Starting phenix.real_space_refine on Mon Mar 18 01:57:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5odv_3785/03_2024/5odv_3785.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5odv_3785/03_2024/5odv_3785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5odv_3785/03_2024/5odv_3785.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5odv_3785/03_2024/5odv_3785.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5odv_3785/03_2024/5odv_3785.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5odv_3785/03_2024/5odv_3785.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.009 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: 6 Type Number sf(0) Gaussians P 120 5.49 5 S 264 5.16 5 C 26184 2.51 5 N 7200 2.21 5 O 8520 1.98 5 H 40368 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 82656 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3293 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "a" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "B" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3293 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "b" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "C" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3293 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "c" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "D" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3293 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "d" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "E" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3293 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "e" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "F" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3293 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "f" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "G" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3293 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "g" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "H" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3293 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "h" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "I" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3293 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "i" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "J" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3293 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "j" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "K" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3293 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "k" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "L" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3293 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "l" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "M" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3293 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "m" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "N" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3293 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "n" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "O" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3293 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "o" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "P" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3293 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "p" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "Q" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3293 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "q" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "R" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3293 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "r" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "S" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3293 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "s" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "T" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3293 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "t" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "U" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3293 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "u" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "V" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3293 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "v" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "W" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3293 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "w" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "X" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3293 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "x" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Time building chain proxies: 26.54, per 1000 atoms: 0.32 Number of scatterers: 82656 At special positions: 0 Unit cell: (151.8, 152.9, 209, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 264 16.00 P 120 15.00 O 8520 8.00 N 7200 7.00 C 26184 6.00 H 40368 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 46.47 Conformation dependent library (CDL) restraints added in 6.2 seconds 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9408 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 24 sheets defined 47.8% alpha, 1.9% beta 0 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 25.42 Creating SS restraints... Processing helix chain 'A' and resid 84 through 88 removed outlier: 4.019A pdb=" N GLU A 87 " --> pdb=" O HIS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 96 removed outlier: 3.739A pdb=" N PHE A 96 " --> pdb=" O VAL A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 117 removed outlier: 3.891A pdb=" N LYS A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 137 removed outlier: 3.774A pdb=" N VAL A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N TRP A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 166 removed outlier: 4.009A pdb=" N VAL A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 179 through 193 Processing helix chain 'A' and resid 197 through 202 removed outlier: 3.566A pdb=" N LEU A 201 " --> pdb=" O PRO A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 214 removed outlier: 3.807A pdb=" N ALA A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG A 212 " --> pdb=" O GLU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 239 removed outlier: 3.675A pdb=" N ALA A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 88 removed outlier: 4.019A pdb=" N GLU B 87 " --> pdb=" O HIS B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 96 removed outlier: 3.740A pdb=" N PHE B 96 " --> pdb=" O VAL B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 117 removed outlier: 3.890A pdb=" N LYS B 113 " --> pdb=" O TYR B 109 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 137 removed outlier: 3.774A pdb=" N VAL B 132 " --> pdb=" O ASN B 128 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N TRP B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 166 removed outlier: 4.008A pdb=" N VAL B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 179 through 193 Processing helix chain 'B' and resid 197 through 202 removed outlier: 3.566A pdb=" N LEU B 201 " --> pdb=" O PRO B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 removed outlier: 3.807A pdb=" N ALA B 211 " --> pdb=" O ARG B 208 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG B 212 " --> pdb=" O GLU B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 239 removed outlier: 3.675A pdb=" N ALA B 231 " --> pdb=" O ARG B 227 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA B 233 " --> pdb=" O ARG B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 88 removed outlier: 4.019A pdb=" N GLU C 87 " --> pdb=" O HIS C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 96 removed outlier: 3.740A pdb=" N PHE C 96 " --> pdb=" O VAL C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 117 removed outlier: 3.891A pdb=" N LYS C 113 " --> pdb=" O TYR C 109 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 137 removed outlier: 3.774A pdb=" N VAL C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N TRP C 133 " --> pdb=" O GLY C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 166 removed outlier: 4.009A pdb=" N VAL C 164 " --> pdb=" O LEU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 176 Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 197 through 202 removed outlier: 3.565A pdb=" N LEU C 201 " --> pdb=" O PRO C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 removed outlier: 3.807A pdb=" N ALA C 211 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARG C 212 " --> pdb=" O GLU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 239 removed outlier: 3.675A pdb=" N ALA C 231 " --> pdb=" O ARG C 227 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA C 233 " --> pdb=" O ARG C 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 88 removed outlier: 4.019A pdb=" N GLU D 87 " --> pdb=" O HIS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 96 removed outlier: 3.740A pdb=" N PHE D 96 " --> pdb=" O VAL D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 117 removed outlier: 3.891A pdb=" N LYS D 113 " --> pdb=" O TYR D 109 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 137 removed outlier: 3.774A pdb=" N VAL D 132 " --> pdb=" O ASN D 128 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TRP D 133 " --> pdb=" O GLY D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 166 removed outlier: 4.009A pdb=" N VAL D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 176 Processing helix chain 'D' and resid 179 through 193 Processing helix chain 'D' and resid 197 through 202 removed outlier: 3.567A pdb=" N LEU D 201 " --> pdb=" O PRO D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 214 removed outlier: 3.807A pdb=" N ALA D 211 " --> pdb=" O ARG D 208 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG D 212 " --> pdb=" O GLU D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 239 removed outlier: 3.676A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 88 removed outlier: 4.019A pdb=" N GLU E 87 " --> pdb=" O HIS E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 96 removed outlier: 3.740A pdb=" N PHE E 96 " --> pdb=" O VAL E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 117 removed outlier: 3.891A pdb=" N LYS E 113 " --> pdb=" O TYR E 109 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU E 115 " --> pdb=" O ALA E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 137 removed outlier: 3.775A pdb=" N VAL E 132 " --> pdb=" O ASN E 128 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N TRP E 133 " --> pdb=" O GLY E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 166 removed outlier: 4.008A pdb=" N VAL E 164 " --> pdb=" O LEU E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 176 Processing helix chain 'E' and resid 179 through 193 Processing helix chain 'E' and resid 197 through 202 removed outlier: 3.566A pdb=" N LEU E 201 " --> pdb=" O PRO E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 214 removed outlier: 3.807A pdb=" N ALA E 211 " --> pdb=" O ARG E 208 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG E 212 " --> pdb=" O GLU E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 239 removed outlier: 3.675A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 88 removed outlier: 4.019A pdb=" N GLU F 87 " --> pdb=" O HIS F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 96 removed outlier: 3.740A pdb=" N PHE F 96 " --> pdb=" O VAL F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 117 removed outlier: 3.891A pdb=" N LYS F 113 " --> pdb=" O TYR F 109 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL F 114 " --> pdb=" O SER F 110 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU F 115 " --> pdb=" O ALA F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 137 removed outlier: 3.774A pdb=" N VAL F 132 " --> pdb=" O ASN F 128 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TRP F 133 " --> pdb=" O GLY F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 166 removed outlier: 4.008A pdb=" N VAL F 164 " --> pdb=" O LEU F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 176 Processing helix chain 'F' and resid 179 through 193 Processing helix chain 'F' and resid 197 through 202 removed outlier: 3.566A pdb=" N LEU F 201 " --> pdb=" O PRO F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 214 removed outlier: 3.807A pdb=" N ALA F 211 " --> pdb=" O ARG F 208 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG F 212 " --> pdb=" O GLU F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 239 removed outlier: 3.676A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 88 removed outlier: 4.020A pdb=" N GLU G 87 " --> pdb=" O HIS G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 96 removed outlier: 3.741A pdb=" N PHE G 96 " --> pdb=" O VAL G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 117 removed outlier: 3.891A pdb=" N LYS G 113 " --> pdb=" O TYR G 109 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU G 115 " --> pdb=" O ALA G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 137 removed outlier: 3.773A pdb=" N VAL G 132 " --> pdb=" O ASN G 128 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N