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 230 Processing helix chain 'E' and resid 5 through 7 No H-bonds generated for 'chain 'E' and resid 5 through 7' Processing helix chain 'E' and resid 22 through 33 removed outlier: 3.556A pdb=" N ALA E 30 " --> pdb=" O TYR E 26 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS E 33 " --> pdb=" O GLU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 103 Processing helix chain 'E' and resid 109 through 124 removed outlier: 3.625A pdb=" N TYR E 123 " --> pdb=" O GLN E 119 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 179 Processing helix chain 'E' and resid 186 through 200 removed outlier: 3.630A pdb=" N SER E 200 " --> pdb=" O ALA E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 230 Processing helix chain 'F' and resid 5 through 7 No H-bonds generated for 'chain 'F' and resid 5 through 7' Processing helix chain 'F' and resid 22 through 33 removed outlier: 3.555A pdb=" N ALA F 30 " --> pdb=" O TYR F 26 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS F 33 " --> pdb=" O GLU F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 103 Processing helix chain 'F' and resid 109 through 124 removed outlier: 3.624A pdb=" N TYR F 123 " --> pdb=" O GLN F 119 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR F 124 " --> pdb=" O MET F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 179 Processing helix chain 'F' and resid 186 through 200 removed outlier: 3.630A pdb=" N SER F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 230 Processing helix chain 'G' and resid 5 through 7 No H-bonds generated for 'chain 'G' and resid 5 through 7' Processing helix chain 'G' and resid 22 through 33 removed outlier: 3.556A pdb=" N ALA G 30 " --> pdb=" O TYR G 26 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS G 33 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 103 Processing helix chain 'G' and resid 109 through 124 removed outlier: 3.624A pdb=" N TYR G 123 " --> pdb=" O GLN G 119 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR G 124 " --> pdb=" O MET G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 179 Processing helix chain 'G' and resid 186 through 200 removed outlier: 3.629A pdb=" N SER G 200 " --> pdb=" O ALA G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 230 Processing helix chain 'O' and resid 5 through 7 No H-bonds generated for 'chain 'O' and resid 5 through 7' Processing helix chain 'O' and resid 22 through 33 removed outlier: 3.556A pdb=" N ALA O 30 " --> pdb=" O TYR O 26 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS O 33 " --> pdb=" O GLU O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 103 Processing helix chain 'O' and resid 109 through 124 removed outlier: 3.624A pdb=" N TYR O 123 " --> pdb=" O GLN O 119 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR O 124 " --> pdb=" O MET O 120 " (cutoff:3.500A) Processing helix chain 'O' and resid 169 through 179 Processing helix chain 'O' and resid 186 through 200 removed outlier: 3.630A pdb=" N SER O 200 " --> pdb=" O ALA O 196 " (cutoff:3.500A) Processing helix chain 'O' and resid 226 through 230 Processing helix chain 'P' and resid 5 through 7 No H-bonds generated for 'chain 'P' and resid 5 through 7' Processing helix chain 'P' and resid 22 through 33 removed outlier: 3.556A pdb=" N ALA P 30 " --> pdb=" O TYR P 26 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS P 33 " --> pdb=" O GLU P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 103 Processing helix chain 'P' and resid 109 through 124 removed outlier: 3.625A pdb=" N TYR P 123 " --> pdb=" O GLN P 119 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR P 124 " --> pdb=" O MET P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 169 through 179 Processing helix chain 'P' and resid 186 through 200 removed outlier: 3.630A pdb=" N SER P 200 " --> pdb=" O ALA P 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 226 through 230 Processing helix chain 'Q' and resid 5 through 7 No H-bonds generated for 'chain 'Q' and resid 5 through 7' Processing helix chain 'Q' and resid 22 through 33 removed outlier: 3.556A pdb=" N ALA Q 30 " --> pdb=" O TYR Q 26 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS Q 33 " --> pdb=" O GLU Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 103 Processing helix chain 'Q' and resid 109 through 124 removed outlier: 3.624A pdb=" N TYR Q 123 " --> pdb=" O GLN Q 119 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR Q 124 " --> pdb=" O MET Q 120 " (cutoff:3.500A) Processing helix chain 'Q' and resid 169 through 179 Processing helix chain 'Q' and resid 186 through 200 removed outlier: 3.630A pdb=" N SER Q 200 " --> pdb=" O ALA Q 196 " (cutoff:3.500A) Processing helix chain 'Q' and resid 226 through 230 Processing helix chain 'R' and resid 5 through 7 No H-bonds generated for 'chain 'R' and resid 5 through 7' Processing helix chain 'R' and resid 22 through 33 removed outlier: 3.557A pdb=" N ALA R 30 " --> pdb=" O TYR R 26 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS R 33 " --> pdb=" O GLU R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 103 Processing helix chain 'R' and resid 109 through 124 removed outlier: 3.624A pdb=" N TYR R 123 " --> pdb=" O GLN R 119 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR R 124 " --> pdb=" O MET R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 179 Processing helix chain 'R' and resid 186 through 200 removed outlier: 3.630A pdb=" N SER R 200 " --> pdb=" O ALA R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 230 Processing helix chain 'S' and resid 5 through 7 No H-bonds generated for 'chain 'S' and resid 5 through 7' Processing helix chain 'S' and resid 22 through 33 removed outlier: 3.556A pdb=" N ALA S 30 " --> pdb=" O TYR S 26 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS S 33 " --> pdb=" O GLU S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 103 Processing helix chain 'S' and resid 109 through 124 removed outlier: 3.623A pdb=" N TYR S 123 " --> pdb=" O GLN S 119 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR S 124 " --> pdb=" O MET S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 169 through 179 