Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 02:02:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6o_33024/04_2023/7x6o_33024.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6o_33024/04_2023/7x6o_33024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6o_33024/04_2023/7x6o_33024.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6o_33024/04_2023/7x6o_33024.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6o_33024/04_2023/7x6o_33024.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6o_33024/04_2023/7x6o_33024.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 13581 2.51 5 N 3678 2.21 5 O 4254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "C ARG 72": "NH1" <-> "NH2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 24": "NH1" <-> "NH2" Residue "D TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 67": "NH1" <-> "NH2" Residue "I ARG 72": "NH1" <-> "NH2" Residue "I PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 24": "NH1" <-> "NH2" Residue "K TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 67": "NH1" <-> "NH2" Residue "J ARG 72": "NH1" <-> "NH2" Residue "J PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 21609 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2514 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 301} Chain breaks: 1 Chain: "B" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1335 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 1, 'TRANS': 163} Chain: "C" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1719 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 218} Chain: "D" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1635 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "E" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2514 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 301} Chain breaks: 1 Chain: "G" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1335 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 1, 'TRANS': 163} Chain: "I" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1719 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 218} Chain: "K" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1635 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "F" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2514 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 301} Chain breaks: 1 Chain: "H" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1335 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 1, 'TRANS': 163} Chain: "J" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1719 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 218} Chain: "L" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1635 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Time building chain proxies: 11.24, per 1000 atoms: 0.52 Number of scatterers: 21609 At special positions: 0 Unit cell: (185.838, 176.612, 142.344, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 4254 8.00 N 3678 7.00 C 13581 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 285 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 77 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 146 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 313 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 102 " - pdb=" SG CYS C 107 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 213 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 285 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS E 100 " - pdb=" SG CYS E 146 " distance=2.03 Simple disulfide: pdb=" SG CYS E 289 " - pdb=" SG CYS E 313 " distance=2.03 Simple disulfide: pdb=" SG CYS G 144 " - pdb=" SG CYS G 148 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 102 " - pdb=" SG CYS I 107 " distance=2.03 Simple disulfide: pdb=" SG CYS I 157 " - pdb=" SG CYS I 213 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.03 Simple disulfide: pdb=" SG CYS F 52 " - pdb=" SG CYS F 285 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 100 " - pdb=" SG CYS F 146 " distance=2.03 Simple disulfide: pdb=" SG CYS F 289 " - pdb=" SG CYS F 313 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 148 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 102 " - pdb=" SG CYS J 107 " distance=2.03 Simple disulfide: pdb=" SG CYS J 157 " - pdb=" SG CYS J 213 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.86 Conformation dependent library (CDL) restraints added in 3.4 seconds 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5142 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 60 sheets defined 15.6% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 66 through 72 removed outlier: 3.610A pdb=" N LEU A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.830A pdb=" N GLU A 78 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 115 removed outlier: 3.675A pdb=" N LEU A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 202 removed outlier: 3.510A pdb=" N GLN A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 53 removed outlier: 3.541A pdb=" N ILE B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 124 removed outlier: 3.941A pdb=" N LEU B 80 " --> pdb=" O ARG B 76 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 96 " --> pdb=" O TRP B 92 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 removed outlier: 3.620A pdb=" N VAL B 152 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS B 153 " --> pdb=" O MET B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 167 removed outlier: 