TRP G 133 " --> pdb=" O GLY G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 166 removed outlier: 4.009A pdb=" N VAL G 164 " --> pdb=" O LEU G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 176 Processing helix chain 'G' and resid 179 through 193 Processing helix chain 'G' and resid 197 through 202 removed outlier: 3.566A pdb=" N LEU G 201 " --> pdb=" O PRO G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 214 removed outlier: 3.808A pdb=" N ALA G 211 " --> pdb=" O ARG G 208 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG G 212 " --> pdb=" O GLU G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 239 removed outlier: 3.675A pdb=" N ALA G 231 " --> pdb=" O ARG G 227 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA G 233 " --> pdb=" O ARG G 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 88 removed outlier: 4.019A pdb=" N GLU H 87 " --> pdb=" O HIS H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 96 removed outlier: 3.739A pdb=" N PHE H 96 " --> pdb=" O VAL H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 117 removed outlier: 3.891A pdb=" N LYS H 113 " --> pdb=" O TYR H 109 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU H 115 " --> pdb=" O ALA H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 137 removed outlier: 3.774A pdb=" N VAL H 132 " --> pdb=" O ASN H 128 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N TRP H 133 " --> pdb=" O GLY H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 166 removed outlier: 4.009A pdb=" N VAL H 164 " --> pdb=" O LEU H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 176 Processing helix chain 'H' and resid 179 through 193 Processing helix chain 'H' and resid 197 through 202 removed outlier: 3.565A pdb=" N LEU H 201 " --> pdb=" O PRO H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 214 removed outlier: 3.807A pdb=" N ALA H 211 " --> pdb=" O ARG H 208 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG H 212 " --> pdb=" O GLU H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 239 removed outlier: 3.675A pdb=" N ALA H 231 " --> pdb=" O ARG H 227 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA H 233 " --> pdb=" O ARG H 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 88 removed outlier: 4.020A pdb=" N GLU I 87 " --> pdb=" O HIS I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 96 removed outlier: 3.740A pdb=" N PHE I 96 " --> pdb=" O VAL I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 117 removed outlier: 3.890A pdb=" N LYS I 113 " --> pdb=" O TYR I 109 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL I 114 " --> pdb=" O SER I 110 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU I 115 " --> pdb=" O ALA I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 137 removed outlier: 3.774A pdb=" N VAL I 132 " --> pdb=" O ASN I 128 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N TRP I 133 " --> pdb=" O GLY I 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 166 removed outlier: 4.009A pdb=" N VAL I 164 " --> pdb=" O LEU I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 176 Processing helix chain 'I' and resid 179 through 193 Processing helix chain 'I' and resid 197 through 202 removed outlier: 3.566A pdb=" N LEU I 201 " --> pdb=" O PRO I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 214 removed outlier: 3.807A pdb=" N ALA I 211 " --> pdb=" O ARG I 208 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARG I 212 " --> pdb=" O GLU I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 239 removed outlier: 3.675A pdb=" N ALA I 231 " --> pdb=" O ARG I 227 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA I 233 " --> pdb=" O ARG I 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 88 removed outlier: 4.019A pdb=" N GLU J 87 " --> pdb=" O HIS J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 96 removed outlier: 3.741A pdb=" N PHE J 96 " --> pdb=" O VAL J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 117 removed outlier: 3.891A pdb=" N LYS J 113 " --> pdb=" O TYR J 109 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL J 114 " --> pdb=" O SER J 110 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU J 115 " --> pdb=" O ALA J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 137 removed outlier: 3.774A pdb=" N VAL J 132 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TRP J 133 " --> pdb=" O GLY J 129 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 166 removed outlier: 4.009A pdb=" N VAL J 164 " --> pdb=" O LEU J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 176 Processing helix chain 'J' and resid 179 through 193 Processing helix chain 'J' and resid 197 through 202 removed outlier: 3.566A pdb=" N LEU J 201 " --> pdb=" O PRO J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 207 through 214 removed outlier: 3.807A pdb=" N ALA J 211 " --> pdb=" O ARG J 208 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG J 212 " --> pdb=" O GLU J 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 239 removed outlier: 3.675A pdb=" N ALA J 231 " --> pdb=" O ARG J 227 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA J 233 " --> pdb=" O ARG J 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 88 removed outlier: 4.019A pdb=" N GLU K 87 " --> pdb=" O HIS K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 96 removed outlier: 3.740A pdb=" N PHE K 96 " --> pdb=" O VAL K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 117 removed outlier: 3.891A pdb=" N LYS K 113 " --> pdb=" O TYR K 109 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL K 114 " --> pdb=" O SER K 110 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU K 115 " --> pdb=" O ALA K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 137 removed outlier: 3.774A pdb=" N VAL K 132 " --> pdb=" O ASN K 128 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TRP K 133 " --> pdb=" O GLY K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 166 removed outlier: 4.008A pdb=" N VAL K 164 " --> pdb=" O LEU K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 176 Processing helix chain 'K' and resid 179 through 193 Processing helix chain 'K' and resid 197 through 202 removed outlier: 3.566A pdb=" N LEU K 201 " --> pdb=" O PRO K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 214 removed outlier: 3.808A pdb=" N ALA K 211 " --> pdb=" O ARG K 208 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG K 212 " --> pdb=" O GLU K 209 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 239 removed outlier: 3.676A pdb=" N ALA K 231 " --> pdb=" O ARG K 227 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA K 233 " --> pdb=" O ARG K 229 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 88 removed outlier: 4.019A pdb=" N GLU L 87 " --> pdb=" O HIS L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 96 removed outlier: 3.740A pdb=" N PHE L 96 " --> pdb=" O VAL L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 101 through 117 removed outlier: 3.891A pdb=" N LYS L 113 " --> pdb=" O TYR L 109 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL L 114 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU L 115 " --> pdb=" O ALA L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 137 removed outlier: 3.775A pdb=" N VAL L 132 " --> pdb=" O ASN L 128 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TRP L 133 " --> pdb=" O GLY L 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 166 removed outlier: 4.008A pdb=" N VAL L 164 " --> pdb=" O LEU L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 171 through 176 Processing helix chain 'L' and resid 179 through 193 Processing helix chain 'L' and resid 197 through 202 removed outlier: 3.565A pdb=" N LEU L 201 " --> pdb=" O PRO L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 207 through 214 removed outlier: 3.807A pdb=" N ALA L 211 " --> pdb=" O ARG L 208 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG L 212 " --> pdb=" O GLU L 209 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 239 removed outlier: 3.674A pdb=" N ALA L 231 " --> pdb=" O ARG L 227 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA L 233 " --> pdb=" O ARG L 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 88 removed outlier: 4.018A pdb=" N GLU M 87 " --> pdb=" O HIS M 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 96 removed outlier: 3.740A pdb=" N PHE M 96 " --> pdb=" O VAL M 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 101 through 117 removed outlier: 3.892A pdb=" N LYS M 113 " --> pdb=" O TYR M 109 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL M 114 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU M 115 " --> pdb=" O ALA M 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 137 removed outlier: 3.775A pdb=" N VAL M 132 " --> pdb=" O ASN M 128 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TRP M 133 " --> pdb=" O GLY M 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 166 removed outlier: 4.008A pdb=" N VAL M 164 " --> pdb=" O LEU M 160 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 176 Processing helix chain 'M' and resid 179 through 193 Processing helix chain 'M' and resid 197 through 202 removed outlier: 3.567A pdb=" N LEU M 201 " --> pdb=" O PRO M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 207 through 214 removed outlier: 3.806A pdb=" N ALA M 211 " --> pdb=" O ARG M 208 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARG M 212 " --> pdb=" O GLU M 209 " (cutoff:3.500A) Processing helix chain 'M' and resid 227 through 239 removed outlier: 3.676A pdb=" N ALA M 231 " --> pdb=" O ARG M 227 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA M 233 " --> pdb=" O ARG M 229 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 88 removed outlier: 4.019A pdb=" N GLU N 87 " --> pdb=" O HIS N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 91 through 96 removed outlier: 3.741A pdb=" N PHE N 96 " --> pdb=" O VAL N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 117 removed outlier: 3.891A pdb=" N LYS N 113 " --> pdb=" O TYR N 109 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL N 114 " --> pdb=" O SER N 110 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU N 115 " --> pdb=" O ALA N 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 122 through 137 removed outlier: 3.774A pdb=" N VAL N 132 " --> pdb=" O ASN N 128 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N TRP N 133 " --> pdb=" O GLY N 129 " (cutoff:3.500A) Processing helix chain 'N' and resid 160 through 166 removed outlier: 4.009A pdb=" N VAL N 164 " --> pdb=" O LEU N 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 176 Processing helix chain 'N' and resid 179 through 193 Processing helix chain 'N' and resid 197 through 202 removed outlier: 3.565A pdb=" N LEU N 201 " --> pdb=" O PRO N 197 " (cutoff:3.500A) Processing helix chain 'N' and resid 207 through 214 removed outlier: 3.807A pdb=" N ALA N 211 " --> pdb=" O ARG N 208 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARG N 212 " --> pdb=" O GLU N 209 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 239 removed outlier: 3.676A pdb=" N ALA N 231 " --> pdb=" O ARG N 227 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA N 233 " --> pdb=" O ARG N 229 " (cutoff:3.500A) Processing helix chain 'O' and resid 84 through 88 removed outlier: 4.018A pdb=" N GLU O 87 " --> pdb=" O HIS O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 91 through 96 removed outlier: 3.740A pdb=" N PHE O 96 " --> pdb=" O VAL O 93 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 117 removed outlier: 3.890A pdb=" N LYS O 113 " --> pdb=" O TYR O 109 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL O 114 " --> pdb=" O SER O 110 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU O 115 " --> pdb=" O ALA O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 122 through 137 removed outlier: 3.775A pdb=" N VAL O 132 " --> pdb=" O ASN O 128 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N TRP O 133 " --> pdb=" O GLY O 129 " (cutoff:3.500A) Processing helix chain 'O' and resid 160 through 166 removed outlier: 4.008A pdb=" N VAL O 164 " --> pdb=" O LEU O 160 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 176 Processing helix chain 'O' and resid 179 through 193 Processing helix chain 'O' and resid 197 through 202 removed outlier: 3.566A pdb=" N LEU O 201 " --> pdb=" O PRO O 197 " (cutoff:3.500A) Processing helix chain 'O' and resid 207 through 214 removed outlier: 3.807A pdb=" N ALA O 211 " --> pdb=" O ARG O 208 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG O 212 " --> pdb=" O GLU O 209 " (cutoff:3.500A) Processing helix chain 'O' and resid 227 through 239 removed outlier: 3.676A pdb=" N ALA O 231 " --> pdb=" O ARG O 227 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA O 233 " --> pdb=" O ARG O 229 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 88 removed outlier: 4.019A pdb=" N GLU P 87 " --> pdb=" O HIS P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 96 removed outlier: 3.739A pdb=" N PHE P 96 " --> pdb=" O VAL P 93 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 117 removed outlier: 3.891A pdb=" N LYS P 113 " --> pdb=" O TYR P 109 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL P 114 " --> pdb=" O SER P 110 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU P 115 " --> pdb=" O ALA P 111 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 137 