Processing helix chain 'S' and resid 186 through 200 removed outlier: 3.630A pdb=" N SER S 200 " --> pdb=" O ALA S 196 " (cutoff:3.500A) Processing helix chain 'S' and resid 226 through 230 Processing helix chain 'T' and resid 5 through 7 No H-bonds generated for 'chain 'T' and resid 5 through 7' Processing helix chain 'T' and resid 22 through 33 removed outlier: 3.556A pdb=" N ALA T 30 " --> pdb=" O TYR T 26 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS T 33 " --> pdb=" O GLU T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 103 Processing helix chain 'T' and resid 109 through 124 removed outlier: 3.624A pdb=" N TYR T 123 " --> pdb=" O GLN T 119 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR T 124 " --> pdb=" O MET T 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 169 through 179 Processing helix chain 'T' and resid 186 through 200 removed outlier: 3.630A pdb=" N SER T 200 " --> pdb=" O ALA T 196 " (cutoff:3.500A) Processing helix chain 'T' and resid 226 through 230 Processing helix chain 'U' and resid 5 through 7 No H-bonds generated for 'chain 'U' and resid 5 through 7' Processing helix chain 'U' and resid 22 through 33 removed outlier: 3.555A pdb=" N ALA U 30 " --> pdb=" O TYR U 26 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS U 33 " --> pdb=" O GLU U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 103 Processing helix chain 'U' and resid 109 through 124 removed outlier: 3.625A pdb=" N TYR U 123 " --> pdb=" O GLN U 119 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR U 124 " --> pdb=" O MET U 120 " (cutoff:3.500A) Processing helix chain 'U' and resid 169 through 179 Processing helix chain 'U' and resid 186 through 200 removed outlier: 3.630A pdb=" N SER U 200 " --> pdb=" O ALA U 196 " (cutoff:3.500A) Processing helix chain 'U' and resid 226 through 230 Processing sheet with id= A, first strand: chain 'A' and resid 162 through 165 Processing sheet with id= B, first strand: chain 'A' and resid 67 through 69 removed outlier: 3.571A pdb=" N ASN A 158 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 124 through 127 Processing sheet with id= D, first strand: chain 'H' and resid 119 through 121 removed outlier: 3.592A pdb=" N THR H 41 " --> pdb=" O ASP H 38 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET H 43 " --> pdb=" O GLN H 36 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLN H 36 " --> pdb=" O MET H 43 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ILE H 45 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU H 34 " --> pdb=" O ILE H 45 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'I' and resid 124 through 127 Processing sheet with id= F, first strand: chain 'I' and resid 119 through 121 removed outlier: 3.591A pdb=" N THR I 41 " --> pdb=" O ASP I 38 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET I 43 " --> pdb=" O GLN I 36 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN I 36 " --> pdb=" O MET I 43 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ILE I 45 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU I 34 " --> pdb=" O ILE I 45 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 124 through 127 Processing sheet with id= H, first strand: chain 'J' and resid 119 through 121 removed outlier: 3.592A pdb=" N THR J 41 " --> pdb=" O ASP J 38 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N MET J 43 " --> pdb=" O GLN J 36 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLN J 36 " --> pdb=" O MET J 43 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ILE J 45 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU J 34 " --> pdb=" O ILE J 45 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'K' and resid 124 through 127 Processing sheet with id= J, first strand: chain 'K' and resid 119 through 121 removed outlier: 3.592A pdb=" N THR K 41 " --> pdb=" O ASP K 38 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET K 43 " --> pdb=" O GLN K 36 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLN K 36 " --> pdb=" O MET K 43 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ILE K 45 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU K 34 " --> pdb=" O ILE K 45 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'L' and resid 124 through 127 Processing sheet with id= L, first strand: chain 'L' and resid 119 through 121 removed outlier: 3.592A pdb=" N THR L 41 " --> pdb=" O ASP L 38 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET L 43 " --> pdb=" O GLN L 36 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN L 36 " --> pdb=" O MET L 43 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ILE L 45 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU L 34 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'M' and resid 124 through 127 Processing sheet with id= N, first strand: chain 'M' and resid 119 through 121 removed outlier: 3.592A pdb=" N THR M 41 " --> pdb=" O ASP M 38 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET M 43 " --> pdb=" O GLN M 36 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLN M 36 " --> pdb=" O MET M 43 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ILE M 45 " --> pdb=" O LEU M 34 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU M 34 " --> pdb=" O ILE M 45 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'N' and resid 124 through 127 Processing sheet with id= P, first strand: chain 'N' and resid 119 through 121 removed outlier: 3.592A pdb=" N THR N 41 " --> pdb=" O ASP N 38 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET N 43 " --> pdb=" O GLN N 36 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLN N 36 " --> pdb=" O MET N 43 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ILE N 45 " --> pdb=" O LEU N 34 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU N 34 " --> pdb=" O ILE N 45 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'V' and resid 124 through 127 Processing sheet with id= R, first strand: chain 'V' and resid 119 through 121 removed outlier: 3.591A pdb=" N THR V 41 " --> pdb=" O ASP V 38 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET V 43 " --> pdb=" O GLN V 36 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLN V 36 " --> pdb=" O