3.799A pdb=" N TYR B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B 166 " --> pdb=" O TYR B 162 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.767A pdb=" N THR C 91 " --> pdb=" O ASP C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 175 No H-bonds generated for 'chain 'C' and resid 173 through 175' Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.963A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 removed outlier: 3.643A pdb=" N LEU D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 121 through 126' Processing helix chain 'D' and resid 183 through 187 removed outlier: 3.818A pdb=" N GLU D 187 " --> pdb=" O LYS D 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 183 through 187' Processing helix chain 'D' and resid 212 through 214 No H-bonds generated for 'chain 'D' and resid 212 through 214' Processing helix chain 'E' and resid 66 through 72 removed outlier: 3.606A pdb=" N LEU E 72 " --> pdb=" O ALA E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 78 removed outlier: 3.777A pdb=" N GLU E 78 " --> pdb=" O PRO E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 115 removed outlier: 3.667A pdb=" N LEU E 111 " --> pdb=" O ASP E 107 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU E 113 " --> pdb=" O GLU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 202 removed outlier: 3.540A pdb=" N GLN E 199 " --> pdb=" O THR E 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 53 Processing helix chain 'G' and resid 74 through 124 removed outlier: 3.790A pdb=" N LEU G 80 " --> pdb=" O ARG G 76 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY G 87 " --> pdb=" O LYS G 83 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA G 96 " --> pdb=" O TRP G 92 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU G 97 " --> pdb=" O THR G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 155 removed outlier: 3.643A pdb=" N VAL G 152 " --> pdb=" O CYS G 148 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS G 153 " --> pdb=" O MET G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 167 removed outlier: 3.628A pdb=" N TYR G 162 " --> pdb=" O ASP G 158 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU G 164 " --> pdb=" O PRO G 160 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N GLU G 165 " --> pdb=" O LYS G 161 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA G 166 " --> pdb=" O TYR G 162 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS G 167 " --> pdb=" O SER G 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.788A pdb=" N THR I 91 " --> pdb=" O ASP I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 173 through 175 No H-bonds generated for 'chain 'I' and resid 173 through 175' Processing helix chain 'K' and resid 79 through 83 removed outlier: 4.004A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 126 removed outlier: 3.671A pdb=" N LEU K 125 " --> pdb=" O SER K 121 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS K 126 " --> pdb=" O ASP K 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 121 through 126' Processing helix chain 'K' and resid 183 through 189 removed outlier: 3.799A pdb=" N GLU K 187 " --> pdb=" O LYS K 183 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS K 188 " --> pdb=" O ALA K 184 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS K 189 " --> pdb=" O ASP K 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 183 through 189' Processing helix chain 'K' and resid 212 through 214 No H-bonds generated for 'chain 'K' and resid 212 through 214' Processing helix chain 'F' and resid 66 through 72 removed outlier: 3.623A pdb=" N LEU F 72 " --> pdb=" O ALA F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 78 removed outlier: 3.729A pdb=" N GLU F 78 " --> pdb=" O PRO F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 115 removed outlier: 3.669A pdb=" N LEU F 111 " --> pdb=" O ASP F 107 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU F 113 " --> pdb=" O GLU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 202 removed outlier: 3.532A pdb=" N GLN F 199 " --> pdb=" O THR F 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 53 Processing helix chain 'H' and resid 74 through 124 removed outlier: 3.804A pdb=" N LEU H 80 " --> pdb=" O ARG H 76 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY H 87 " --> pdb=" O LYS H 83 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA H 96 " --> pdb=" O TRP H 92 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU H 97 " --> pdb=" O THR H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 155 removed outlier: 3.648A pdb=" N VAL H 152 " --> pdb=" O CYS H 148 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS H 153 " --> pdb=" O MET H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 167 removed outlier: 3.773A pdb=" N TYR H 162 " --> pdb=" O ASP H 158 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU H 164 " --> pdb=" O PRO H 160 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N GLU H 165 " --> pdb=" O LYS H 161 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA H 166 " --> pdb=" O TYR H 162 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.791A pdb=" N THR J 91 " --> pdb=" O ASP J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 175 No H-bonds generated for 'chain 'J' and resid 173 through 175' Processing helix chain 'J' and resid 204 through 206 No H-bonds generated for 'chain 'J' and resid 204 through 206' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.965A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 