removed outlier: 3.774A pdb=" N VAL P 132 " --> pdb=" O ASN P 128 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TRP P 133 " --> pdb=" O GLY P 129 " (cutoff:3.500A) Processing helix chain 'P' and resid 160 through 166 removed outlier: 4.007A pdb=" N VAL P 164 " --> pdb=" O LEU P 160 " (cutoff:3.500A) Processing helix chain 'P' and resid 171 through 176 Processing helix chain 'P' and resid 179 through 193 Processing helix chain 'P' and resid 197 through 202 removed outlier: 3.566A pdb=" N LEU P 201 " --> pdb=" O PRO P 197 " (cutoff:3.500A) Processing helix chain 'P' and resid 207 through 214 removed outlier: 3.807A pdb=" N ALA P 211 " --> pdb=" O ARG P 208 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG P 212 " --> pdb=" O GLU P 209 " (cutoff:3.500A) Processing helix chain 'P' and resid 227 through 239 removed outlier: 3.676A pdb=" N ALA P 231 " --> pdb=" O ARG P 227 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA P 233 " --> pdb=" O ARG P 229 " (cutoff:3.500A) Processing helix chain 'Q' and resid 84 through 88 removed outlier: 4.019A pdb=" N GLU Q 87 " --> pdb=" O HIS Q 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 96 removed outlier: 3.740A pdb=" N PHE Q 96 " --> pdb=" O VAL Q 93 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 117 removed outlier: 3.890A pdb=" N LYS Q 113 " --> pdb=" O TYR Q 109 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL Q 114 " --> pdb=" O SER Q 110 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU Q 115 " --> pdb=" O ALA Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 122 through 137 removed outlier: 3.774A pdb=" N VAL Q 132 " --> pdb=" O ASN Q 128 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TRP Q 133 " --> pdb=" O GLY Q 129 " (cutoff:3.500A) Processing helix chain 'Q' and resid 160 through 166 removed outlier: 4.009A pdb=" N VAL Q 164 " --> pdb=" O LEU Q 160 " (cutoff:3.500A) Processing helix chain 'Q' and resid 171 through 176 Processing helix chain 'Q' and resid 179 through 193 Processing helix chain 'Q' and resid 197 through 202 removed outlier: 3.566A pdb=" N LEU Q 201 " --> pdb=" O PRO Q 197 " (cutoff:3.500A) Processing helix chain 'Q' and resid 207 through 214 removed outlier: 3.807A pdb=" N ALA Q 211 " --> pdb=" O ARG Q 208 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG Q 212 " --> pdb=" O GLU Q 209 " (cutoff:3.500A) Processing helix chain 'Q' and resid 227 through 239 removed outlier: 3.675A pdb=" N ALA Q 231 " --> pdb=" O ARG Q 227 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA Q 233 " --> pdb=" O ARG Q 229 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 88 removed outlier: 4.018A pdb=" N GLU R 87 " --> pdb=" O HIS R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 96 removed outlier: 3.740A pdb=" N PHE R 96 " --> pdb=" O VAL R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 117 removed outlier: 3.891A pdb=" N LYS R 113 " --> pdb=" O TYR R 109 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL R 114 " --> pdb=" O SER R 110 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU R 115 " --> pdb=" O ALA R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 122 through 137 removed outlier: 3.774A pdb=" N VAL R 132 " --> pdb=" O ASN R 128 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TRP R 133 " --> pdb=" O GLY R 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 166 removed outlier: 4.007A pdb=" N VAL R 164 " --> pdb=" O LEU R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 176 Processing helix chain 'R' and resid 179 through 193 Processing helix chain 'R' and resid 197 through 202 removed outlier: 3.566A pdb=" N LEU R 201 " --> pdb=" O PRO R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 214 removed outlier: 3.808A pdb=" N ALA R 211 " --> pdb=" O ARG R 208 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG R 212 " --> pdb=" O GLU R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 239 removed outlier: 3.676A pdb=" N ALA R 231 " --> pdb=" O ARG R 227 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA R 233 " --> pdb=" O ARG R 229 " (cutoff:3.500A) Processing helix chain 'S' and resid 84 through 88 removed outlier: 4.018A pdb=" N GLU S 87 " --> pdb=" O HIS S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 91 through 96 removed outlier: 3.739A pdb=" N PHE S 96 " --> pdb=" O VAL S 93 " (cutoff:3.500A) Processing helix chain 'S' and resid 101 through 117 removed outlier: 3.891A pdb=" N LYS S 113 " --> pdb=" O TYR S 109 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL S 114 " --> pdb=" O SER S 110 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU S 115 " --> pdb=" O ALA S 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 122 through 137 removed outlier: 3.775A pdb=" N VAL S 132 " --> pdb=" O ASN S 128 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TRP S 133 " --> pdb=" O GLY S 129 " (cutoff:3.500A) Processing helix chain 'S' and resid 160 through 166 removed outlier: 4.008A pdb=" N VAL S 164 " --> pdb=" O LEU S 160 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 176 Processing helix chain 'S' and resid 179 through 193 Processing helix chain 'S' and resid 197 through 202 removed outlier: 3.565A pdb=" N LEU S 201 " --> pdb=" O PRO S 197 " (cutoff:3.500A) Processing helix chain 'S' and resid 207 through 214 removed outlier: 3.807A pdb=" N ALA S 211 " --> pdb=" O ARG S 208 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG S 212 " --> pdb=" O GLU S 209 " (cutoff:3.500A) Processing helix chain 'S' and resid 227 through 239 removed outlier: 3.676A pdb=" N ALA S 231 " --> pdb=" O ARG S 227 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA S 233 " --> pdb=" O ARG S 229 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 88 removed outlier: 4.019A pdb=" N GLU T 87 " --> pdb=" O HIS T 84 " (cutoff:3.500A) Processing helix chain 'T' and resid 91 through 96 removed outlier: 3.739A pdb=" N PHE T 96 " --> pdb=" O VAL T 93 " (cutoff:3.500A) Processing helix chain 'T' and resid 101 through 117 removed outlier: 3.891A pdb=" N LYS T 113 " --> pdb=" O TYR T 109 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL T 114 " --> pdb=" O SER T 110 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU T 115 " --> pdb=" O ALA T 111 " (cutoff:3.500A) Processing helix chain 'T' and resid 122 through 137 removed outlier: 3.775A pdb=" N VAL T 132 " --> pdb=" O ASN T 128 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N TRP T 133 " --> pdb=" O GLY T 129 " (cutoff:3.500A) Processing helix chain 'T' and resid 160 through 166 removed outlier: 4.009A pdb=" N VAL T 164 " --> pdb=" O LEU T 160 " (cutoff:3.500A) Processing helix chain 'T' and resid 171 through 176 Processing helix chain 'T' and resid 179 through 193 Processing helix chain 'T' and resid 197 through 202 removed outlier: 3.565A pdb=" N LEU T 201 " --> pdb=" O PRO T 197 " (cutoff:3.500A) Processing helix chain 'T' and resid 207 through 214 removed outlier: 3.807A pdb=" N ALA T 211 " --> pdb=" O ARG T 208 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG T 212 " --> pdb=" O GLU T 209 " (cutoff:3.500A) Processing helix chain 'T' and resid 227 through 239 removed outlier: 3.677A pdb=" N ALA T 231 " --> pdb=" O ARG T 227 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA T 233 " --> pdb=" O ARG T 229 " (cutoff:3.500A) Processing helix chain 'U' and resid 84 through 88 removed outlier: 4.018A pdb=" N GLU U 87 " --> pdb=" O HIS U 84 " (cutoff:3.500A) Processing helix chain 'U' and resid 91 through 96 removed outlier: 3.739A pdb=" N PHE U 96 " --> pdb=" O VAL U 93 " (cutoff:3.500A) Processing helix chain 'U' and resid 101 through 117 removed outlier: 3.891A pdb=" N LYS U 113 " --> pdb=" O TYR U 109 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL U 114 " --> pdb=" O SER U 110 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU U 115 " --> pdb=" O ALA U 111 " (cutoff:3.500A) Processing helix chain 'U' and resid 122 through 137 removed outlier: 3.775A pdb=" N VAL U 132 " --> pdb=" O ASN U 128 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N TRP U 133 " --> pdb=" O GLY U 129 " (cutoff:3.500A) Processing helix chain 'U' and resid 160 through 166 removed outlier: 4.009A pdb=" N VAL U 164 " --> pdb=" O LEU U 160 " (cutoff:3.500A) Processing helix chain 'U' and resid 171 through 176 Processing helix chain 'U' and resid 179 through 193 Processing helix chain 'U' and resid 197 through 202 removed outlier: 3.565A pdb=" N LEU U 201 " --> pdb=" O PRO U 197 " (cutoff:3.500A) Processing helix chain 'U' and resid 207 through 214 removed outlier: 3.807A pdb=" N ALA U 211 " --> pdb=" O ARG U 208 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG U 212 " --> pdb=" O GLU U 209 " (cutoff:3.500A) Processing helix chain 'U' and resid 227 through 239 removed outlier: 3.675A pdb=" N ALA U 231 " --> pdb=" O ARG U 227 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA U 233 " --> pdb=" O ARG U 229 " (cutoff:3.500A) Processing helix chain 'V' and resid 84 through 88 removed outlier: 4.019A pdb=" N GLU V 87 " --> pdb=" O HIS V 84 " (cutoff:3.500A) Processing helix chain 'V' and resid 91 through 96 removed outlier: 3.740A pdb=" N PHE V 96 " --> pdb=" O VAL V 93 " (cutoff:3.500A) Processing helix chain 'V' and resid 101 through 117 removed outlier: 3.892A pdb=" N LYS V 113 " --> pdb=" O TYR V 109 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL V 114 " --> pdb=" O SER V 110 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU V 115 " --> pdb=" O ALA V 111 " (cutoff:3.500A) Processing helix chain 'V' and resid 122 through 137 removed outlier: 3.775A pdb=" N VAL V 132 " --> pdb=" O ASN V 128 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TRP V 133 " --> pdb=" O GLY V 129 " (cutoff:3.500A) Processing helix chain 'V' and resid 160 through 166 removed outlier: 4.009A pdb=" N VAL V 164 " --> pdb=" O LEU V 160 " (cutoff:3.500A) Processing helix chain 'V' and resid 171 through 176 Processing helix chain 'V' and resid 179 through 193 Processing helix chain 'V' and resid 197 through 202 removed outlier: 3.566A pdb=" N LEU V 201 " --> pdb=" O PRO V 197 " (cutoff:3.500A) Processing helix chain 'V' and resid 207 through 214 removed outlier: 3.807A pdb=" N ALA V 211 " --> pdb=" O ARG V 208 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARG V 212 " --> pdb=" O GLU V 209 " (cutoff:3.500A) Processing helix chain 'V' and resid 227 through 239 removed outlier: 3.677A pdb=" N ALA V 231 " --> pdb=" O ARG V 227 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA V 233 " --> pdb=" O ARG V 229 " (cutoff:3.500A) Processing helix chain 'W' and resid 84 through 88 removed outlier: 4.018A pdb=" N GLU W 87 " --> pdb=" O HIS W 84 " (cutoff:3.500A) Processing helix chain 'W' and resid 91 through 96 removed outlier: 3.740A pdb=" N PHE W 96 " --> pdb=" O VAL W 93 " (cutoff:3.500A) Processing helix chain 'W' and resid 101 through 117 removed outlier: 3.890A pdb=" N LYS W 113 " --> pdb=" O TYR W 109 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL W 114 " --> pdb=" O SER W 110 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU W 115 " --> pdb=" O ALA W 111 " (cutoff:3.500A) Processing helix chain 'W' and resid 122 through 137 removed outlier: 3.774A pdb=" N VAL W 132 " --> pdb=" O ASN W 128 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N TRP W 133 " --> pdb=" O GLY W 129 " (cutoff:3.500A) Processing helix chain 'W' and resid 160 through 166 removed outlier: 4.007A pdb=" N VAL W 164 " --> pdb=" O LEU W 160 " (cutoff:3.500A) Processing helix chain 'W' and resid 171 through 176 Processing helix chain 'W' and resid 179 through 193 Processing helix chain 'W' and resid 197 through 202 removed outlier: 3.566A pdb=" N LEU W 201 " --> pdb=" O PRO W 197 " (cutoff:3.500A) Processing helix chain 'W' and resid 207 through 214 removed outlier: 3.807A pdb=" N ALA W 211 " --> pdb=" O ARG W 208 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARG W 212 " --> pdb=" O GLU W 209 " (cutoff:3.500A) Processing helix chain 'W' and resid 227 through 239 removed outlier: 3.675A pdb=" N ALA W 231 " --> pdb=" O ARG W 227 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA W 233 " --> pdb=" O ARG W 229 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 88 removed outlier: 4.019A pdb=" N GLU X 87 " --> pdb=" O HIS X 84 " (cutoff:3.500A) Processing helix chain 'X' and resid 91 through 96 removed outlier: 3.740A pdb=" N PHE X 96 " --> pdb=" O VAL X 93 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 117 removed outlier: 3.890A pdb=" N LYS X 113 " --> pdb=" O TYR X 109 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL X 114 " --> pdb=" O SER X 110 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU X 115 " --> pdb=" O ALA X 111 " (cutoff:3.500A) Processing helix chain 'X' and resid 122 through 137 removed outlier: 3.775A pdb=" N VAL X 132 " --> pdb=" O ASN X 128 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TRP X 133 " --> pdb=" O GLY X 129 " (cutoff:3.500A) Processing helix chain 'X' and resid 160 through 166 removed outlier: 4.009A pdb=" N VAL X 164 " --> pdb=" O LEU X 160 " (cutoff:3.500A) Processing helix chain 'X' and resid 171 through 176 Processing helix chain 'X' and resid 179 through 193 Processing helix chain 'X' and resid 197 through 202 removed outlier: 3.566A pdb=" N LEU X 201 " --> pdb=" O PRO X 197 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 214 removed outlier: 3.808A pdb=" N ALA X 211 " --> pdb=" O