MET V 43 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ILE V 45 " --> pdb=" O LEU V 34 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU V 34 " --> pdb=" O ILE V 45 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'W' and resid 124 through 127 Processing sheet with id= T, first strand: chain 'W' and resid 119 through 121 removed outlier: 3.592A pdb=" N THR W 41 " --> pdb=" O ASP W 38 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET W 43 " --> pdb=" O GLN W 36 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLN W 36 " --> pdb=" O MET W 43 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ILE W 45 " --> pdb=" O LEU W 34 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU W 34 " --> pdb=" O ILE W 45 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'X' and resid 124 through 127 Processing sheet with id= V, first strand: chain 'X' and resid 119 through 121 removed outlier: 3.592A pdb=" N THR X 41 " --> pdb=" O ASP X 38 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET X 43 " --> pdb=" O GLN X 36 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLN X 36 " --> pdb=" O MET X 43 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ILE X 45 " --> pdb=" O LEU X 34 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU X 34 " --> pdb=" O ILE X 45 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Y' and resid 124 through 127 Processing sheet with id= X, first strand: chain 'Y' and resid 119 through 121 removed outlier: 3.591A pdb=" N THR Y 41 " --> pdb=" O ASP Y 38 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET Y 43 " --> pdb=" O GLN Y 36 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLN Y 36 " --> pdb=" O MET Y 43 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ILE Y 45 " --> pdb=" O LEU Y 34 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU Y 34 " --> pdb=" O ILE Y 45 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'Z' and resid 124 through 127 Processing sheet with id= Z, first strand: chain 'Z' and resid 119 through 121 removed outlier: 3.592A pdb=" N THR Z 41 " --> pdb=" O ASP Z 38 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET Z 43 " --> pdb=" O GLN Z 36 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN Z 36 " --> pdb=" O MET Z 43 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ILE Z 45 " --> pdb=" O LEU Z 34 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU Z 34 " --> pdb=" O ILE Z 45 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'a' and resid 124 through 127 Processing sheet with id= AB, first strand: chain 'a' and resid 119 through 121 removed outlier: 3.591A pdb=" N THR a 41 " --> pdb=" O ASP a 38 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET a 43 " --> pdb=" O GLN a 36 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLN a 36 " --> pdb=" O MET a 43 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ILE a 45 " --> pdb=" O LEU a 34 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU a 34 " --> pdb=" O ILE a 45 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'b' and resid 124 through 127 Processing sheet with id= AD, first strand: chain 'b' and resid 119 through 121 removed outlier: 3.592A pdb=" N THR b 41 " --> pdb=" O ASP b 38 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET b 43 " --> pdb=" O GLN b 36 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLN b 36 " --> pdb=" O MET b 43 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ILE b 45 " --> pdb=" O LEU b 34 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU b 34 " --> pdb=" O ILE b 45 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'B' and resid 162 through 165 Processing sheet with id= AF, first strand: chain 'B' and resid 67 through 69 removed outlier: 3.571A pdb=" N ASN B 158 " --> pdb=" O ASP B 150 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 162 through 165 Processing sheet with id= AH, first strand: chain 'C' and resid 67 through 69 removed outlier: 3.571A pdb=" N ASN C 158 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'D' and resid 162 through 165 Processing sheet with id= AJ, first strand: chain 'D' and resid 67 through 69 removed outlier: 3.571A pdb=" N ASN D 158 " --> pdb=" O ASP D 150 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'E' and resid 162 through 165 Processing sheet with id= AL, first strand: chain 'E' and resid 67 through 69 removed outlier: 3.571A pdb=" N ASN E 158 " --> pdb=" O ASP E 150 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'F' and resid 162 through 165 Processing sheet with id= AN, first strand: chain 'F' and resid 67 through 69 removed outlier: 3.571A pdb=" N ASN F 158 " --> pdb=" O ASP F 150 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'G' and resid 162 through 165 Processing sheet with id= AP, first strand: chain 'G' and resid 67 through 69 removed outlier: 3.571A pdb=" N ASN G 158 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'O' and resid 162 through 165 Processing sheet with id= AR, first strand: chain 'O' and resid 67 through 69 removed outlier: 3.572A pdb=" N ASN O 158 " --> pdb=" O ASP O 150 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'P' and resid 162 through 165 Processing sheet with id= AT, first strand: chain 'P' and resid 67 through 69 removed outlier: 3.571A pdb=" N ASN P 158 " --> pdb=" O ASP P 150 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'Q' and resid 162 through 165 Processing sheet with id= AV, first strand: chain 'Q' and resid 67 through 69 removed outlier: 3.571A pdb=" N ASN Q 158 " --> pdb=" O ASP Q 150 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'R' and resid 162 through 165 Processing sheet with id= AX, first strand: chain 'R' and resid 67 through 69 removed outlier: 3.571A pdb=" N ASN R 158 " --> pdb=" O ASP R 150 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'S' and resid 162 through 165 Processing sheet with id= AZ, first strand: chain 'S' and resid 67 through 69 removed outlier: 3.571A pdb=" N ASN S 158 " --> pdb=" O ASP S 150 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'T' and resid 162 through 165 Processing sheet with id= BB, first strand: chain 'T' and resid 67 through 69 removed outlier: 3.571A pdb=" N ASN T 158 " --> pdb=" O ASP T 150 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'U' and resid 162 through 165 Processing sheet with id= BD, first strand: chain 'U' and resid 67 through 69 removed outlier: 3.571A pdb=" N ASN U 158 " --> pdb=" O ASP U 150 " (cutoff:3.500A) 2398 hydrogen bonds defined for protein. 