removed outlier: 3.623A pdb=" N LEU L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 121 through 126' Processing helix chain 'L' and resid 183 through 187 removed outlier: 3.804A pdb=" N GLU L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 183 through 187' Processing sheet with id=AA1, first strand: chain 'B' and resid 32 through 36 removed outlier: 3.509A pdb=" N GLY B 33 " --> pdb=" O HIS B 26 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS A 14 " --> pdb=" O HIS B 25 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B 139 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 40 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 7.453A pdb=" N LEU A 51 " --> pdb=" O CYS A 285 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N THR A 287 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LYS A 53 " --> pdb=" O THR A 287 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 60 through 61 removed outlier: 7.699A pdb=" N LEU A 60 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 122 through 124 removed outlier: 3.514A pdb=" N ALA A 266 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU A 186 " --> pdb=" O PRO A 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 122 through 124 removed outlier: 3.514A pdb=" N ALA A 266 " --> pdb=" O GLU A 122 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 171 through 176 removed outlier: 3.514A pdb=" N ALA A 254 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR A 175 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 211 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 294 through 296 removed outlier: 3.651A pdb=" N THR A 291 " --> pdb=" O GLY A 294 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE A 296 " --> pdb=" O CYS A 289 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS A 289 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR B 64 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.878A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.928A pdb=" N GLY C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR C 127 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C 12 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.928A pdb=" N GLY C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR C 127 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C 12 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA C 97 " --> pdb=" O ASN C 35 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG C 98 " --> pdb=" O ASP C 118 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N GLY C 116 " --> pdb=" O ARG C 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 137 through 140 removed outlier: 3.641A pdb=" N SER C 197 " --> pdb=" O CYS C 157 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TYR C 193 " --> pdb=" O ASP C 161 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 198 " --> pdb=" O HIS C 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 137 through 140 removed outlier: 3.641A pdb=" N SER C 197 " --> pdb=" O CYS C 157 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TYR C 193 " --> pdb=" O ASP C 161 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 167 through 171 removed outlier: 3.746A pdb=" N TYR C 211 " --> pdb=" O VAL C 228 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.513A pdb=" N SER D 65 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.454A pdb=" N VAL D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR D 49 " --> pdb=" O ARG D 53 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG D 53 " --> pdb=" O TYR D 49 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 114 through 118 removed outlier: 3.639A pdb=" N ASN D 137 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL D 133 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN D 138 " --> pdb=" O TYR D 173 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 145 through 150 removed outlier: 3.641A pdb=" N LYS D 145 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS D 149 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR D 192 " --> pdb=" O PHE D 209 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS D 207 " --> pdb=" O CYS D 194 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL D 205 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 32 through 36 removed outlier: 3.528A pdb=" N GLY G 33 " --> pdb=" O HIS G 26 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N CYS E 14 " --> pdb=" O HIS G 25 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU G 139 " --> pdb=" O LYS G 131 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 25 through 26 Processing sheet with id=AC5, first strand: chain 'E' and resid 39 through 40 Processing sheet with id=AC6, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AC7, first strand: chain 'E' and resid 51 through 54 removed outlier: 5.559A pdb=" N LEU E 51 " --> pdb=" O HIS E 283 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N CYS E 285 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 60 through 61 removed outlier: 7.683A pdb=" N LEU E 60 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 122 through 124 removed outlier: 3.586A pdb=" N ALA E 266 " --> pdb=" O GLU E 122 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N LEU E 186 " --> pdb=" O PRO E 261 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 122 through 124 removed outlier: 3.586A pdb=" N ALA E 266 " --> pdb=" O GLU E 122 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 