ARG X 208 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG X 212 " --> pdb=" O GLU X 209 " (cutoff:3.500A) Processing helix chain 'X' and resid 227 through 239 removed outlier: 3.676A pdb=" N ALA X 231 " --> pdb=" O ARG X 227 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA X 233 " --> pdb=" O ARG X 229 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 146 through 148 removed outlier: 3.583A pdb=" N TRP A 147 " --> pdb=" O TYR A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 146 through 148 removed outlier: 3.584A pdb=" N TRP B 147 " --> pdb=" O TYR B 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 146 through 148 removed outlier: 3.584A pdb=" N TRP C 147 " --> pdb=" O TYR C 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 146 through 148 removed outlier: 3.584A pdb=" N TRP D 147 " --> pdb=" O TYR D 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.585A pdb=" N TRP E 147 " --> pdb=" O TYR E 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 146 through 148 removed outlier: 3.584A pdb=" N TRP F 147 " --> pdb=" O TYR F 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 146 through 148 removed outlier: 3.584A pdb=" N TRP G 147 " --> pdb=" O TYR G 158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.584A pdb=" N TRP H 147 " --> pdb=" O TYR H 158 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 146 through 148 removed outlier: 3.584A pdb=" N TRP I 147 " --> pdb=" O TYR I 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 146 through 148 removed outlier: 3.584A pdb=" N TRP J 147 " --> pdb=" O TYR J 158 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 146 through 148 removed outlier: 3.583A pdb=" N TRP K 147 " --> pdb=" O TYR K 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 146 through 148 removed outlier: 3.584A pdb=" N TRP L 147 " --> pdb=" O TYR L 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 146 through 148 removed outlier: 3.584A pdb=" N TRP M 147 " --> pdb=" O TYR M 158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 146 through 148 removed outlier: 3.585A pdb=" N TRP N 147 " --> pdb=" O TYR N 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 146 through 148 removed outlier: 3.584A pdb=" N TRP O 147 " --> pdb=" O TYR O 158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 146 through 148 removed outlier: 3.584A pdb=" N TRP P 147 " --> pdb=" O TYR P 158 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Q' and resid 146 through 148 removed outlier: 3.583A pdb=" N TRP Q 147 " --> pdb=" O TYR Q 158 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'R' and resid 146 through 148 removed outlier: 3.584A pdb=" N TRP R 147 " --> pdb=" O TYR R 158 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.584A pdb=" N TRP S 147 " --> pdb=" O TYR S 158 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'T' and resid 146 through 148 removed outlier: 3.585A pdb=" N TRP T 147 " --> pdb=" O TYR T 158 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'U' and resid 146 through 148 removed outlier: 3.584A pdb=" N TRP U 147 " --> pdb=" O TYR U 158 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'V' and resid 146 through 148 removed outlier: 3.583A pdb=" N TRP V 147 " --> pdb=" O TYR V 158 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'W' and resid 146 through 148 removed outlier: 3.584A pdb=" N TRP W 147 " --> pdb=" O TYR W 158 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 146 through 148 removed outlier: 3.583A pdb=" N TRP X 147 " --> pdb=" O TYR X 158 " (cutoff:3.500A) 1200 hydrogen bonds defined for protein. 3168 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 26.17 Time building geometry restraints manager: 49.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 40344 1.03 - 1.22: 169 1.22 - 1.42: 17909 1.42 - 1.61: 24786 1.61 - 1.80: 504 Bond restraints: 83712 Sorted by residual: bond pdb=" CA ASP C 207 " pdb=" CB ASP C 207 " ideal model delta sigma weight residual 1.526 1.562 -0.036 1.26e-02 6.30e+03 8.26e+00 bond pdb=" CA ASP H 207 " pdb=" CB ASP H 207 " ideal model delta sigma weight residual 1.526 1.562 -0.036 1.26e-02 6.30e+03 8.11e+00 bond pdb=" CA ASP P 207 " pdb=" CB ASP P 207 " ideal model delta sigma weight residual 1.526 1.562 -0.036 1.26e-02 6.30e+03 8.10e+00 bond pdb=" CA ASP U 207 " pdb=" CB ASP U 207 " ideal model delta sigma weight residual 1.526 1.562 -0.036 1.26e-02 6.30e+03 8.05e+00 bond pdb=" CA ASP D 207 " pdb=" CB ASP D 207 " ideal model delta sigma weight residual 1.526 1.562 -0.036 1.26e-02 6.30e+03 8.04e+00 ... (remaining 83707 not shown) Histogram of bond angle deviations from ideal: 99.41 - 106.36: 2456 106.36 - 113.31: 95655 113.31 - 120.26: 27041 120.26 - 127.21: 25306 127.21 - 134.16: 478 Bond angle restraints: 150936 Sorted by residual: angle pdb=" C ARG C 206 " pdb=" N ASP C 207 " pdb=" CA ASP C 207 " ideal model delta sigma weight residual 121.99 117.51 4.48 1.49e+00 4.50e-01 9.03e+00 angle pdb=" C ARG E 206 " pdb=" N ASP E 207 " pdb=" CA ASP E 207 " ideal model delta sigma weight residual 121.99 117.53 4.46 1.49e+00 4.50e-01 8.97e+00 angle pdb=" C ARG B 206 " pdb=" N ASP B 207 " pdb=" CA ASP B 207 " ideal model delta sigma weight residual 121.99 117.53 4.46 1.49e+00 4.50e-01 8.96e+00 angle pdb=" C ARG A 206 " pdb=" N ASP A 207 " pdb=" CA ASP A 207 " ideal model delta sigma weight residual 121.99 117.53 4.46 1.49e+00 4.50e-01 8.95e+00 angle pdb=" C ARG P 206 " pdb=" N ASP P 207 " pdb=" CA ASP P 207 " ideal model delta sigma weight residual 121.99 117.54 4.45 1.49e+00 4.50e-01 8.94e+00 ... (remaining 150931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 37277 17.30 - 34.60: 1459 34.60 - 51.90: 696 51.90 - 69.20: 312 69.20 - 86.50: 72 Dihedral angle restraints: 39816 sinusoidal: 22824 harmonic: 16992 Sorted by residual: dihedral pdb=" CA PHE L 215 " pdb=" C PHE L 215 " pdb=" N ASP L 216 " pdb=" CA ASP L 216 " ideal model delta harmonic sigma weight residual 180.00 154.48 25.52 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA PHE O 215 " pdb=" C PHE O 215 " pdb=" N ASP O 216 " pdb=" CA ASP O 216 " ideal model delta harmonic sigma weight residual 180.00 154.49 25.51 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA PHE C 215 " pdb=" C PHE C 215 " pdb=" N ASP C 216 " pdb=" CA ASP C 216 " ideal model delta harmonic sigma weight residual 180.00 154.49 25.51 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 39813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 4839 0.052 - 0.103: 1418 0.103 - 0.155: 271 0.155 - 0.207: 0 0.207 - 0.258: 24 Chirality restraints: 6552 Sorted by residual: chirality pdb=" C1' U u 2 " pdb=" O4' U u 2 " pdb=" C2' U u 2 " pdb=" N1 U u 2 " both_signs ideal model delta sigma weight residual False 2.47 2.21 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C1' U e 2 " pdb=" O4' U e 2 " pdb=" C2' U e 2 " pdb=" N1 U e 2 " both_signs ideal model delta sigma weight residual False 2.47 2.21 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C1' U f 2 " pdb=" O4' U f 2 " pdb=" C2' U f 2 " pdb=" N1 U f 2 " both_signs ideal model delta sigma weight residual False 2.47 2.21 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 6549 not shown) Planarity restraints: 12048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN P 70 " 0.072 2.00e-02 2.50e+03 7.35e-02 8.10e+01 pdb=" CG ASN P 70 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN P 70 " -0.060 2.00e-02 2.50e+03 pdb=" ND2 ASN P 70 " -0.005 2.00e-02 2.50e+03 pdb="HD21 ASN P 70 " -0.104 2.00e-02 2.50e+03 pdb="HD22 ASN P 70 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN V 70 " 0.071 2.00e-02 2.50e+03 7.33e-02 8.07e+01 pdb=" CG ASN V 70 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN V 70 " -0.060 2.00e-02 2.50e+03 pdb=" ND2 ASN V 70 " -0.006 2.00e-02 2.50e+03 pdb="HD21 ASN V 70 " -0.104 2.00e-02 2.50e+03 pdb="HD22 ASN V 70 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN Q 70 " 0.072 2.00e-02 2.50e+03 7.33e-02 8.05e+01 pdb=" CG ASN Q 70 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN Q 70 " -0.060 2.00e-02 2.50e+03 pdb=" ND2 ASN Q 70 " -0.006 2.00e-02 2.50e+03 pdb="HD21 ASN Q 70 " -0.104 2.00e-02 2.50e+03 pdb="HD22 ASN Q 70 " 0.112 2.00e-02 2.50e+03 ... (remaining 12045 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.03: 632 2.03 - 2.67: 118996 2.67 - 3.32: 212837 3.32 - 3.96: 255806 3.96 - 4.60: 403279 Nonbonded interactions: 991550 Sorted by model distance: nonbonded pdb=" OE1 GLN K 155 " pdb=" H LYS L 102 " model vdw 1.388 1.850 nonbonded pdb=" OE1 GLN S 155 " pdb=" H LYS T 102 " model vdw 1.388 1.850 nonbonded pdb=" OE1 GLN G 155 " pdb=" H LYS H 102 " model vdw 1.388 1.850 nonbonded pdb=" OE1 GLN J 155 " pdb=" H LYS K 102 " model vdw 1.389 1.850 nonbonded pdb=" OE1 GLN O 155 " pdb=" H LYS P 102 " model vdw 1.389 1.850 ... (remaining 991545 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' } 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: 0.670 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: 0.970 Extract box with map and model: 6.070 Check model and map are aligned: 0.900 Set scattering table: 0.570 Process input model: 204.560 Find NCS groups from input model: 3.290 Set up NCS constraints: 0.800 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 220.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 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 : 0.008 0.066 43344 Z= 0.503 Angle : 0.798 5.404 59064 Z= 0.438 Chirality : 0.049 0.258 6552 Planarity : 0.006 0.044 7320 Dihedral : 12.012 69.541 17280 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.17 % Favored : 86.83 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.48 (0.10), residues: 4920 helix: -3.43 (0.08), residues: 1680 sheet: None (None), residues: 0 loop : -2.89 (0.11), residues: 3240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP Q 133 HIS 0.006 0.002 HIS S 176 PHE 0.022 0.003 PHE H 215 TYR 0.010 0.001 TYR P 218 ARG 0.006 0.001 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1358 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1358 time to evaluate : 4.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.7349 (mptt) cc_final: 0.6720 (ptmt) REVERT: A 109 TYR cc_start: 0.8081 (t80) cc_final: 0.7727 (t80) REVERT: A 165 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7257 (mt-10) REVERT: A 173 GLN cc_start: 0.7725 (tp-100) cc_final: 0.7449 (tp-100) REVERT: A 206 ARG cc_start: 0.7078 (mmt90) cc_final: 0.4104 (ptt-90) REVERT: A 222 SER cc_start: 0.7817 (p) cc_final: 0.7563 (p) REVERT: B 61 ARG cc_start: 0.6835 (mtm-85) cc_final: 0.5464 (mmt180) REVERT: C 61 ARG cc_start: 0.6877 (mtm-85) cc_final: 0.5656 (mmt180) REVERT: C 173 GLN cc_start: 0.7430 (tp-100) cc_final: 0.7103 (tp-100) REVERT: D 61 ARG cc_start: 0.7180 (mtm-85) cc_final: 0.5609 (mmm160) REVERT: D 109 TYR cc_start: 0.7986 (t80) cc_final: 0.7693 (t80) REVERT: D 190 ASN cc_start: 0.8258 (t0) cc_final: 0.7924 (t0) REVERT: E 117 ASP cc_start: 0.7326 (t0) cc_final: 0.6858 (p0) REVERT: F 105 PHE cc_start: 0.8317 (t80) cc_final: 0.8047 (t80) REVERT: F 109 TYR cc_start: 0.8251 (t80) cc_final: 0.7735 (t80) REVERT: F 131 MET cc_start: 0.5077 (ptm) cc_final: 0.4777 (ptm) REVERT: F 261 THR cc_start: 0.4822 (p) cc_final: 0.4439 (p) REVERT: G 117 ASP cc_start: 0.7838 (t0) cc_final: 0.7518 (p0) REVERT: H 61 ARG cc_start: 0.7105 (mtm-85) cc_final: 0.5508 (mmm160) REVERT: H 70 ASN cc_start: 0.7454 (p0) cc_final: 0.5863 (p0) REVERT: H 109 TYR cc_start: 0.8172 (t80) cc_final: 0.7828 (t80) REVERT: I 82 LEU cc_start: 0.7362 (mt) cc_final: 0.7097 (mt) REVERT: I 117 ASP cc_start: 0.7422 (t0) cc_final: 0.6918 (p0) REVERT: J 61 ARG cc_start: 0.6581 (mtm-85) cc_final: 0.5852 (mmt180) REVERT: J 117 ASP cc_start: 0.7698 (t0) cc_final: 0.7349 (p0) REVERT: J 131 MET cc_start: 0.5169 (ptm) cc_final: 0.4895 (ptm) REVERT: L 117 ASP cc_start: 0.7714 (t0) cc_final: 0.6954 (p0) REVERT: L 190 ASN cc_start: 0.7890 (t0) cc_final: 0.7635 (t0) REVERT: M 117 ASP cc_start: 0.8200 (t0) cc_final: 0.7799 (p0) REVERT: O 251 ASP cc_start: 0.7784 (t70) cc_final: 0.7406 (t70) REVERT: P 117 ASP cc_start: 0.7534 (t0) cc_final: 0.7201 (p0) REVERT: P 251 ASP cc_start: 0.7529 (t70) cc_final: 0.7201 (t70) REVERT: Q 253 ASN cc_start: 0.7983 (t0) cc_final: 0.7581 (t0) REVERT: R 98 THR cc_start: 0.9141 (p) cc_final: 0.8934 (t) REVERT: T 264 HIS cc_start: 0.5813 (m-70) cc_final: 0.5350 (p90) REVERT: W 165 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6603 (tp30) REVERT: X 165 GLU cc_start: 0.7647 (mt-10) cc_final: 0.6813 (tp30) outliers start: 0 outliers final: 0 residues processed: 1358 average time/residue: 1.0703 time to fit residues: 2361.9754 Evaluate side-chains 866 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 866 time to evaluate : 4.