6900 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: 40.10 Time building geometry restraints manager: 63.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 47964 1.04 - 1.24: 3450 1.24 - 1.43: 16185 1.43 - 1.63: 27867 1.63 - 1.83: 406 Bond restraints: 95872 Sorted by residual: bond pdb=" C3 XIB G 301 " pdb=" N1 XIB G 301 " ideal model delta sigma weight residual 1.455 1.333 0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" C3 XIB P 301 " pdb=" N1 XIB P 301 " ideal model delta sigma weight residual 1.455 1.333 0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" C3 XIB C 301 " pdb=" N1 XIB C 301 " ideal model delta sigma weight residual 1.455 1.333 0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C3 XIB Q 301 " pdb=" N1 XIB Q 301 " ideal model delta sigma weight residual 1.455 1.333 0.122 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C3 XIB O 301 " pdb=" N1 XIB O 301 " ideal model delta sigma weight residual 1.455 1.334 0.121 2.00e-02 2.50e+03 3.69e+01 ... (remaining 95867 not shown) Histogram of bond angle deviations from ideal: 100.76 - 108.07: 17848 108.07 - 115.39: 107673 115.39 - 122.71: 37055 122.71 - 130.02: 10940 130.02 - 137.34: 56 Bond angle restraints: 173572 Sorted by residual: angle pdb=" C2 XIB R 301 " pdb=" N1 XIB R 301 " pdb=" C3 XIB R 301 " ideal model delta sigma weight residual 120.00 137.34 -17.34 3.00e+00 1.11e-01 3.34e+01 angle pdb=" C2 XIB Q 301 " pdb=" N1 XIB Q 301 " pdb=" C3 XIB Q 301 " ideal model delta sigma weight residual 120.00 137.33 -17.33 3.00e+00 1.11e-01 3.34e+01 angle pdb=" C2 XIB S 301 " pdb=" N1 XIB S 301 " pdb=" C3 XIB S 301 " ideal model delta sigma weight residual 120.00 137.33 -17.33 3.00e+00 1.11e-01 3.34e+01 angle pdb=" C2 XIB A 301 " pdb=" N1 XIB A 301 " pdb=" C3 XIB A 301 " ideal model delta sigma weight residual 120.00 137.33 -17.33 3.00e+00 1.11e-01 3.34e+01 angle pdb=" C2 XIB F 301 " pdb=" N1 XIB F 301 " pdb=" C3 XIB F 301 " ideal model delta sigma weight residual 120.00 137.32 -17.32 3.00e+00 1.11e-01 3.33e+01 ... (remaining 173567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 41468 17.82 - 35.63: 1806 35.63 - 53.45: 942 53.45 - 71.27: 332 71.27 - 89.09: 98 Dihedral angle restraints: 44646 sinusoidal: 25130 harmonic: 19516 Sorted by residual: dihedral pdb=" CD ARG R 28 " pdb=" NE ARG R 28 " pdb=" CZ ARG R 28 " pdb=" NH1 ARG R 28 " ideal model delta sinusoidal sigma weight residual 0.00 66.84 -66.84 1 1.00e+01 1.00e-02 5.82e+01 dihedral pdb=" CD ARG Q 28 " pdb=" NE ARG Q 28 " pdb=" CZ ARG Q 28 " pdb=" NH1 ARG Q 28 " ideal model delta sinusoidal sigma weight residual 0.00 66.84 -66.84 1 1.00e+01 1.00e-02 5.82e+01 dihedral pdb=" CD ARG B 28 " pdb=" NE ARG B 28 " pdb=" CZ ARG B 28 " pdb=" NH1 ARG B 28 " ideal model delta sinusoidal sigma weight residual 0.00 66.84 -66.84 1 1.00e+01 1.00e-02 5.82e+01 ... (remaining 44643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 5620 0.045 - 0.090: 1156 0.090 - 0.135: 578 0.135 - 0.181: 66 0.181 - 0.226: 42 Chirality restraints: 7462 Sorted by residual: chirality pdb=" CA MET K 22 " pdb=" N MET K 22 " pdb=" C MET K 22 " pdb=" CB MET K 22 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA MET b 22 " pdb=" N MET b 22 " pdb=" C MET b 22 " pdb=" CB MET b 22 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA MET W 22 " pdb=" N MET W 22 " pdb=" C MET W 22 " pdb=" CB MET W 22 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 7459 not shown) Planarity restraints: 14210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG O 28 " 0.749 9.50e-02 1.11e+02 3.77e-01 1.87e+03 pdb=" NE ARG O 28 " -0.244 2.00e-02 2.50e+03 pdb=" CZ ARG O 28 " -0.066 2.00e-02 2.50e+03 pdb=" NH1 ARG O 28 " 0.050 2.00e-02 2.50e+03 pdb=" NH2 ARG O 28 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG O 28 " 0.060 2.00e-02 2.50e+03 pdb="HH12 ARG O 28 " 0.124 2.00e-02 2.50e+03 pdb="HH21 ARG O 28 " -0.542 2.00e-02 2.50e+03 pdb="HH22 ARG O 28 " 0.585 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 28 " -0.749 9.50e-02 1.11e+02 3.77e-01 1.87e+03 pdb=" NE ARG F 28 " 0.245 2.00e-02 2.50e+03 pdb=" CZ ARG F 28 " 0.066 2.00e-02 2.50e+03 pdb=" NH1 ARG F 28 " -0.050 2.00e-02 2.50e+03 pdb=" NH2 ARG F 28 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG F 28 " -0.059 2.00e-02 2.50e+03 pdb="HH12 ARG F 28 " -0.124 2.00e-02 2.50e+03 pdb="HH21 ARG F 28 " 0.542 2.00e-02 2.50e+03 pdb="HH22 ARG F 28 " -0.585 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 28 " -0.748 9.50e-02 1.11e+02 3.77e-01 1.87e+03 pdb=" NE ARG C 28 " 0.244 2.00e-02 2.50e+03 pdb=" CZ ARG C 28 " 0.066 2.00e-02 2.50e+03 pdb=" NH1 ARG C 28 " -0.050 2.00e-02 2.50e+03 pdb=" NH2 ARG C 28 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG C 28 " -0.059 2.00e-02 2.50e+03 pdb="HH12 ARG C 28 " -0.124 2.00e-02 2.50e+03 pdb="HH21 ARG C 28 " 0.542 2.00e-02 2.50e+03 pdb="HH22 ARG C 28 " -0.585 2.00e-02 2.50e+03 ... (remaining 14207 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.86: 457 1.86 - 2.55: 84038 2.55 - 3.23: 302203 3.23 - 3.92: 392213 3.92 - 4.60: 616785 Nonbonded interactions: 1395696 Sorted by model distance: nonbonded pdb=" HH TYR T 126 " pdb=" HH TYR U 123 " model vdw 1.181 2.100 nonbonded pdb=" HH TYR A 126 " pdb=" HH TYR B 123 " model vdw 1.183 2.100 nonbonded pdb=" HH TYR E 126 " pdb=" HH TYR F 123 " model vdw 1.189 2.100 nonbonded pdb=" HH TYR S 126 " pdb=" HH TYR T 123 " model vdw 1.195 2.100 nonbonded pdb=" HH TYR B 126 " pdb=" HH TYR C 123 " model vdw 1.202 2.100 ... (remaining 1395691 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = (chain 'H' and (resid 1 through 88 or resid 91 through 202)) selection = (chain 'I' and (resid 1 through 88 or resid 91 through 202)) selection = (chain 'J' and (resid 1 through 88 or resid 91 through 202)) selection = (chain 'K' and (resid 1 through 88 or resid 91 through 202)) selection = (chain 'L' and (resid 1 through 88 or