171 through 176 removed outlier: 3.619A pdb=" N TYR E 175 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL E 211 " --> pdb=" O LYS E 218 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 294 through 296 removed outlier: 3.531A pdb=" N THR E 291 " --> pdb=" O GLY E 294 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE E 296 " --> pdb=" O CYS E 289 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS E 289 " --> pdb=" O ILE E 296 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE E 310 " --> pdb=" O GLN E 290 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR G 64 " --> pdb=" O GLY E 311 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.868A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.842A pdb=" N GLY I 10 " --> pdb=" O THR I 125 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR I 127 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL I 12 " --> pdb=" O THR I 127 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N MET I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N TYR I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.842A pdb=" N GLY I 10 " --> pdb=" O THR I 125 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR I 127 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL I 12 " --> pdb=" O THR I 127 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA I 97 " --> pdb=" O ASN I 35 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG I 98 " --> pdb=" O ASP I 118 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLY I 116 " --> pdb=" O ARG I 100 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 137 through 140 removed outlier: 3.609A pdb=" N SER I 197 " --> pdb=" O CYS I 157 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TYR I 193 " --> pdb=" O ASP I 161 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL I 198 " --> pdb=" O HIS I 181 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 137 through 140 removed outlier: 3.609A pdb=" N SER I 197 " --> pdb=" O CYS I 157 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TYR I 193 " --> pdb=" O ASP I 161 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 167 through 171 removed outlier: 3.793A pdb=" N TYR I 211 " --> pdb=" O VAL I 228 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.637A pdb=" N SER K 65 " --> pdb=" O THR K 72 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.535A pdb=" N VAL K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR K 49 " --> pdb=" O ARG K 53 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG K 53 " --> pdb=" O TYR K 49 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 114 through 118 removed outlier: 3.642A pdb=" N ASN K 137 " --> pdb=" O SER K 114 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL K 133 " --> pdb=" O PHE K 118 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN K 138 " --> pdb=" O TYR K 173 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR K 173 " --> pdb=" O ASN K 138 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 145 through 150 removed outlier: 3.607A pdb=" N LYS K 145 " --> pdb=" O THR K 197 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS K 149 " --> pdb=" O ALA K 193 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR K 192 " --> pdb=" O PHE K 209 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS K 207 " --> pdb=" O CYS K 194 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL K 205 " --> pdb=" O VAL K 196 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 32 through 36 removed outlier: 3.534A pdb=" N GLY H 33 " --> pdb=" O HIS H 26 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS F 14 " --> pdb=" O HIS H 25 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU H 139 " --> pdb=" O LYS H 131 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 25 through 26 Processing sheet with id=AE7, first strand: chain 'F' and resid 39 through 40 Processing sheet with id=AE8, first strand: chain 'F' and resid 43 through 44 removed outlier: 3.535A pdb=" N GLU F 44 " --> pdb=" O PHE F 302 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 51 through 54 removed outlier: 7.479A pdb=" N LEU F 51 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N THR F 287 " --> pdb=" O LEU F 51 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LYS F 53 " --> pdb=" O THR F 287 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'F' and resid 60 through 61 removed outlier: 7.689A pdb=" N LEU F 60 " --> pdb=" O VAL F 90 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 122 through 124 removed outlier: 3.545A pdb=" N ALA F 266 " --> pdb=" O GLU F 122 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N LEU F 186 " --> pdb=" O PRO F 261 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 122 through 124 removed outlier: 3.545A pdb=" N ALA F 266 " --> pdb=" O GLU F 122 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 171 through 176 removed outlier: 3.507A pdb=" N ALA F 254 " --> pdb=" O LEU F 171 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR F 175 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL F 211 " --> pdb=" O LYS F 218 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 294 through 296 removed outlier: 3.638A pdb=" N THR F 291 " --> pdb=" O GLY F 294 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE F 296 " --> pdb=" O CYS F 289 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS F 289 " --> pdb=" O ILE F 296 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE F 310 " --> pdb=" O GLN F 290 