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 405 optimal weight: 9.9990 chunk 363 optimal weight: 0.6980 chunk 201 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 245 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 376 optimal weight: 8.9990 chunk 145 optimal weight: 7.9990 chunk 228 optimal weight: 3.9990 chunk 280 optimal weight: 9.9990 chunk 435 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN A 176 HIS B 128 ASN B 176 HIS C 176 HIS ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 HIS ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 ASN E 176 HIS ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 HIS G 128 ASN G 176 HIS H 128 ASN H 176 HIS ** I 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 HIS J 128 ASN J 176 HIS ** K 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 HIS ** L 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 176 HIS M 128 ASN ** N 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 70 ASN O 128 ASN O 176 HIS O 244 ASN P 70 ASN P 128 ASN P 176 HIS Q 70 ASN Q 128 ASN Q 176 HIS Q 264 HIS R 84 HIS R 176 HIS S 84 HIS S 128 ASN S 176 HIS S 264 HIS T 84 HIS U 97 ASN U 128 ASN U 176 HIS V 70 ASN V 176 HIS W 70 ASN W 176 HIS X 176 HIS Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 43344 Z= 0.274 Angle : 0.658 4.804 59064 Z= 0.365 Chirality : 0.044 0.225 6552 Planarity : 0.006 0.056 7320 Dihedral : 13.381 60.752 7320 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 1.81 % Allowed : 9.91 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.11), residues: 4920 helix: -1.34 (0.13), residues: 1608 sheet: None (None), residues: 0 loop : -2.87 (0.10), residues: 3312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 133 HIS 0.013 0.002 HIS T 84 PHE 0.031 0.003 PHE R 96 TYR 0.013 0.002 TYR M 109 ARG 0.007 0.001 ARG S 172 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1104 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1026 time to evaluate : 5.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASN cc_start: 0.8321 (m-40) cc_final: 0.7882 (p0) REVERT: A 222 SER cc_start: 0.7780 (p) cc_final: 0.7385 (p) REVERT: B 61 ARG cc_start: 0.6914 (mtm-85) cc_final: 0.5463 (mmt180) REVERT: B 115 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7935 (mt-10) REVERT: B 117 ASP cc_start: 0.7600 (t0) cc_final: 0.7126 (p0) REVERT: B 127 MET cc_start: 0.7087 (mmm) cc_final: 0.6816 (mmm) REVERT: C 61 ARG cc_start: 0.7039 (mtm-85) cc_final: 0.5677 (mmt180) REVERT: D 109 TYR cc_start: 0.8204 (t80) cc_final: 0.7801 (t80) REVERT: D 251 ASP cc_start: 0.8618 (m-30) cc_final: 0.8328 (m-30) REVERT: E 83 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7729 (m-30) REVERT: E 117 ASP cc_start: 0.7233 (t0) cc_final: 0.7028 (p0) REVERT: F 109 TYR cc_start: 0.8396 (t80) cc_final: 0.8135 (t80) REVERT: G 109 TYR cc_start: 0.8548 (t80) cc_final: 0.8285 (t80) REVERT: G 117 ASP cc_start: 0.8041 (t0) cc_final: 0.7602 (p0) REVERT: G 121 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6822 (mm-30) REVERT: G 127 MET cc_start: 0.7291 (mmm) cc_final: 0.7088 (mmp) REVERT: G 173 GLN cc_start: 0.8240 (tp-100) cc_final: 0.8025 (tp-100) REVERT: H 173 GLN cc_start: 0.8068 (tp-100) cc_final: 0.7847 (tp-100) REVERT: J 61 ARG cc_start: 0.6748 (mtm-85) cc_final: 0.5975 (mmt180) REVERT: J 117 ASP cc_start: 0.7899 (t0) cc_final: 0.7608 (p0) REVERT: J 251 ASP cc_start: 0.7840 (t70) cc_final: 0.7420 (t70) REVERT: K 117 ASP cc_start: 0.7765 (t0) cc_final: 0.7545 (t70) REVERT: K 251 ASP cc_start: 0.7948 (t70) cc_final: 0.7564 (t70) REVERT: L 127 MET cc_start: 0.7217 (mmm) cc_final: 0.6896 (mmp) REVERT: L 251 ASP cc_start: 0.8320 (t70) cc_final: 0.7842 (t70) REVERT: N 123 MET cc_start: 0.6818 (mmm) cc_final: 0.6283 (mmt) REVERT: O 190 ASN cc_start: 0.8398 (t0) cc_final: 0.7911 (t0) REVERT: O 251 ASP cc_start: 0.8110 (t70) cc_final: 0.7782 (t70) REVERT: P 196 MET cc_start: 0.8272 (mmm) cc_final: 0.7946 (mmm) REVERT: P 251 ASP cc_start: 0.7913 (t70) cc_final: 0.7620 (t70) REVERT: T 87 GLU cc_start: 0.7375 (pm20) cc_final: 0.7092 (pt0) REVERT: T 106 GLU cc_start: 0.8159 (tp30) cc_final: 0.7699 (tp30) REVERT: T 150 MET cc_start: 0.8217 (ptm) cc_final: 0.7963 (ptm) REVERT: T 264 HIS cc_start: 0.5629 (m-70) cc_final: 0.5187 (p90) REVERT: U 127 MET cc_start: 0.7783 (mmm) cc_final: 0.7374 (mmt) REVERT: V 82 LEU cc_start: 0.8234 (mt) cc_final: 0.7980 (mt) REVERT: W 93 VAL cc_start: 0.9133 (p) cc_final: 0.8707 (p) REVERT: W 123 MET cc_start: 0.5676 (mmp) cc_final: 0.5423 (mmp) REVERT: X 123 MET cc_start: 0.6419 (mmm) cc_final: 0.6097 (mmp) REVERT: X 165 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7231 (tp30) REVERT: X 177 HIS cc_start: 0.7662 (OUTLIER) cc_final: 0.7371 (m170) outliers start: 78 outliers final: 48 residues processed: 1067 average time/residue: 1.0076 time to fit residues: 1800.4508 Evaluate side-chains 910 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 859 time to evaluate : 4.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 84 HIS Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain F residue 84 HIS Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain I residue 84 HIS Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain J residue 223 LYS Chi-restraints excluded: chain K residue 84 HIS Chi-restraints excluded: chain M residue 188 MET Chi-restraints excluded: chain M residue 245 SER Chi-restraints excluded: chain N residue 84 HIS Chi-restraints excluded: chain N residue 91 ASN Chi-restraints excluded: chain N residue 226 ASN Chi-restraints excluded: chain O residue 210 LEU Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 84 HIS Chi-restraints excluded: chain Q residue 188 MET Chi-restraints excluded: chain Q residue 251 ASP Chi-restraints excluded: chain R residue 84 HIS Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain R residue 251 ASP Chi-restraints excluded: chain S residue 84 HIS Chi-restraints excluded: chain S residue 245 SER Chi-restraints excluded: chain T residue 84 HIS Chi-restraints excluded: chain T residue 174 ILE Chi-restraints excluded: chain U residue 245 SER Chi-restraints excluded: chain V residue 70 ASN Chi-restraints excluded: chain V residue 106 GLU Chi-restraints excluded: chain V residue 216 ASP Chi-restraints excluded: chain V residue 245 SER Chi-restraints excluded: chain W residue 226 ASN Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 216 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 362 optimal weight: 6.9990 chunk 296 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 chunk 436 optimal weight: 10.0000 chunk 471 optimal weight: 0.9990 chunk 388 optimal weight: 5.9990 chunk 433 optimal weight: 0.4980 chunk 148 optimal weight: 0.0050 chunk 350 optimal weight: 5.9990 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN E 166 ASN ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 104 GLN ** K 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 137 ASN ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 264 HIS S 84 HIS S 264 HIS T 176 HIS V 84 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 43344 Z= 0.169 Angle : 0.510 4.281 59064 Z= 0.281 Chirality : 0.040 0.218 6552 Planarity : 0.005 0.044 7320 Dihedral : 13.181 60.647 7320 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.57 % Allowed : 12.41 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.12), residues: 4920 helix: -0.30 (0.14), residues: 1608 sheet: None (None), residues: 0 loop : -2.61 (0.11), residues: 3312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 147 HIS 0.012 0.001 HIS V 84 PHE 0.014 0.001 PHE S 215 TYR 0.014 0.001 TYR C 213 ARG 0.008 0.000 ARG V 203 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 911 time to evaluate : 4.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASN cc_start: 0.8235 (m-40) cc_final: 0.7956 (p0) REVERT: A 222 SER cc_start: 0.7803 (p) cc_final: 0.7407 (p) REVERT: B 61 ARG cc_start: 0.6880 (mtm-85) cc_final: 0.5439 (mmt180) REVERT: B 117 ASP cc_start: 0.7495 (t0) cc_final: 0.7104 (p0) REVERT: B 204 ASN cc_start: 0.8291 (m-40) cc_final: 0.8082 (p0) REVERT: C 61 ARG cc_start: 0.6935 (mtm-85) cc_final: 0.5558 (mmt180) REVERT: C 177 HIS cc_start: 0.8101 (OUTLIER) cc_final: 0.7307 (m170) REVERT: D 109 TYR cc_start: 0.8038 (t80) cc_final: 0.7805 (t80) REVERT: D 251 ASP cc_start: 0.8674 (m-30) cc_final: 0.8366 (m-30) REVERT: E 117 ASP cc_start: 0.7160 (t0) cc_final: 0.6755 (p0) REVERT: G 109 TYR cc_start: 0.8531 (t80) cc_final: 0.8225 (t80) REVERT: G 117 ASP cc_start: 0.8140 (t0) cc_final: 0.7667 (p0) REVERT: G 121 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6697 (mm-30) REVERT: H 262 GLU cc_start: 0.7446 (tt0) cc_final: 0.6902 (tp30) REVERT: J 61 ARG cc_start: 0.6801 (mtm-85) cc_final: 0.5913 (mmm160) REVERT: J 117 ASP cc_start: 0.7928 (t0) cc_final: 0.7692 (p0) REVERT: J 251 ASP cc_start: 0.7858 (t70) cc_final: 0.7424 (t70) REVERT: K 251 ASP cc_start: 0.8018 (t70) cc_final: 0.7634 (t70) REVERT: L 127 MET cc_start: 0.7144 (mmm) cc_final: 0.6751 (mmp) REVERT: L 251 ASP cc_start: 0.8260 (t70) cc_final: 0.7794 (t70) REVERT: P 190 ASN cc_start: 0.8373 (t0) cc_final: 0.8152 (t0) REVERT: P 251 ASP cc_start: 0.7873 (t70) cc_final: 0.7610 (t70) REVERT: S 235 MET cc_start: 0.7855 (mtt) cc_final: 0.7558 (mtm) REVERT: T 106 GLU cc_start: 0.8142 (tp30) cc_final: 0.7781 (tp30) REVERT: T 264 HIS cc_start: 0.5777 (m-70) cc_final: 0.5147 (p90) REVERT: U 127 MET cc_start: 0.7952 (mmm) cc_final: 0.7510 (mmt) REVERT: V 196 MET cc_start: 0.8684 (mmm) cc_final: 0.8345 (mmm) REVERT: W 127 MET cc_start: 0.7827 (mmm) cc_final: 0.7571 (mmp) REVERT: X 123 MET cc_start: 0.6368 (mmm) cc_final: 0.6005 (mmp) REVERT: X 177 HIS cc_start: 0.7360 (OUTLIER) cc_final: 0.6916 (m170) outliers start: 68 outliers final: 41 residues processed: 946 average time/residue: 0.9568 time to fit residues: 1538.3362 Evaluate side-chains 895 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 851 time to evaluate : 4.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain B residue 84 HIS Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 177 HIS Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 244 ASN Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain E residue 84 HIS Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain I residue 131 MET Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 245 SER Chi-restraints excluded: chain K residue 84 HIS Chi-restraints excluded: chain K residue 151 ASP Chi-restraints excluded: chain L residue 131 MET Chi-restraints excluded: chain M residue 151 ASP Chi-restraints excluded: chain M residue 188 MET Chi-restraints excluded: chain M residue 245 SER Chi-restraints excluded: chain N residue 84 HIS Chi-restraints excluded: chain N residue 122 GLN Chi-restraints excluded: chain N residue 174 ILE Chi-restraints excluded: chain Q residue 84 HIS Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain Q residue 188 MET Chi-restraints excluded: chain S residue 188 MET Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain U residue 216 ASP Chi-restraints excluded: chain V residue 84 HIS Chi-restraints excluded: chain V residue 125 VAL Chi-restraints excluded: chain V residue 188 MET Chi-restraints excluded: chain V residue 222 SER Chi-restraints excluded: chain V residue 245 SER Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 219 GLU Chi-restraints excluded: chain W residue 226 ASN Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 216 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 10.0000 chunk 328 optimal weight: 4.9990 chunk 226 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 208 optimal weight: 6.9990 chunk 293 optimal weight: 5.9990 chunk 438 optimal weight: 8.9990 chunk 463 optimal weight: 9.9990 chunk 228 optimal weight: 4.9990 chunk 415 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 244 ASN I 104 GLN ** I 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 128 ASN R 84 HIS S 264 HIS T 84 HIS U 84 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.6490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 43344 Z= 0.368 Angle : 0.701 8.134 59064 Z= 0.391 Chirality : 0.047 0.271 6552 Planarity : 0.006 0.060 7320 Dihedral : 13.014 61.731 7320 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.18 % Favored : 89.80 % Rotamer: Outliers : 3.15 % Allowed : 11.64 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.11), residues: 4920 helix: -1.05 (0.12), residues: 1872 sheet: None (None), residues: 0 loop : -3.19 (0.10), residues: 3048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP S 147 HIS 0.067 0.002 HIS V 84 PHE 0.028 0.002 PHE M 215 TYR 0.020 0.002 TYR C 116 ARG 0.007 0.001 ARG J 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1200 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1064 time to evaluate : 4.