resid 91 through 202)) selection = (chain 'M' and (resid 1 through 88 or resid 91 through 202)) selection = (chain 'N' and (resid 1 through 88 or resid 91 through 202)) selection = (chain 'V' and (resid 1 through 88 or resid 91 through 202)) selection = (chain 'W' and (resid 1 through 88 or resid 91 through 202)) selection = (chain 'X' and (resid 1 through 88 or resid 91 through 202)) selection = (chain 'Y' and (resid 1 through 88 or resid 91 through 202)) selection = (chain 'Z' and (resid 1 through 88 or resid 91 through 202)) selection = (chain 'a' and (resid 1 through 88 or resid 91 through 202)) selection = (chain 'b' and (resid 1 through 88 or resid 91 through 202)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.840 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: 1.420 Extract box with map and model: 20.070 Check model and map are aligned: 1.110 Set scattering table: 0.670 Process input model: 259.190 Find NCS groups from input model: 4.430 Set up NCS constraints: 0.760 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: 0.020 Load rotamer database and sin/cos tables:13.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 306.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 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 0.122 47894 Z= 0.299 Angle : 0.678 17.341 64624 Z= 0.396 Chirality : 0.047 0.226 7462 Planarity : 0.021 0.453 8316 Dihedral : 12.068 89.086 18256 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.39 % Allowed : 3.06 % Favored : 95.56 % 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: 1.42 (0.11), residues: 6034 helix: 2.03 (0.10), residues: 2296 sheet: 0.83 (0.13), residues: 1512 loop : -0.06 (0.14), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS V 109 PHE 0.011 0.001 PHE D 232 TYR 0.009 0.001 TYR F 160 ARG 0.002 0.000 ARG D 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 670 time to evaluate : 6.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 14 MET cc_start: 0.7879 (mtp) cc_final: 0.7629 (mtp) REVERT: L 17 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6794 (pp20) REVERT: N 17 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6674 (pp20) REVERT: V 17 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6773 (pp20) REVERT: a 14 MET cc_start: 0.7907 (mtp) cc_final: 0.7670 (mtp) REVERT: a 17 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6694 (pp20) REVERT: b 17 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6708 (pp20) REVERT: E 120 MET cc_start: 0.7349 (mtp) cc_final: 0.7132 (mtp) outliers start: 70 outliers final: 32 residues processed: 740 average time/residue: 3.7753 time to fit residues: 3342.0769 Evaluate side-chains 582 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 545 time to evaluate : 5.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 202 ILE Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 202 ILE Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain M residue 202 ILE Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 202 ILE Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 202 ILE Chi-restraints excluded: chain W residue 202 ILE Chi-restraints excluded: chain X residue 202 ILE Chi-restraints excluded: chain Y residue 149 ASP Chi-restraints excluded: chain Y residue 202 ILE Chi-restraints excluded: chain Z residue 202 ILE Chi-restraints excluded: chain a residue 17 GLU Chi-restraints excluded: chain a residue 202 ILE Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 149 ASP Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain O residue 233 LEU Chi-restraints excluded: chain P residue 233 LEU Chi-restraints excluded: chain Q residue 233 LEU Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain T residue 233 LEU Chi-restraints excluded: chain U residue 233 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 508 optimal weight: 0.0970 chunk 456 optimal weight: 4.9990 chunk 253 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 307 optimal weight: 6.9990 chunk 243 optimal weight: 0.6980 chunk 471 optimal weight: 0.9990 chunk 182 optimal weight: 4.9990 chunk 286 optimal weight: 0.9980 chunk 351 optimal weight: 4.9990 chunk 546 optimal weight: 6.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN S 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 47894 Z= 0.169 Angle : 0.517 5.961 64624 Z= 0.285 Chirality : 0.044 0.164 7462 Planarity : 0.005 0.059 8316 Dihedral : 11.000 89.651 7065 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.75 % Allowed : 8.75 % Favored : 90.50 % 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: 1.59 (0.11), residues: 6034 helix: 2.51 (0.10), residues: 2310 sheet: 1.00 (0.13), residues: 1428 loop : -0.42 (0.13), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 109 PHE 0.008 0.001 PHE Z 133 TYR 0.013 0.001 TYR N 66 ARG 0.009 0.001 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 558 time to evaluate : 6.023 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 20 residues processed: 592 average time/residue: 3.3037 time to fit residues: 2397.2571 Evaluate side-chains 562 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 542 time to evaluate : 5.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 202 ILE Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain K residue 202 ILE Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain M residue 202 ILE Chi-restraints excluded: chain N residue 202 ILE Chi-restraints excluded: chain V residue 202 ILE Chi-restraints excluded: chain W residue 202 ILE Chi-restraints excluded: chain X residue 202 ILE Chi-restraints excluded: chain Y residue 202 ILE Chi-restraints excluded: chain Z residue 202 ILE Chi-restraints excluded: chain a residue 202 ILE Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain T residue 207 LEU Chi-restraints excluded: chain T residue 233 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 303 optimal weight: 8.9990 chunk 169 optimal weight: 3.9990 chunk 454 optimal weight: 4.9990 chunk 372 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 547 optimal weight: 2.9990 chunk 591 optimal weight: 3.9990 chunk 487 optimal weight: 8.9990 chunk 543 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 439 