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR H 64 " --> pdb=" O GLY F 311 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.840A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER J 25 " --> pdb=" O GLN J 3 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.885A pdb=" N GLY J 10 " --> pdb=" O THR J 125 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR J 127 " --> pdb=" O GLY J 10 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL J 12 " --> pdb=" O THR J 127 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR J 124 " --> pdb=" O TYR J 94 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N MET J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N TYR J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.885A pdb=" N GLY J 10 " --> pdb=" O THR J 125 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR J 127 " --> pdb=" O GLY J 10 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL J 12 " --> pdb=" O THR J 127 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR J 124 " --> pdb=" O TYR J 94 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA J 97 " --> pdb=" O ASN J 35 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG J 98 " --> pdb=" O ASP J 118 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N GLY J 116 " --> pdb=" O ARG J 100 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 137 through 140 removed outlier: 3.642A pdb=" N SER J 197 " --> pdb=" O CYS J 157 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR J 193 " --> pdb=" O ASP J 161 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL J 198 " --> pdb=" O HIS J 181 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 137 through 140 removed outlier: 3.642A pdb=" N SER J 197 " --> pdb=" O CYS J 157 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR J 193 " --> pdb=" O ASP J 161 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 167 through 171 removed outlier: 3.745A pdb=" N TYR J 211 " --> pdb=" O VAL J 228 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.548A pdb=" N SER L 65 " --> pdb=" O THR L 72 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.499A pdb=" N VAL L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR L 49 " --> pdb=" O ARG L 53 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.655A pdb=" N ASN L 137 " --> pdb=" O SER L 114 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN L 138 " --> pdb=" O TYR L 173 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 145 through 150 removed outlier: 3.645A pdb=" N LYS L 145 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS L 149 " --> pdb=" O ALA L 193 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR L 192 " --> pdb=" O PHE L 209 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL L 205 " --> pdb=" O VAL L 196 " (cutoff:3.500A) 750 hydrogen bonds defined for protein. 1950 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: 7.74 Time building geometry restraints manager: 9.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7002 1.34 - 1.46: 5243 1.46 - 1.58: 9730 1.58 - 1.70: 0 1.70 - 1.81: 123 Bond restraints: 22098 Sorted by residual: bond pdb=" N SER A 299 " pdb=" CA SER A 299 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.90e-02 2.77e+03 4.34e+00 bond pdb=" N SER E 299 " pdb=" CA SER E 299 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.24e+00 bond pdb=" N SER F 299 " pdb=" CA SER F 299 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.22e+00 bond pdb=" C THR F 298 " pdb=" N SER F 299 " ideal model delta sigma weight residual 1.329 1.353 -0.024 1.40e-02 5.10e+03 2.84e+00 bond pdb=" C THR E 298 " pdb=" N SER E 299 " ideal model delta sigma weight residual 1.329 1.352 -0.023 1.40e-02 5.10e+03 2.66e+00 ... (remaining 22093 not shown) Histogram of bond angle deviations from ideal: 100.64 - 107.54: 816 107.54 - 114.44: 12757 114.44 - 121.34: 9880 121.34 - 128.24: 6361 128.24 - 135.14: 177 Bond angle restraints: 29991 Sorted by residual: angle pdb=" C THR E 298 " pdb=" N SER E 299 " pdb=" CA SER E 299 " ideal model delta sigma weight residual 121.70 135.14 -13.44 1.80e+00 3.09e-01 5.57e+01 angle pdb=" C THR F 298 " pdb=" N SER F 299 " pdb=" CA SER F 299 " ideal model delta sigma weight residual 121.70 135.10 -13.40 1.80e+00 3.09e-01 5.54e+01 angle pdb=" C THR A 298 " pdb=" N SER A 299 " pdb=" CA SER A 299 " ideal model delta sigma weight residual 121.70 134.87 -13.17 1.80e+00 3.09e-01 5.36e+01 angle pdb=" N VAL G 66 " pdb=" CA VAL G 66 " pdb=" C VAL G 66 " ideal model delta sigma weight residual 111.81 108.61 3.20 8.60e-01 1.35e+00 1.38e+01 angle pdb=" N VAL B 66 " pdb=" CA VAL B 66 " pdb=" C VAL B 66 " ideal model delta sigma weight residual 111.81 108.73 3.08 8.60e-01 1.35e+00 1.28e+01 ... (remaining 29986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.70: 12644 14.70 - 29.41: 414 29.41 - 44.11: 135 44.11 - 58.82: 16 58.82 - 73.52: 3 Dihedral angle restraints: 13212 sinusoidal: 5163 harmonic: 8049 Sorted by residual: dihedral pdb=" CA HIS G 72 " pdb=" C HIS G 72 " pdb=" N LEU G 73 " pdb=" CA LEU G 73 " ideal model delta harmonic sigma weight residual 180.00 163.20 16.80 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA HIS B 72 " pdb=" C HIS B 72 " pdb=" N LEU B 73 " pdb=" CA LEU B 73 " ideal model delta harmonic sigma weight residual 180.00 163.52 16.48 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA HIS H 72 " pdb=" C HIS H 72 " pdb=" N LEU H 73 " pdb=" CA LEU H 73 " ideal model delta harmonic sigma weight residual 180.00 164.12 