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7895 (ppp) cc_final: 0.7452 (ttp) REVERT: A 174 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8411 (mt) REVERT: A 177 HIS cc_start: 0.8677 (OUTLIER) cc_final: 0.7782 (m-70) REVERT: A 204 ASN cc_start: 0.8817 (m-40) cc_final: 0.8252 (p0) REVERT: B 61 ARG cc_start: 0.7124 (mtm-85) cc_final: 0.5581 (mmt180) REVERT: B 94 ASP cc_start: 0.8523 (t0) cc_final: 0.7892 (t0) REVERT: B 117 ASP cc_start: 0.7652 (t0) cc_final: 0.7201 (p0) REVERT: B 196 MET cc_start: 0.8440 (mmm) cc_final: 0.8026 (mmm) REVERT: B 204 ASN cc_start: 0.8803 (m-40) cc_final: 0.8441 (p0) REVERT: B 207 ASP cc_start: 0.8072 (t0) cc_final: 0.7863 (t0) REVERT: C 61 ARG cc_start: 0.7132 (mtm-85) cc_final: 0.5624 (mmt180) REVERT: C 177 HIS cc_start: 0.8868 (OUTLIER) cc_final: 0.7945 (m170) REVERT: C 204 ASN cc_start: 0.8512 (m-40) cc_final: 0.8056 (p0) REVERT: D 109 TYR cc_start: 0.8533 (t80) cc_final: 0.8199 (t80) REVERT: E 89 LYS cc_start: 0.8655 (mttt) cc_final: 0.8436 (mttp) REVERT: E 117 ASP cc_start: 0.7305 (t0) cc_final: 0.6880 (p0) REVERT: E 173 GLN cc_start: 0.7663 (tp-100) cc_final: 0.7382 (tp-100) REVERT: E 183 GLU cc_start: 0.8074 (tp30) cc_final: 0.7667 (tt0) REVERT: E 196 MET cc_start: 0.8573 (mmm) cc_final: 0.8306 (mmm) REVERT: G 117 ASP cc_start: 0.8114 (t0) cc_final: 0.7598 (p0) REVERT: G 121 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7616 (mm-30) REVERT: G 150 MET cc_start: 0.7870 (ttp) cc_final: 0.7592 (ptm) REVERT: G 204 ASN cc_start: 0.8911 (m-40) cc_final: 0.7929 (p0) REVERT: H 196 MET cc_start: 0.8647 (mmm) cc_final: 0.8420 (mmm) REVERT: H 204 ASN cc_start: 0.8984 (m-40) cc_final: 0.8247 (p0) REVERT: H 207 ASP cc_start: 0.7887 (t0) cc_final: 0.7612 (t0) REVERT: I 150 MET cc_start: 0.8024 (ttp) cc_final: 0.7787 (ttp) REVERT: I 158 TYR cc_start: 0.8557 (m-80) cc_final: 0.8325 (m-80) REVERT: J 61 ARG cc_start: 0.6853 (mtm-85) cc_final: 0.5926 (mmm160) REVERT: J 117 ASP cc_start: 0.7927 (t0) cc_final: 0.7666 (t70) REVERT: J 251 ASP cc_start: 0.8165 (t70) cc_final: 0.7865 (t70) REVERT: J 261 THR cc_start: 0.8587 (m) cc_final: 0.8173 (p) REVERT: K 251 ASP cc_start: 0.8383 (t70) cc_final: 0.8108 (t70) REVERT: L 109 TYR cc_start: 0.8985 (t80) cc_final: 0.8779 (t80) REVERT: L 251 ASP cc_start: 0.8470 (t70) cc_final: 0.8080 (t70) REVERT: M 128 ASN cc_start: 0.8420 (OUTLIER) cc_final: 0.8202 (t0) REVERT: M 196 MET cc_start: 0.8580 (mmm) cc_final: 0.8287 (ttm) REVERT: N 174 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8960 (tt) REVERT: O 122 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7432 (pm20) REVERT: O 123 MET cc_start: 0.7108 (mmm) cc_final: 0.6827 (mmm) REVERT: O 158 TYR cc_start: 0.8497 (m-80) cc_final: 0.8211 (m-80) REVERT: P 69 MET cc_start: 0.7649 (tpp) cc_final: 0.7281 (tpp) REVERT: P 123 MET cc_start: 0.6830 (mmm) cc_final: 0.6377 (mmp) REVERT: P 158 TYR cc_start: 0.8639 (m-80) cc_final: 0.8434 (m-80) REVERT: P 196 MET cc_start: 0.8795 (mmm) cc_final: 0.8527 (mmm) REVERT: P 204 ASN cc_start: 0.8736 (m-40) cc_final: 0.8492 (m-40) REVERT: S 63 GLN cc_start: 0.6879 (mm-40) cc_final: 0.6588 (mm-40) REVERT: T 63 GLN cc_start: 0.6736 (mm-40) cc_final: 0.6494 (mm-40) REVERT: T 106 GLU cc_start: 0.8405 (tp30) cc_final: 0.8124 (tp30) REVERT: T 118 LEU cc_start: 0.6805 (tp) cc_final: 0.6315 (tp) REVERT: T 177 HIS cc_start: 0.8805 (OUTLIER) cc_final: 0.7764 (m-70) REVERT: U 127 MET cc_start: 0.8914 (mmm) cc_final: 0.8711 (mmp) REVERT: U 132 VAL cc_start: 0.8367 (m) cc_final: 0.8137 (t) REVERT: V 196 MET cc_start: 0.8965 (mmm) cc_final: 0.8703 (mmm) REVERT: W 106 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7664 (tm-30) REVERT: W 127 MET cc_start: 0.8481 (mmm) cc_final: 0.8170 (mmt) REVERT: X 122 GLN cc_start: 0.7037 (mt0) cc_final: 0.6751 (mt0) REVERT: X 165 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7509 (tp30) REVERT: X 187 GLU cc_start: 0.8014 (tp30) cc_final: 0.7813 (tp30) REVERT: X 199 TYR cc_start: 0.8746 (t80) cc_final: 0.8541 (t80) REVERT: X 223 LYS cc_start: 0.8173 (mmtp) cc_final: 0.7554 (mtmt) outliers start: 136 outliers final: 89 residues processed: 1136 average time/residue: 0.9580 time to fit residues: 1838.2742 Evaluate side-chains 1023 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 926 time to evaluate : 4.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain B residue 84 HIS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 177 HIS Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 84 HIS Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 84 HIS Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 84 HIS Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 232 ILE Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 70 ASN Chi-restraints excluded: chain I residue 84 HIS Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain I residue 245 SER Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 70 ASN Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 70 ASN Chi-restraints excluded: chain K residue 84 HIS Chi-restraints excluded: chain K residue 151 ASP Chi-restraints excluded: chain K residue 188 MET Chi-restraints excluded: chain K residue 204 ASN Chi-restraints excluded: chain L residue 131 MET Chi-restraints excluded: chain L residue 245 SER Chi-restraints excluded: chain M residue 128 ASN Chi-restraints excluded: chain M residue 151 ASP Chi-restraints excluded: chain M residue 188 MET Chi-restraints excluded: chain M residue 245 SER Chi-restraints excluded: chain N residue 84 HIS Chi-restraints excluded: chain N residue 151 ASP Chi-restraints excluded: chain N residue 174 ILE Chi-restraints excluded: chain N residue 210 LEU Chi-restraints excluded: chain O residue 84 HIS Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 122 GLN Chi-restraints excluded: chain O residue 210 LEU Chi-restraints excluded: chain O residue 245 SER Chi-restraints excluded: chain P residue 84 HIS Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 174 ILE Chi-restraints excluded: chain P residue 210 LEU Chi-restraints excluded: chain Q residue 84 HIS Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 157 GLU Chi-restraints excluded: chain Q residue 188 MET Chi-restraints excluded: chain Q residue 222 SER Chi-restraints excluded: chain Q residue 251 ASP Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 222 SER Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain R residue 251 ASP Chi-restraints excluded: chain S residue 245 SER Chi-restraints excluded: chain S residue 251 ASP Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 115 GLU Chi-restraints excluded: chain T residue 177 HIS Chi-restraints excluded: chain U residue 84 HIS Chi-restraints excluded: chain U residue 148 VAL Chi-restraints excluded: chain U residue 190 ASN Chi-restraints excluded: chain U residue 245 SER Chi-restraints excluded: chain U residue 251 ASP Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 84 HIS Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 188 MET Chi-restraints excluded: chain V residue 245 SER Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 110 SER Chi-restraints excluded: chain W residue 188 MET Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain X residue 84 HIS Chi-restraints excluded: chain X residue 177 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 3.9990 chunk 263 optimal weight: 6.9990 chunk 6 optimal weight: 0.2980 chunk 345 optimal weight: 9.9990 chunk 191 optimal weight: 2.9990 chunk 395 optimal weight: 0.6980 chunk 320 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 236 optimal weight: 0.0040 chunk 416 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN B 137 ASN C 137 ASN D 137 ASN ** I 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 ASN K 137 ASN L 128 ASN L 137 ASN N 137 ASN T 137 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.6761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 43344 Z= 0.165 Angle : 0.518 4.428 59064 Z= 0.281 Chirality : 0.039 0.235 6552 Planarity : 0.005 0.057 7320 Dihedral : 13.004 60.749 7320 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.45 % Allowed : 15.28 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.12), residues: 4920 helix: -0.51 (0.12), residues: 1896 sheet: None (None), residues: 0 loop : -2.95 (0.10), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 147 HIS 0.015 0.001 HIS U 84 PHE 0.014 0.001 PHE P 215 TYR 0.012 0.001 TYR R 116 ARG 0.004 0.001 ARG S 203 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1097 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 991 time to evaluate : 5.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7757 (ppp) cc_final: 0.7446 (ttp) REVERT: A 175 MET cc_start: 0.9169 (tpp) cc_final: 0.8926 (tpp) REVERT: A 204 ASN cc_start: 0.8773 (m-40) cc_final: 0.8292 (p0) REVERT: A 251 ASP cc_start: 0.8376 (m-30) cc_final: 0.7894 (m-30) REVERT: B 61 ARG cc_start: 0.7050 (mtm-85) cc_final: 0.5526 (mmt180) REVERT: B 94 ASP cc_start: 0.8384 (t0) cc_final: 0.7878 (t0) REVERT: B 117 ASP cc_start: 0.7613 (t0) cc_final: 0.7297 (p0) REVERT: B 204 ASN cc_start: 0.8670 (m-40) cc_final: 0.8343 (p0) REVERT: B 207 ASP cc_start: 0.8047 (t0) cc_final: 0.7809 (t0) REVERT: C 61 ARG cc_start: 0.7052 (mtm-85) cc_final: 0.5597 (mmt180) REVERT: C 92 GLN cc_start: 0.8576 (tp40) cc_final: 0.8023 (tp40) REVERT: C 177 HIS cc_start: 0.8729 (OUTLIER) cc_final: 0.8126 (m170) REVERT: C 204 ASN cc_start: 0.8425 (m-40) cc_final: 0.8053 (p0) REVERT: D 204 ASN cc_start: 0.8635 (m-40) cc_final: 0.7862 (p0) REVERT: E 89 LYS cc_start: 0.8575 (mttt) cc_final: 0.8351 (mttp) REVERT: E 117 ASP cc_start: 0.7496 (t0) cc_final: 0.6645 (p0) REVERT: E 173 GLN cc_start: 0.7554 (tp-100) cc_final: 0.7199 (tp-100) REVERT: E 196 MET cc_start: 0.8514 (mmm) cc_final: 0.8226 (mmm) REVERT: E 204 ASN cc_start: 0.8918 (OUTLIER) cc_final: 0.8091 (p0) REVERT: F 63 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7564 (mm-40) REVERT: F 92 GLN cc_start: 0.8252 (tp40) cc_final: 0.7393 (tp40) REVERT: G 121 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7631 (mm-30) REVERT: H 136 ASP cc_start: 0.8396 (m-30) cc_final: 0.8174 (t0) REVERT: H 196 MET cc_start: 0.8605 (mmm) cc_final: 0.8347 (mmm) REVERT: H 251 ASP cc_start: 0.8031 (t0) cc_final: 0.7561 (m-30) REVERT: J 61 ARG cc_start: 0.6766 (mtm-85) cc_final: 0.5834 (mmm160) REVERT: J 117 ASP cc_start: 0.7865 (t0) cc_final: 0.7623 (t70) REVERT: J 251 ASP cc_start: 0.8067 (t70) cc_final: 0.7723 (t70) REVERT: K 251 ASP cc_start: 0.8315 (t70) cc_final: 0.7970 (t70) REVERT: L 226 ASN cc_start: 0.8640 (m-40) cc_final: 0.8426 (m110) REVERT: L 251 ASP cc_start: 0.8449 (t70) cc_final: 0.8079 (t70) REVERT: L 253 ASN cc_start: 0.8994 (t0) cc_final: 0.8787 (t0) REVERT: M 122 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7790 (pm20) REVERT: M 196 MET cc_start: 0.8634 (mmm) cc_final: 0.8282 (ttm) REVERT: N 204 ASN cc_start: 0.8660 (m-40) cc_final: 0.8426 (m-40) REVERT: O 158 TYR cc_start: 0.8367 (m-80) cc_final: 0.8113 (m-80) REVERT: P 69 MET cc_start: 0.7514 (tpp) cc_final: 0.7168 (tpp) REVERT: P 117 ASP cc_start: 0.7931 (t0) cc_final: 0.7536 (p0) REVERT: P 187 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8161 (tm-30) REVERT: P 190 ASN cc_start: 0.8284 (t0) cc_final: 0.7932 (t0) REVERT: P 196 MET cc_start: 0.8756 (mmm) cc_final: 0.8487 (mmm) REVERT: Q 150 MET cc_start: 0.8323 (ptm) cc_final: 0.8108 (ptp) REVERT: R 127 MET cc_start: 0.8424 (mmm) cc_final: 0.8138 (mmm) REVERT: R 250 LEU cc_start: 0.8589 (tp) cc_final: 0.8330 (tt) REVERT: S 63 GLN cc_start: 0.6854 (mm-40) cc_final: 0.6625 (mm-40) REVERT: T 106 GLU cc_start: 0.8336 (tp30) cc_final: 0.8023 (tp30) REVERT: U 235 MET cc_start: 0.8105 (mtt) cc_final: 0.7834 (mtm) REVERT: V 196 MET cc_start: 0.9044 (mmm) cc_final: 0.8764 (mmm) REVERT: W 196 MET cc_start: 0.8944 (tpp) cc_final: 0.8609 (mmm) outliers start: 106 outliers final: 76 residues processed: 1043 average time/residue: 0.9053 time to fit residues: 1609.1643 Evaluate side-chains 997 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 917 time to evaluate : 4.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 84 HIS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 177 HIS Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain D residue 84 HIS Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain E residue 84 HIS Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain F residue 84 HIS Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain I residue 84 HIS Chi-restraints excluded: chain I residue 135 ILE Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 188 MET Chi-restraints excluded: chain J residue 70 ASN Chi-restraints excluded: chain J residue 84 HIS Chi-restraints excluded: chain K residue 84 HIS Chi-restraints excluded: chain K residue 151 ASP Chi-restraints excluded: chain K residue 188 MET Chi-restraints excluded: chain K residue 222 SER Chi-restraints excluded: chain L residue 84 HIS Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 188 MET Chi-restraints excluded: chain L residue 245 SER Chi-restraints excluded: chain M residue 122 GLN Chi-restraints excluded: chain M residue 151 ASP Chi-restraints excluded: chain M residue 222 SER Chi-restraints excluded: chain M residue 245 SER Chi-restraints excluded: chain N residue 84 HIS Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 137 ASN Chi-restraints excluded: chain O residue 84 HIS Chi-restraints excluded: chain O residue 210 LEU Chi-restraints excluded: chain P residue 84 HIS Chi-restraints excluded: chain P residue 174 ILE Chi-restraints excluded: chain P residue 188 MET Chi-restraints excluded: chain Q residue 84 HIS Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 149 MET Chi-restraints excluded: chain Q residue 157 GLU Chi-restraints excluded: chain Q residue 245 SER Chi-restraints excluded: chain R residue 116 TYR Chi-restraints excluded: chain R residue 188 MET Chi-restraints excluded: chain S residue 220 VAL Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 216 ASP Chi-restraints excluded: chain T residue 220 VAL Chi-restraints excluded: chain T residue 222 SER Chi-restraints excluded: chain U residue 188 MET Chi-restraints excluded: chain U residue 222 SER Chi-restraints excluded: chain V residue 84 HIS Chi-restraints excluded: chain V residue 188 MET Chi-restraints excluded: chain V residue 201 LEU Chi-restraints excluded: chain W residue 115 GLU Chi-restraints excluded: chain W residue 135 ILE Chi-restraints excluded: chain W residue 188 MET Chi-restraints excluded: chain X residue 84 HIS Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 222 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 6.9990 chunk 417 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 272 optimal weight: 7.9990 chunk 114 optimal weight: 0.7980 chunk 464 optimal weight: 10.0000 chunk 385 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 153 optimal weight: 7.9990 chunk 243 optimal weight: 2.