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN C 143 GLN D 143 GLN S 143 GLN T 143 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 47894 Z= 0.341 Angle : 0.548 6.630 64624 Z= 0.305 Chirality : 0.045 0.169 7462 Planarity : 0.004 0.052 8316 Dihedral : 10.570 89.761 7018 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.77 % Allowed : 8.93 % Favored : 90.30 % 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: 1.41 (0.11), residues: 6034 helix: 2.28 (0.10), residues: 2324 sheet: 0.87 (0.13), residues: 1428 loop : -0.43 (0.13), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS a 28 PHE 0.009 0.001 PHE M 25 TYR 0.019 0.002 TYR Z 66 ARG 0.005 0.001 ARG C 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 544 time to evaluate : 6.064 Fit side-chains revert: symmetry clash REVERT: Z 71 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.6802 (mmm160) outliers start: 39 outliers final: 24 residues processed: 575 average time/residue: 3.2893 time to fit residues: 2316.7296 Evaluate side-chains 559 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 534 time to evaluate : 5.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 202 ILE Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain K residue 202 ILE Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain M residue 202 ILE Chi-restraints excluded: chain N residue 202 ILE Chi-restraints excluded: chain V residue 202 ILE Chi-restraints excluded: chain W residue 202 ILE Chi-restraints excluded: chain X residue 202 ILE Chi-restraints excluded: chain Y residue 202 ILE Chi-restraints excluded: chain Z residue 71 ARG Chi-restraints excluded: chain Z residue 202 ILE Chi-restraints excluded: chain a residue 202 ILE Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain Q residue 207 LEU Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain T residue 207 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 541 optimal weight: 2.9990 chunk 411 optimal weight: 4.9990 chunk 284 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 261 optimal weight: 0.8980 chunk 367 optimal weight: 3.9990 chunk 549 optimal weight: 5.9990 chunk 581 optimal weight: 4.9990 chunk 287 optimal weight: 4.9990 chunk 520 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 47894 Z= 0.167 Angle : 0.483 6.083 64624 Z= 0.266 Chirality : 0.043 0.168 7462 Planarity : 0.004 0.044 8316 Dihedral : 10.097 89.867 7014 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.71 % Allowed : 9.13 % Favored : 90.16 % 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: 1.61 (0.11), residues: 6034 helix: 2.58 (0.10), residues: 2324 sheet: 0.86 (0.13), residues: 1428 loop : -0.39 (0.13), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 28 PHE 0.006 0.001 PHE B 15 TYR 0.012 0.001 TYR N 66 ARG 0.003 0.000 ARG K 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 538 time to evaluate : 6.033 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 24 residues processed: 569 average time/residue: 3.3250 time to fit residues: 2315.1812 Evaluate side-chains 552 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 528 time to evaluate : 5.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 202 ILE Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain K residue 202 ILE Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain M residue 202 ILE Chi-restraints excluded: chain N residue 202 ILE Chi-restraints excluded: chain V residue 202 ILE Chi-restraints excluded: chain W residue 202 ILE Chi-restraints excluded: chain X residue 202 ILE Chi-restraints excluded: chain Y residue 202 ILE Chi-restraints excluded: chain Z residue 202 ILE Chi-restraints excluded: chain a residue 202 ILE Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain Q residue 207 LEU Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain T residue 207 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 484 optimal weight: 8.9990 chunk 330 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 433 optimal weight: 0.7980 chunk 240 optimal weight: 4.9990 chunk 496 optimal weight: 2.9990 chunk 402 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 297 optimal weight: 3.9990 chunk 522 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 47894 Z= 0.263 Angle : 0.502 5.860 64624 Z= 0.280 Chirality : 0.043 0.166 7462 Planarity : 0.004 0.059 8316 Dihedral : 9.911 89.907 7014 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.71 % Allowed : 9.40 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.11), residues: 6034 helix: 2.51 (0.10), residues: 2324 sheet: 0.80 (0.13), residues: 1428 loop : -0.33 (0.14), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS I 28 PHE 0.008 0.001 PHE E 149 TYR 0.017 0.001 TYR I 66 ARG 0.006 0.000 ARG O 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 535 time to evaluate : 6.012 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 27 residues processed: 567 average time/residue: 3.2210 time to fit residues: 2248.2565 Evaluate side-chains 544 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 517 time to evaluate : 5.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 202 ILE Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain K residue 202 ILE Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain M residue 202 ILE Chi-restraints excluded: chain N residue 202 ILE Chi-restraints excluded: chain V residue 202 ILE Chi-restraints excluded: chain W residue 202 ILE Chi-restraints excluded: chain X residue 202 ILE Chi-restraints excluded: chain Y residue 202 ILE Chi-restraints excluded: chain Z residue 202 ILE Chi-restraints excluded: chain a residue 202 ILE Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain Q residue 207 LEU Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain T residue 207 LEU Chi-restraints excluded: chain U residue 207 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 195 optimal weight: 4.9990 chunk 524 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 341 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 582 optimal weight: 0.9990 chunk 483 optimal weight: 8.9990 chunk 269 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 305 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN T 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 47894 Z= 0.230 Angle : 0.487 6.179 64624 Z= 0.270 Chirality : 0.043 0.168 7462 Planarity : 0.004 0.051 8316 Dihedral : 9.723 89.088 7014 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.62 % Allowed : 9.90 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.11), residues: 6034 helix: 2.59 (0.10), residues: 2324 sheet: 0.81 (0.13), residues: 1428 loop : -0.33 (0.14), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 28 PHE 0.007 0.001 PHE P 15 TYR 0.014 0.001 TYR X 66 ARG 0.003 0.000 ARG O 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 529 time to evaluate : 6.417 Fit side-chains outliers start: 31 outliers final: 27 residues processed: 556 average time/residue: 3.2125 time to fit residues: 2199.0310 Evaluate side-chains 539 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 512 time to evaluate : 5.