15.88 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 13209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2504 0.041 - 0.081: 504 0.081 - 0.122: 286 0.122 - 0.162: 18 0.162 - 0.203: 3 Chirality restraints: 3315 Sorted by residual: chirality pdb=" CA SER F 299 " pdb=" N SER F 299 " pdb=" C SER F 299 " pdb=" CB SER F 299 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA SER E 299 " pdb=" N SER E 299 " pdb=" C SER E 299 " pdb=" CB SER E 299 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA SER A 299 " pdb=" N SER A 299 " pdb=" C SER A 299 " pdb=" CB SER A 299 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.74e-01 ... (remaining 3312 not shown) Planarity restraints: 3864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN K 79 " -0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO K 80 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO K 80 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO K 80 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN L 79 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO L 80 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 79 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO D 80 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 80 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 80 " -0.026 5.00e-02 4.00e+02 ... (remaining 3861 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 5723 2.81 - 3.33: 16250 3.33 - 3.85: 36637 3.85 - 4.38: 39644 4.38 - 4.90: 70741 Nonbonded interactions: 168995 Sorted by model distance: nonbonded pdb=" OG1 THR E 287 " pdb=" O ILE E 296 " model vdw 2.283 2.440 nonbonded pdb=" O LEU B 89 " pdb=" OG1 THR B 93 " model vdw 2.311 2.440 nonbonded pdb=" O CYS A 52 " pdb=" OH TYR A 88 " model vdw 2.312 2.440 nonbonded pdb=" O LEU H 89 " pdb=" OG1 THR H 93 " model vdw 2.314 2.440 nonbonded pdb=" O LEU G 89 " pdb=" OG1 THR G 93 " model vdw 2.319 2.440 ... (remaining 168990 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 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.380 Check model and map are aligned: 0.330 Set scattering table: 0.190 Process input model: 55.820 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5249 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 : 0.002 0.040 22098 Z= 0.136 Angle : 0.487 13.437 29991 Z= 0.280 Chirality : 0.042 0.203 3315 Planarity : 0.005 0.049 3864 Dihedral : 8.088 73.519 7980 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % 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: -3.07 (0.13), residues: 2757 helix: -4.02 (0.11), residues: 300 sheet: -1.37 (0.17), residues: 822 loop : -2.03 (0.13), residues: 1635 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 527 time to evaluate : 2.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 10 residues processed: 560 average time/residue: 0.3276 time to fit residues: 283.6257 Evaluate side-chains 438 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 428 time to evaluate : 2.432 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2088 time to fit residues: 7.3806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 1.9990 chunk 206 optimal weight: 0.3980 chunk 114 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 139 optimal weight: 0.0040 chunk 110 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 159 optimal weight: 40.0000 chunk 247 optimal weight: 20.0000 overall best weight: 1.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS A 166 ASN A 203 GLN ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 HIS B 25 HIS B 50 ASN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN B 129 ASN C 56 ASN E 203 GLN G 25 HIS G 42 GLN ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 ASN ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 ASN H 25 HIS H 81 ASN ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 ASN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5618 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 22098 Z= 0.307 Angle : 0.694 9.927 29991 Z= 0.368 Chirality : 0.047 0.235 3315 Planarity : 0.005 0.059 3864 Dihedral : 4.066 19.536 3003 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 2.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % 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: -1.90 (0.15), residues: 2757 helix: -1.74 (0.23), residues: 297 sheet: -0.94 (0.17), residues: 819 loop : -1.32 (0.14), residues: 1641 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 482 time to evaluate : 2.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 36 residues processed: 515 average time/residue: 0.3568 time to fit residues: 277.2212 Evaluate side-chains 485 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 449 time to evaluate : 2.510 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.1913 time to fit residues: 16.7951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 206 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 268 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 246 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 199 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN B 50 ASN B 62 GLN B 129 ASN D 37 GLN D 90 GLN E 233 GLN G 62 GLN ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 ASN ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 ASN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5667 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 22098 Z= 0.257 Angle : 0.639 12.923 29991 Z= 0.329 Chirality : 0.046 0.216 3315 Planarity : 0.004 0.041 