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN B 137 ASN C 137 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 ASN ** I 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 ASN L 137 ASN N 137 ASN P 137 ASN ** P 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 264 HIS U 70 ASN V 84 HIS ** V 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.7178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 43344 Z= 0.243 Angle : 0.543 4.451 59064 Z= 0.296 Chirality : 0.041 0.240 6552 Planarity : 0.004 0.041 7320 Dihedral : 13.007 60.887 7320 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 2.96 % Allowed : 15.83 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.12), residues: 4920 helix: -0.42 (0.13), residues: 1896 sheet: None (None), residues: 0 loop : -2.86 (0.11), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 147 HIS 0.010 0.001 HIS Q 264 PHE 0.030 0.001 PHE T 215 TYR 0.013 0.001 TYR S 199 ARG 0.005 0.001 ARG S 203 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1104 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 976 time to evaluate : 4.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7840 (ppp) cc_final: 0.7469 (ttp) REVERT: A 204 ASN cc_start: 0.8734 (m-40) cc_final: 0.8235 (p0) REVERT: B 61 ARG cc_start: 0.7119 (mtm-85) cc_final: 0.5551 (mmt180) REVERT: B 94 ASP cc_start: 0.8382 (t0) cc_final: 0.7843 (t0) REVERT: B 204 ASN cc_start: 0.8768 (m-40) cc_final: 0.8422 (p0) REVERT: B 207 ASP cc_start: 0.8140 (t0) cc_final: 0.7884 (t0) REVERT: B 251 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.8004 (m-30) REVERT: C 61 ARG cc_start: 0.7090 (mtm-85) cc_final: 0.5610 (mmt180) REVERT: C 177 HIS cc_start: 0.8830 (OUTLIER) cc_final: 0.8214 (m170) REVERT: C 204 ASN cc_start: 0.8421 (m-40) cc_final: 0.7958 (p0) REVERT: D 109 TYR cc_start: 0.8435 (t80) cc_final: 0.8201 (t80) REVERT: D 201 LEU cc_start: 0.8624 (mt) cc_final: 0.8282 (tp) REVERT: D 204 ASN cc_start: 0.8771 (m-40) cc_final: 0.7965 (p0) REVERT: E 89 LYS cc_start: 0.8660 (mttt) cc_final: 0.8422 (mttp) REVERT: E 117 ASP cc_start: 0.7486 (t0) cc_final: 0.6615 (p0) REVERT: E 173 GLN cc_start: 0.7623 (tp-100) cc_final: 0.7226 (tp-100) REVERT: E 196 MET cc_start: 0.8653 (mmm) cc_final: 0.8360 (mmm) REVERT: F 63 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7552 (mm-40) REVERT: F 173 GLN cc_start: 0.7567 (tp-100) cc_final: 0.7247 (tp-100) REVERT: H 136 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8165 (t0) REVERT: H 196 MET cc_start: 0.8693 (mmm) cc_final: 0.8403 (mmm) REVERT: H 251 ASP cc_start: 0.8297 (t0) cc_final: 0.7873 (m-30) REVERT: J 61 ARG cc_start: 0.6820 (mtm-85) cc_final: 0.5988 (mmt180) REVERT: J 117 ASP cc_start: 0.7882 (t0) cc_final: 0.7632 (t70) REVERT: J 251 ASP cc_start: 0.8232 (t70) cc_final: 0.7917 (t70) REVERT: K 251 ASP cc_start: 0.8400 (t70) cc_final: 0.8084 (t70) REVERT: L 251 ASP cc_start: 0.8471 (t70) cc_final: 0.8127 (t70) REVERT: M 122 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8028 (pm20) REVERT: M 196 MET cc_start: 0.8649 (mmm) cc_final: 0.8385 (ttm) REVERT: N 188 MET cc_start: 0.7809 (ptm) cc_final: 0.7481 (tmm) REVERT: O 158 TYR cc_start: 0.8367 (m-80) cc_final: 0.8071 (m-80) REVERT: P 116 TYR cc_start: 0.8840 (OUTLIER) cc_final: 0.8092 (m-80) REVERT: P 117 ASP cc_start: 0.7969 (t0) cc_final: 0.7515 (p0) REVERT: P 187 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8125 (tm-30) REVERT: P 196 MET cc_start: 0.8834 (mmm) cc_final: 0.8499 (mmm) REVERT: Q 116 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.6067 (t80) REVERT: R 127 MET cc_start: 0.8539 (mmm) cc_final: 0.8281 (mmm) REVERT: S 63 GLN cc_start: 0.6829 (mm-40) cc_final: 0.6489 (mm-40) REVERT: S 123 MET cc_start: 0.6787 (mmm) cc_final: 0.6583 (mmm) REVERT: T 106 GLU cc_start: 0.8381 (tp30) cc_final: 0.8038 (tp30) REVERT: T 177 HIS cc_start: 0.8814 (OUTLIER) cc_final: 0.7779 (m-70) REVERT: T 264 HIS cc_start: 0.5232 (m-70) cc_final: 0.4659 (m-70) REVERT: V 196 MET cc_start: 0.9024 (mmm) cc_final: 0.8726 (mmm) REVERT: W 180 ASP cc_start: 0.8494 (m-30) cc_final: 0.8183 (m-30) REVERT: X 188 MET cc_start: 0.8332 (ptm) cc_final: 0.7965 (tmm) REVERT: X 198 ARG cc_start: 0.7602 (ttt90) cc_final: 0.7210 (ttm170) outliers start: 128 outliers final: 109 residues processed: 1032 average time/residue: 0.9049 time to fit residues: 1587.0024 Evaluate side-chains 1036 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 920 time to evaluate : 4.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain B residue 84 HIS Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 177 HIS Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain D residue 84 HIS Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain E residue 84 HIS Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 84 HIS Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 245 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain H residue 136 ASP Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain I residue 84 HIS Chi-restraints excluded: chain I residue 135 ILE Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 188 MET Chi-restraints excluded: chain I residue 204 ASN Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 70 ASN Chi-restraints excluded: chain J residue 84 HIS Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 245 SER Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 84 HIS Chi-restraints excluded: chain K residue 151 ASP Chi-restraints excluded: chain K residue 188 MET Chi-restraints excluded: chain K residue 204 ASN Chi-restraints excluded: chain L residue 84 HIS Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 121 GLU Chi-restraints excluded: chain L residue 188 MET Chi-restraints excluded: chain L residue 245 SER Chi-restraints excluded: chain M residue 70 ASN Chi-restraints excluded: chain M residue 122 GLN Chi-restraints excluded: chain M residue 151 ASP Chi-restraints excluded: chain M residue 245 SER Chi-restraints excluded: chain N residue 84 HIS Chi-restraints excluded: chain N residue 157 GLU Chi-restraints excluded: chain O residue 84 HIS Chi-restraints excluded: chain O residue 210 LEU Chi-restraints excluded: chain O residue 245 SER Chi-restraints excluded: chain P residue 84 HIS Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 116 TYR Chi-restraints excluded: chain P residue 174 ILE Chi-restraints excluded: chain P residue 188 MET Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain Q residue 84 HIS Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 116 TYR Chi-restraints excluded: chain Q residue 149 MET Chi-restraints excluded: chain Q residue 157 GLU Chi-restraints excluded: chain Q residue 188 MET Chi-restraints excluded: chain Q residue 222 SER Chi-restraints excluded: chain Q residue 245 SER Chi-restraints excluded: chain Q residue 264 HIS Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 116 TYR Chi-restraints excluded: chain R residue 188 MET Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain S residue 245 SER Chi-restraints excluded: chain S residue 251 ASP Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 115 GLU Chi-restraints excluded: chain T residue 177 HIS Chi-restraints excluded: chain T residue 245 SER Chi-restraints excluded: chain U residue 70 ASN Chi-restraints excluded: chain U residue 135 ILE Chi-restraints excluded: chain U residue 188 MET Chi-restraints excluded: chain U residue 190 ASN Chi-restraints excluded: chain U residue 245 SER Chi-restraints excluded: chain U residue 251 ASP Chi-restraints excluded: chain V residue 84 HIS Chi-restraints excluded: chain V residue 135 ILE Chi-restraints excluded: chain V residue 188 MET Chi-restraints excluded: chain V residue 201 LEU Chi-restraints excluded: chain V residue 204 ASN Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 115 GLU Chi-restraints excluded: chain W residue 135 ILE Chi-restraints excluded: chain W residue 188 MET Chi-restraints excluded: chain W residue 204 ASN Chi-restraints excluded: chain W residue 219 GLU Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain X residue 84 HIS Chi-restraints excluded: chain X residue 135 ILE Chi-restraints excluded: chain X residue 177 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 264 optimal weight: 10.0000 chunk 339 optimal weight: 0.0070 chunk 262 optimal weight: 9.9990 chunk 390 optimal weight: 6.9990 chunk 259 optimal weight: 0.1980 chunk 462 optimal weight: 0.0980 chunk 289 optimal weight: 2.9990 chunk 282 optimal weight: 9.9990 chunk 213 optimal weight: 8.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN B 137 ASN C 137 ASN ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 ASN N 137 ASN N 226 ASN ** P 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 137 ASN Q 264 HIS V 137 ASN ** V 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.7304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.088 43344 Z= 0.159 Angle : 0.495 6.193 59064 Z= 0.265 Chirality : 0.038 0.202 6552 Planarity : 0.004 0.081 7320 Dihedral : 13.019 60.495 7320 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.90 % Allowed : 17.18 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.12), residues: 4920 helix: -0.03 (0.13), residues: 1896 sheet: None (None), residues: 0 loop : -2.71 (0.11), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 147 HIS 0.029 0.001 HIS Q 264 PHE 0.024 0.001 PHE T 215 TYR 0.014 0.001 TYR S 199 ARG 0.006 0.000 ARG N 203 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1024 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 942 time to evaluate : 4.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7844 (ppp) cc_final: 0.7490 (ttp) REVERT: A 204 ASN cc_start: 0.8785 (m-40) cc_final: 0.8239 (p0) REVERT: A 251 ASP cc_start: 0.8475 (m-30) cc_final: 0.8002 (m-30) REVERT: B 61 ARG cc_start: 0.7079 (mtm-85) cc_final: 0.5523 (mmt180) REVERT: B 94 ASP cc_start: 0.8315 (t0) cc_final: 0.7822 (t0) REVERT: B 117 ASP cc_start: 0.7343 (t0) cc_final: 0.7128 (t70) REVERT: B 204 ASN cc_start: 0.8709 (m-40) cc_final: 0.8436 (p0) REVERT: B 251 ASP cc_start: 0.8466 (m-30) cc_final: 0.8096 (m-30) REVERT: C 61 ARG cc_start: 0.7123 (mtm-85) cc_final: 0.5580 (mmt180) REVERT: C 92 GLN cc_start: 0.8146 (tp40) cc_final: 0.7665 (tp40) REVERT: C 177 HIS cc_start: 0.8698 (OUTLIER) cc_final: 0.8196 (m170) REVERT: C 204 ASN cc_start: 0.8466 (m-40) cc_final: 0.7995 (p0) REVERT: D 109 TYR cc_start: 0.8359 (t80) cc_final: 0.8102 (t80) REVERT: D 201 LEU cc_start: 0.8504 (mt) cc_final: 0.8235 (tp) REVERT: D 204 ASN cc_start: 0.8677 (m-40) cc_final: 0.7883 (p0) REVERT: E 89 LYS cc_start: 0.8592 (mttt) cc_final: 0.8377 (mttp) REVERT: E 117 ASP cc_start: 0.7482 (t0) cc_final: 0.6650 (p0) REVERT: E 173 GLN cc_start: 0.7653 (tp-100) cc_final: 0.7245 (tp-100) REVERT: E 188 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8094 (ptm) REVERT: E 196 MET cc_start: 0.8707 (mmm) cc_final: 0.8404 (mmm) REVERT: E 204 ASN cc_start: 0.8966 (OUTLIER) cc_final: 0.8123 (p0) REVERT: F 63 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7561 (mm-40) REVERT: F 92 GLN cc_start: 0.7735 (tp40) cc_final: 0.7313 (tp40) REVERT: F 173 GLN cc_start: 0.7482 (tp-100) cc_final: 0.7137 (tp-100) REVERT: H 136 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.8120 (t0) REVERT: H 196 MET cc_start: 0.8691 (mmm) cc_final: 0.8316 (mmm) REVERT: H 201 LEU cc_start: 0.8484 (mm) cc_final: 0.8024 (tp) REVERT: H 251 ASP cc_start: 0.8166 (t0) cc_final: 0.7659 (m-30) REVERT: J 61 ARG cc_start: 0.6790 (mtm-85) cc_final: 0.5988 (mmt180) REVERT: J 117 ASP cc_start: 0.7859 (t0) cc_final: 0.7606 (t70) REVERT: J 148 VAL cc_start: 0.9094 (OUTLIER) cc_final: 0.8872 (p) REVERT: J 251 ASP cc_start: 0.8122 (t70) cc_final: 0.7776 (t70) REVERT: J 261 THR cc_start: 0.8645 (m) cc_final: 0.8279 (p) REVERT: K 131 MET cc_start: 0.8338 (ttp) cc_final: 0.8092 (ttt) REVERT: K 251 ASP cc_start: 0.8373 (t70) cc_final: 0.8070 (t70) REVERT: L 251 ASP cc_start: 0.8528 (t70) cc_final: 0.8161 (t70) REVERT: M 120 ASP cc_start: 0.8253 (t0) cc_final: 0.8048 (t0) REVERT: M 122 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7849 (pm20) REVERT: O 131 MET cc_start: 0.7666 (ttt) cc_final: 0.6984 (ttt) REVERT: O 158 TYR cc_start: 0.8224 (m-80) cc_final: 0.7949 (m-80) REVERT: P 117 ASP cc_start: 0.7886 (t0) cc_final: 0.7462 (p0) REVERT: P 196 MET cc_start: 0.8852 (mmm) cc_final: 0.8454 (mmm) REVERT: Q 116 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.5894 (t80) REVERT: R 127 MET cc_start: 0.8421 (mmm) cc_final: 0.8182 (mmm) REVERT: S 63 GLN cc_start: 0.6836 (mm-40) cc_final: 0.6584 (mm-40) REVERT: T 106 GLU cc_start: 0.8352 (tp30) cc_final: 0.7942 (tp30) REVERT: T 132 VAL cc_start: 0.7236 (m) cc_final: 0.6946 (m) REVERT: T 264 HIS cc_start: 0.5240 (m-70) cc_final: 0.4672 (m-70) REVERT: V 196 MET cc_start: 0.9143 (mmm) cc_final: 0.8865 (mmm) REVERT: W 196 MET cc_start: 0.8940 (tpp) cc_final: 0.8724 (mmm) REVERT: X 188 MET cc_start: 0.8123 (ptm) cc_final: 0.7858 (tmm) outliers start: 82 outliers final: 62 residues processed: 979 average time/residue: 0.9065 time to fit residues: 1504.3197 Evaluate side-chains 974 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 905 time to evaluate : 4.