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 202 ILE Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain K residue 202 ILE Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain M residue 202 ILE Chi-restraints excluded: chain N residue 202 ILE Chi-restraints excluded: chain V residue 202 ILE Chi-restraints excluded: chain W residue 202 ILE Chi-restraints excluded: chain X residue 202 ILE Chi-restraints excluded: chain Y residue 202 ILE Chi-restraints excluded: chain Z residue 202 ILE Chi-restraints excluded: chain a residue 202 ILE Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain Q residue 207 LEU Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain T residue 207 LEU Chi-restraints excluded: chain U residue 207 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 561 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 331 optimal weight: 10.0000 chunk 425 optimal weight: 3.9990 chunk 329 optimal weight: 6.9990 chunk 490 optimal weight: 6.9990 chunk 325 optimal weight: 6.9990 chunk 580 optimal weight: 4.9990 chunk 363 optimal weight: 0.8980 chunk 353 optimal weight: 5.9990 chunk 267 optimal weight: 0.0870 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 47894 Z= 0.218 Angle : 0.481 6.234 64624 Z= 0.267 Chirality : 0.043 0.161 7462 Planarity : 0.004 0.042 8316 Dihedral : 9.552 89.121 7014 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.60 % Allowed : 10.04 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.11), residues: 6034 helix: 2.64 (0.10), residues: 2324 sheet: 0.81 (0.13), residues: 1428 loop : -0.30 (0.14), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS Y 28 PHE 0.007 0.001 PHE F 15 TYR 0.014 0.001 TYR I 66 ARG 0.005 0.000 ARG b 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 514 time to evaluate : 5.971 Fit side-chains revert: symmetry clash REVERT: M 22 MET cc_start: 0.6212 (OUTLIER) cc_final: 0.5937 (ttp) REVERT: W 22 MET cc_start: 0.6211 (OUTLIER) cc_final: 0.5936 (ttp) outliers start: 30 outliers final: 22 residues processed: 539 average time/residue: 3.2590 time to fit residues: 2158.3750 Evaluate side-chains 533 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 509 time to evaluate : 5.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 202 ILE Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain K residue 202 ILE Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain M residue 22 MET Chi-restraints excluded: chain M residue 202 ILE Chi-restraints excluded: chain N residue 202 ILE Chi-restraints excluded: chain V residue 202 ILE Chi-restraints excluded: chain W residue 22 MET Chi-restraints excluded: chain W residue 202 ILE Chi-restraints excluded: chain X residue 202 ILE Chi-restraints excluded: chain Y residue 202 ILE Chi-restraints excluded: chain Z residue 202 ILE Chi-restraints excluded: chain a residue 202 ILE Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain Q residue 207 LEU Chi-restraints excluded: chain T residue 207 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 358 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 346 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 368 optimal weight: 10.0000 chunk 395 optimal weight: 8.9990 chunk 286 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 456 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN T 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 47894 Z= 0.233 Angle : 0.485 6.404 64624 Z= 0.269 Chirality : 0.043 0.164 7462 Planarity : 0.004 0.046 8316 Dihedral : 9.468 89.759 7014 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.65 % Allowed : 10.00 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.11), residues: 6034 helix: 2.64 (0.10), residues: 2324 sheet: 0.80 (0.13), residues: 1428 loop : -0.28 (0.14), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 28 PHE 0.007 0.001 PHE O 149 TYR 0.015 0.001 TYR J 66 ARG 0.002 0.000 ARG O 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 510 time to evaluate : 6.739 Fit side-chains REVERT: J 71 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6636 (mmm160) REVERT: M 22 MET cc_start: 0.6196 (OUTLIER) cc_final: 0.5932 (ttp) REVERT: W 22 MET cc_start: 0.6196 (OUTLIER) cc_final: 0.5930 (ttp) outliers start: 33 outliers final: 24 residues processed: 540 average time/residue: 3.2882 time to fit residues: 2177.3557 Evaluate side-chains 537 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 510 time to evaluate : 5.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain H residue 202 ILE Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain J residue 71 ARG Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain K residue 202 ILE Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain M residue 22 MET Chi-restraints excluded: chain M residue 202 ILE Chi-restraints excluded: chain N residue 202 ILE Chi-restraints excluded: chain V residue 202 ILE Chi-restraints excluded: chain W residue 22 MET Chi-restraints excluded: chain W residue 202 ILE Chi-restraints excluded: chain X residue 202 ILE Chi-restraints excluded: chain Y residue 202 ILE Chi-restraints excluded: chain Z residue 202 ILE Chi-restraints excluded: chain a residue 202 ILE Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain Q residue 207 LEU Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain T residue 207 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 527 optimal weight: 7.9990 chunk 555 optimal weight: 6.9990 chunk 507 optimal weight: 2.9990 chunk 540 optimal weight: 0.0770 chunk 325 optimal weight: 6.9990 chunk 235 optimal weight: 4.9990 chunk 424 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 488 optimal weight: 0.7980 chunk 511 optimal weight: 0.9980 chunk 538 optimal weight: 4.9990 overall best weight: 1.