3864 Dihedral : 4.053 25.344 3003 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % 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 (0.15), residues: 2757 helix: -1.11 (0.25), residues: 312 sheet: -0.59 (0.17), residues: 828 loop : -1.06 (0.15), residues: 1617 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 456 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 23 residues processed: 479 average time/residue: 0.3707 time to fit residues: 269.7440 Evaluate side-chains 460 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 437 time to evaluate : 2.465 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2228 time to fit residues: 13.5207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 20.0000 chunk 186 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 166 optimal weight: 0.0670 chunk 249 optimal weight: 0.9990 chunk 263 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 236 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN B 50 ASN D 3 GLN D 37 GLN E 166 ASN G 42 GLN G 60 ASN ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 ASN ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5644 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 22098 Z= 0.195 Angle : 0.604 10.965 29991 Z= 0.308 Chirality : 0.044 0.204 3315 Planarity : 0.004 0.042 3864 Dihedral : 3.963 22.721 3003 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % 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: -1.07 (0.15), residues: 2757 helix: -1.09 (0.25), residues: 330 sheet: -0.13 (0.18), residues: 789 loop : -0.90 (0.15), residues: 1638 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 443 time to evaluate : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 17 residues processed: 456 average time/residue: 0.3514 time to fit residues: 241.8327 Evaluate side-chains 441 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 424 time to evaluate : 2.312 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2265 time to fit residues: 10.1197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN C 33 ASN C 56 ASN E 74 ASN E 114 GLN E 166 ASN E 233 GLN E 290 GLN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN K 37 GLN K 100 GLN F 290 GLN ** H 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5874 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.074 22098 Z= 0.430 Angle : 0.786 10.343 29991 Z= 0.415 Chirality : 0.050 0.358 3315 Planarity : 0.005 0.068 3864 Dihedral : 5.001 24.512 3003 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer Outliers : 2.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % 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: -1.16 (0.16), residues: 2757 helix: -1.04 (0.27), residues: 294 sheet: -0.34 (0.18), residues: 837 loop : -0.92 (0.15), residues: 1626 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 455 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 33 residues processed: 490 average time/residue: 0.3883 time to fit residues: 292.3006 Evaluate side-chains 462 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 429 time to evaluate : 2.670 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.2956 time to fit residues: 21.2929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 20.0000 chunk 237 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 154 optimal weight: 50.0000 chunk 65 optimal weight: 10.0000 chunk 264 optimal weight: 6.9990 chunk 219 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 87 optimal weight: 20.0000 chunk 138 optimal weight: 0.8980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN A 290 GLN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN E 114 GLN G 42 GLN ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 ASN ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 217 HIS L 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5872 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 22098 Z= 0.355 Angle : 0.724 11.312 29991 Z= 0.381 Chirality : 0.048 0.324 3315 Planarity : 0.004 0.053 3864 Dihedral : 4.982 25.252 3003 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % 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: -1.20 (0.16), residues: 2757 helix: -1.04 (0.27), residues: 300 sheet: -0.25 (0.18), residues: 855 loop : -1.03 (0.15), residues: 1602 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 442 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 21 residues processed: 461 average time/residue: 0.3721 time to fit residues: 258.1168 Evaluate side-chains 453 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 432 time to evaluate : 2.733 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2057 time to fit residues: 12.1462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 222 optimal weight: 0.6980 chunk 147 optimal weight: 8.9990 chunk 263 optimal weight: 0.2980 chunk 164 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN A 306 HIS B 42 GLN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5788 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 22098 Z= 0.206 Angle : 0.651 14.590 29991 Z= 0.337 Chirality : 0.046 0.243 3315 Planarity : 0.004 0.041 3864 Dihedral : 4.646 28.053 3003 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.16), residues: 2757 helix: -0.79 (0.27), residues: 312 sheet: -0.08 (0.18), residues: 822 loop : -0.86 (0.15), residues: 1623 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 447 time to evaluate : 2.