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN T 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 47894 Z= 0.186 Angle : 0.470 6.271 64624 Z= 0.260 Chirality : 0.042 0.160 7462 Planarity : 0.003 0.049 8316 Dihedral : 9.299 89.860 7014 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.56 % Allowed : 10.14 % Favored : 89.31 % 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: 1.78 (0.11), residues: 6034 helix: 2.77 (0.10), residues: 2324 sheet: 0.81 (0.13), residues: 1428 loop : -0.25 (0.14), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 28 PHE 0.007 0.001 PHE P 15 TYR 0.013 0.001 TYR J 66 ARG 0.002 0.000 ARG K 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 515 time to evaluate : 7.097 Fit side-chains REVERT: J 71 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6630 (mmm160) REVERT: a 71 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6626 (mmm160) outliers start: 28 outliers final: 23 residues processed: 541 average time/residue: 3.4133 time to fit residues: 2252.2460 Evaluate side-chains 536 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 511 time to evaluate : 5.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain H residue 202 ILE Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain J residue 71 ARG Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain K residue 202 ILE Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain M residue 202 ILE Chi-restraints excluded: chain N residue 202 ILE Chi-restraints excluded: chain V residue 202 ILE Chi-restraints excluded: chain W residue 202 ILE Chi-restraints excluded: chain X residue 202 ILE Chi-restraints excluded: chain Y residue 202 ILE Chi-restraints excluded: chain Z residue 202 ILE Chi-restraints excluded: chain a residue 71 ARG Chi-restraints excluded: chain a residue 202 ILE Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain Q residue 207 LEU Chi-restraints excluded: chain T residue 207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 355 optimal weight: 6.9990 chunk 571 optimal weight: 4.9990 chunk 348 optimal weight: 7.9990 chunk 271 optimal weight: 2.9990 chunk 397 optimal weight: 5.9990 chunk 599 optimal weight: 4.9990 chunk 551 optimal weight: 0.6980 chunk 477 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 368 optimal weight: 10.0000 chunk 292 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 47894 Z= 0.311 Angle : 0.506 6.539 64624 Z= 0.282 Chirality : 0.044 0.164 7462 Planarity : 0.004 0.067 8316 Dihedral : 9.429 89.366 7014 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.50 % Allowed : 10.38 % Favored : 89.13 % 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: 1.63 (0.11), residues: 6034 helix: 2.58 (0.10), residues: 2324 sheet: 0.78 (0.13), residues: 1428 loop : -0.28 (0.14), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS K 28 PHE 0.008 0.001 PHE O 149 TYR 0.018 0.001 TYR J 66 ARG 0.006 0.000 ARG O 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 509 time to evaluate : 6.073 Fit side-chains REVERT: J 71 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.6625 (mmm160) REVERT: a 71 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6626 (mmm160) outliers start: 25 outliers final: 22 residues processed: 534 average time/residue: 3.3661 time to fit residues: 2194.9053 Evaluate side-chains 528 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 504 time to evaluate : 5.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain H residue 202 ILE Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain J residue 71 ARG Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain K residue 202 ILE Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain M residue 202 ILE Chi-restraints excluded: chain N residue 202 ILE Chi-restraints excluded: chain V residue 202 ILE Chi-restraints excluded: chain W residue 202 ILE Chi-restraints excluded: chain X residue 202 ILE Chi-restraints excluded: chain Y residue 202 ILE Chi-restraints excluded: chain Z residue 202 ILE Chi-restraints excluded: chain a residue 71 ARG Chi-restraints excluded: chain a residue 202 ILE Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain Q residue 207 LEU Chi-restraints excluded: chain T residue 207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 379 optimal weight: 4.9990 chunk 508 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 440 optimal weight: 0.7980 chunk 70 optimal weight: 0.0870 chunk 132 optimal weight: 0.9990 chunk 478 optimal weight: 0.4980 chunk 200 optimal weight: 0.4980 chunk 491 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN D 143 GLN T 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.087244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.055581 restraints weight = 440945.899| |-----------------------------------------------------------------------------| r_work (start): 0.2552 rms_B_bonded: 2.96 r_work: 0.2395 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2277 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2274 r_free = 0.2274 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2274 r_free = 0.2274 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 47894 Z= 0.122 Angle : 0.456 6.216 64624 Z= 0.250 Chirality : 0.042 0.155 7462 Planarity : 0.003 0.066 8316 Dihedral : 9.043 89.984 7014 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.42 % Allowed : 10.44 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.11), residues: 6034 helix: 2.97 (0.10), residues: 2324 sheet: 0.89 (0.13), residues: 1358 loop : -0.21 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 109 PHE 0.006 0.001 PHE Z 35 TYR 0.011 0.001 TYR a 66 ARG 0.005 0.000 ARG O 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35753.82 seconds wall clock time: 614 minutes 38.25 seconds (36878.25 seconds total)