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 456 average time/residue: 0.3641 time to fit residues: 250.7003 Evaluate side-chains 439 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 426 time to evaluate : 2.452 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2135 time to fit residues: 8.6304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 157 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 179 optimal weight: 9.9990 chunk 130 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 206 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5808 moved from start: 0.5467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 22098 Z= 0.237 Angle : 0.668 14.646 29991 Z= 0.345 Chirality : 0.046 0.244 3315 Planarity : 0.004 0.043 3864 Dihedral : 4.656 27.598 3003 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.16), residues: 2757 helix: -0.78 (0.28), residues: 312 sheet: 0.04 (0.19), residues: 816 loop : -0.83 (0.15), residues: 1629 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 433 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 441 average time/residue: 0.3851 time to fit residues: 257.0827 Evaluate side-chains 438 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 426 time to evaluate : 2.719 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2153 time to fit residues: 8.7090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 0.9990 chunk 252 optimal weight: 1.9990 chunk 229 optimal weight: 0.0570 chunk 245 optimal weight: 50.0000 chunk 147 optimal weight: 7.9990 chunk 106 optimal weight: 0.1980 chunk 192 optimal weight: 2.9990 chunk 75 optimal weight: 0.2980 chunk 221 optimal weight: 0.7980 chunk 231 optimal weight: 9.9990 chunk 244 optimal weight: 0.3980 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 GLN ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 ASN H 128 ASN L 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5744 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 22098 Z= 0.181 Angle : 0.656 14.085 29991 Z= 0.334 Chirality : 0.045 0.229 3315 Planarity : 0.004 0.052 3864 Dihedral : 4.488 27.092 3003 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.16), residues: 2757 helix: -0.69 (0.28), residues: 306 sheet: 0.24 (0.19), residues: 813 loop : -0.77 (0.15), residues: 1638 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 440 time to evaluate : 2.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 446 average time/residue: 0.3689 time to fit residues: 249.0689 Evaluate side-chains 439 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 433 time to evaluate : 2.674 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2245 time to fit residues: 6.1457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 5.9990 chunk 259 optimal weight: 4.9990 chunk 158 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 chunk 180 optimal weight: 30.0000 chunk 271 optimal weight: 30.0000 chunk 250 optimal weight: 0.2980 chunk 216 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 167 optimal weight: 7.9990 chunk 132 optimal weight: 0.2980 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN C 33 ASN D 160 GLN ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 HIS H 60 ASN ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 160 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5986 moved from start: 0.6315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.092 22098 Z= 0.533 Angle : 0.906 17.639 29991 Z= 0.476 Chirality : 0.055 0.426 3315 Planarity : 0.006 0.060 3864 Dihedral : 5.777 40.246 3003 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 26.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % 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: -1.27 (0.16), residues: 2757 helix: -1.46 (0.26), residues: 312 sheet: -0.07 (0.19), residues: 801 loop : -1.11 (0.15), residues: 1644 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 451 time to evaluate : 2.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 457 average time/residue: 0.3611 time to fit residues: 247.8954 Evaluate side-chains 444 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 433 time to evaluate : 2.624 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2096 time to fit residues: 7.8104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 2.9990 chunk 230 optimal weight: 0.1980 chunk 66 optimal weight: 0.9980 chunk 199 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 216 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 222 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.218009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.183630 restraints weight = 34038.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.189096 restraints weight = 17958.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.192469 restraints weight = 10860.936| |-----------------------------------------------------------------------------| r_work (final): 0.4503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5803 moved from start: 0.6094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 22098 Z= 0.224 Angle : 0.727 14.555 29991 Z= 0.371 Chirality : 0.048 0.220 3315 Planarity : 0.004 0.051 3864 Dihedral : 5.101 37.680 3003 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.16), residues: 2757 helix: -1.25 (0.26), residues: 336 sheet: 0.07 (0.19), residues: 837 loop : -1.02 (0.15), residues: 1584 =============================================================================== Job complete usr+sys time: 5270.05 seconds wall clock time: 96 minutes 40.75 seconds (5800.75 seconds total)