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 84 HIS Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 177 HIS Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 84 HIS Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain E residue 84 HIS Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain F residue 84 HIS Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain H residue 136 ASP Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain I residue 84 HIS Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 188 MET Chi-restraints excluded: chain J residue 84 HIS Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 84 HIS Chi-restraints excluded: chain K residue 151 ASP Chi-restraints excluded: chain K residue 204 ASN Chi-restraints excluded: chain L residue 84 HIS Chi-restraints excluded: chain L residue 188 MET Chi-restraints excluded: chain M residue 122 GLN Chi-restraints excluded: chain M residue 151 ASP Chi-restraints excluded: chain M residue 245 SER Chi-restraints excluded: chain M residue 253 ASN Chi-restraints excluded: chain N residue 84 HIS Chi-restraints excluded: chain N residue 157 GLU Chi-restraints excluded: chain O residue 84 HIS Chi-restraints excluded: chain O residue 245 SER Chi-restraints excluded: chain P residue 84 HIS Chi-restraints excluded: chain P residue 174 ILE Chi-restraints excluded: chain P residue 188 MET Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain Q residue 84 HIS Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 116 TYR Chi-restraints excluded: chain Q residue 188 MET Chi-restraints excluded: chain Q residue 245 SER Chi-restraints excluded: chain R residue 116 TYR Chi-restraints excluded: chain R residue 188 MET Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 115 GLU Chi-restraints excluded: chain T residue 245 SER Chi-restraints excluded: chain U residue 188 MET Chi-restraints excluded: chain U residue 219 GLU Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 137 ASN Chi-restraints excluded: chain V residue 188 MET Chi-restraints excluded: chain V residue 201 LEU Chi-restraints excluded: chain W residue 115 GLU Chi-restraints excluded: chain W residue 188 MET Chi-restraints excluded: chain W residue 219 GLU Chi-restraints excluded: chain X residue 84 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 9.9990 chunk 184 optimal weight: 10.0000 chunk 276 optimal weight: 5.9990 chunk 139 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 294 optimal weight: 6.9990 chunk 315 optimal weight: 9.9990 chunk 228 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 363 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 264 HIS V 137 ASN ** V 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.7597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 43344 Z= 0.226 Angle : 0.526 5.158 59064 Z= 0.284 Chirality : 0.040 0.215 6552 Planarity : 0.004 0.062 7320 Dihedral : 12.859 61.727 7320 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 2.62 % Allowed : 17.01 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.12), residues: 4920 helix: -0.00 (0.13), residues: 1896 sheet: None (None), residues: 0 loop : -2.66 (0.11), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 147 HIS 0.005 0.001 HIS Q 264 PHE 0.017 0.001 PHE H 215 TYR 0.013 0.001 TYR E 195 ARG 0.007 0.001 ARG S 189 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 945 time to evaluate : 4.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7942 (ppp) cc_final: 0.7532 (ttp) REVERT: A 201 LEU cc_start: 0.8854 (mt) cc_final: 0.8543 (tp) REVERT: A 204 ASN cc_start: 0.8753 (m-40) cc_final: 0.8200 (p0) REVERT: B 61 ARG cc_start: 0.7027 (mtm-85) cc_final: 0.5495 (mmt180) REVERT: B 94 ASP cc_start: 0.8369 (t0) cc_final: 0.7824 (t0) REVERT: B 177 HIS cc_start: 0.8852 (OUTLIER) cc_final: 0.8316 (m-70) REVERT: B 204 ASN cc_start: 0.8808 (m-40) cc_final: 0.8443 (p0) REVERT: B 251 ASP cc_start: 0.8460 (m-30) cc_final: 0.8111 (m-30) REVERT: C 61 ARG cc_start: 0.7162 (mtm-85) cc_final: 0.5606 (mmt180) REVERT: C 177 HIS cc_start: 0.8802 (OUTLIER) cc_final: 0.8213 (m170) REVERT: C 204 ASN cc_start: 0.8476 (m-40) cc_final: 0.7849 (p0) REVERT: C 235 MET cc_start: 0.7756 (mtt) cc_final: 0.7476 (mtt) REVERT: D 109 TYR cc_start: 0.8430 (t80) cc_final: 0.8145 (t80) REVERT: D 201 LEU cc_start: 0.8658 (mt) cc_final: 0.8393 (tp) REVERT: E 89 LYS cc_start: 0.8616 (mttt) cc_final: 0.8393 (mttp) REVERT: E 117 ASP cc_start: 0.7503 (t0) cc_final: 0.6650 (p0) REVERT: E 173 GLN cc_start: 0.7585 (tp-100) cc_final: 0.7143 (tp-100) REVERT: E 188 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.8123 (ptm) REVERT: E 196 MET cc_start: 0.8743 (mmm) cc_final: 0.8377 (mmm) REVERT: F 173 GLN cc_start: 0.7577 (tp-100) cc_final: 0.7229 (tp-100) REVERT: G 123 MET cc_start: 0.6818 (mmm) cc_final: 0.6297 (ttm) REVERT: H 136 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.8118 (t0) REVERT: H 201 LEU cc_start: 0.8656 (mm) cc_final: 0.8206 (tp) REVERT: H 251 ASP cc_start: 0.8329 (t0) cc_final: 0.7905 (m-30) REVERT: I 201 LEU cc_start: 0.8431 (mm) cc_final: 0.8187 (tp) REVERT: J 61 ARG cc_start: 0.6913 (mtm-85) cc_final: 0.6019 (mmt180) REVERT: J 117 ASP cc_start: 0.7892 (t0) cc_final: 0.7664 (t70) REVERT: J 148 VAL cc_start: 0.9153 (OUTLIER) cc_final: 0.8929 (p) REVERT: J 251 ASP cc_start: 0.8238 (t70) cc_final: 0.7909 (t70) REVERT: K 251 ASP cc_start: 0.8414 (t70) cc_final: 0.8109 (t70) REVERT: L 251 ASP cc_start: 0.8557 (t70) cc_final: 0.8169 (t70) REVERT: M 151 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8142 (p0) REVERT: N 188 MET cc_start: 0.7657 (tmm) cc_final: 0.7416 (tmm) REVERT: O 131 MET cc_start: 0.7882 (ttt) cc_final: 0.7154 (ttt) REVERT: O 158 TYR cc_start: 0.8255 (m-80) cc_final: 0.7968 (m-80) REVERT: Q 116 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.6226 (t80) REVERT: R 127 MET cc_start: 0.8603 (mmm) cc_final: 0.8368 (mmm) REVERT: S 63 GLN cc_start: 0.6781 (mm-40) cc_final: 0.6523 (mm-40) REVERT: T 106 GLU cc_start: 0.8441 (tp30) cc_final: 0.7993 (tp30) REVERT: T 264 HIS cc_start: 0.4780 (m-70) cc_final: 0.4272 (m-70) REVERT: V 196 MET cc_start: 0.9170 (mmm) cc_final: 0.8832 (mmm) REVERT: W 180 ASP cc_start: 0.8241 (m-30) cc_final: 0.7919 (m-30) REVERT: W 251 ASP cc_start: 0.7259 (t70) cc_final: 0.6922 (t70) REVERT: X 188 MET cc_start: 0.8172 (ptm) cc_final: 0.7962 (tmm) REVERT: X 198 ARG cc_start: 0.7670 (ttt90) cc_final: 0.7234 (ttm170) REVERT: X 209 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6876 (tm-30) outliers start: 113 outliers final: 95 residues processed: 991 average time/residue: 0.9032 time to fit residues: 1524.9057 Evaluate side-chains 1026 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 924 time to evaluate : 4.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 84 HIS Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 177 HIS Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 177 HIS Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain D residue 84 HIS Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 84 HIS Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain F residue 84 HIS Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 174 ILE Chi-restraints excluded: chain G residue 245 SER Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain H residue 136 ASP Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 232 ILE Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 84 HIS Chi-restraints excluded: chain I residue 135 ILE Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 188 MET Chi-restraints excluded: chain I residue 204 ASN Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 84 HIS Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 84 HIS Chi-restraints excluded: chain K residue 151 ASP Chi-restraints excluded: chain K residue 204 ASN Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 84 HIS Chi-restraints excluded: chain L residue 128 ASN Chi-restraints excluded: chain L residue 188 MET Chi-restraints excluded: chain M residue 84 HIS Chi-restraints excluded: chain M residue 135 ILE Chi-restraints excluded: chain M residue 151 ASP Chi-restraints excluded: chain M residue 245 SER Chi-restraints excluded: chain N residue 84 HIS Chi-restraints excluded: chain N residue 157 GLU Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 84 HIS Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain O residue 210 LEU Chi-restraints excluded: chain O residue 245 SER Chi-restraints excluded: chain P residue 84 HIS Chi-restraints excluded: chain P residue 174 ILE Chi-restraints excluded: chain P residue 188 MET Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain Q residue 84 HIS Chi-restraints excluded: chain Q residue 116 TYR Chi-restraints excluded: chain Q residue 149 MET Chi-restraints excluded: chain Q residue 157 GLU Chi-restraints excluded: chain Q residue 188 MET Chi-restraints excluded: chain Q residue 245 SER Chi-restraints excluded: chain R residue 116 TYR Chi-restraints excluded: chain R residue 188 MET Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 115 GLU Chi-restraints excluded: chain T residue 135 ILE Chi-restraints excluded: chain T residue 245 SER Chi-restraints excluded: chain U residue 135 ILE Chi-restraints excluded: chain U residue 188 MET Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 137 ASN Chi-restraints excluded: chain V residue 188 MET Chi-restraints excluded: chain V residue 204 ASN Chi-restraints excluded: chain W residue 69 MET Chi-restraints excluded: chain W residue 115 GLU Chi-restraints excluded: chain W residue 135 ILE Chi-restraints excluded: chain W residue 188 MET Chi-restraints excluded: chain W residue 204 ASN Chi-restraints excluded: chain W residue 219 GLU Chi-restraints excluded: chain X residue 84 HIS Chi-restraints excluded: chain X residue 135 ILE Chi-restraints excluded: chain X residue 177 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 6.9990 chunk 443 optimal weight: 1.9990 chunk 404 optimal weight: 5.9990 chunk 431 optimal weight: 6.9990 chunk 259 optimal weight: 9.9990 chunk 187 optimal weight: 8.9990 chunk 338 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 389 optimal weight: 7.9990 chunk 407 optimal weight: 6.9990 chunk 429 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 264 HIS T 137 ASN V 137 ASN ** W 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.8195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 43344 Z= 0.308 Angle : 0.615 7.069 59064 Z= 0.336 Chirality : 0.043 0.260 6552 Planarity : 0.005 0.059 7320 Dihedral : 13.099 69.542 7320 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 3.33 % Allowed : 16.97 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.12), residues: 4920 helix: -0.28 (0.13), residues: 1896 sheet: None (None), residues: 0 loop : -2.76 (0.11), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 147 HIS 0.009 0.001 HIS Q 264 PHE 0.024 0.002 PHE M 215 TYR 0.026 0.002 TYR H 158 ARG 0.008 0.001 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1111 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 967 time to evaluate : 4.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.8007 (t0) REVERT: A 150 MET cc_start: 0.8112 (ppp) cc_final: 0.7611 (ttp) REVERT: A 201 LEU cc_start: 0.9020 (mt) cc_final: 0.8784 (tp) REVERT: B 61 ARG cc_start: 0.7104 (mtm-85) cc_final: 0.5534 (mmt180) REVERT: B 94 ASP cc_start: 0.8454 (t0) cc_final: 0.7944 (t0) REVERT: B 204 ASN cc_start: 0.8798 (m-40) cc_final: 0.8262 (p0) REVERT: C 61 ARG cc_start: 0.7209 (mtm-85) cc_final: 0.5659 (mmt180) REVERT: C 177 HIS cc_start: 0.8802 (OUTLIER) cc_final: 0.8007 (m170) REVERT: C 183 GLU cc_start: 0.8352 (tp30) cc_final: 0.7744 (tt0) REVERT: C 235 MET cc_start: 0.7823 (mtt) cc_final: 0.7499 (mtt) REVERT: D 109 TYR cc_start: 0.8593 (t80) cc_final: 0.8388 (t80) REVERT: E 89 LYS cc_start: 0.8698 (mttt) cc_final: 0.8408 (mttp) REVERT: E 117 ASP cc_start: 0.7537 (t0) cc_final: 0.6631 (p0) REVERT: E 201 LEU cc_start: 0.9030 (mm) cc_final: 0.8526 (tp) REVERT: F 216 ASP cc_start: 0.8058 (m-30) cc_final: 0.7806 (m-30) REVERT: G 68 LYS cc_start: 0.3507 (pttt) cc_final: 0.2866 (pttt) REVERT: G 117 ASP cc_start: 0.7874 (t70) cc_final: 0.7500 (t70) REVERT: H 118 LEU cc_start: 0.8734 (mt) cc_final: 0.7996 (mt) REVERT: H 120 ASP cc_start: 0.7708 (m-30) cc_final: 0.7176 (m-30) REVERT: H 123 MET cc_start: 0.7469 (mtp) cc_final: 0.7246 (mmm) REVERT: H 136 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8058 (t0) REVERT: H 196 MET cc_start: 0.8882 (mmm) cc_final: 0.8600 (mmm) REVERT: H 201 LEU cc_start: 0.8800 (mm) cc_final: 0.8437 (tp) REVERT: H 251 ASP cc_start: 0.8540 (t0) cc_final: 0.8267 (m-30) REVERT: I 201 LEU cc_start: 0.8756 (mm) cc_final: 0.8502 (tp) REVERT: J 61 ARG cc_start: 0.7056 (mtm-85) cc_final: 0.6080 (mmt180) REVERT: J 117 ASP cc_start: 0.8027 (t0) cc_final: 0.7708 (t70) REVERT: J 123 MET cc_start: 0.7556 (mmm) cc_final: 0.7309 (tpt) REVERT: J 196 MET cc_start: 0.8937 (mmm) cc_final: 0.8670 (mmm) REVERT: J 251 ASP cc_start: 0.8337 (t70) cc_final: 0.8068 (t70) REVERT: K 127 MET cc_start: 0.8517 (mmp) cc_final: 0.8303 (mmp) REVERT: L 251 ASP cc_start: 0.8569 (t70) cc_final: 0.8234 (t70) REVERT: M 196 MET cc_start: 0.8878 (mmm) cc_final: 0.8486 (ttm) REVERT: N 188 MET cc_start: 0.7820 (tmm) cc_final: 0.7529 (tmm) REVERT: O 131 MET cc_start: 0.8052 (ttt) cc_final: 0.7361 (ttt) REVERT: R 127 MET cc_start: 0.8861 (mmm) cc_final: 0.8644 (mmm) REVERT: T 106 GLU cc_start: 0.8494 (tp30) cc_final: 0.7961 (tp30) REVERT: T 177 HIS cc_start: 0.8940 (OUTLIER) cc_final: 0.7929 (m-70) REVERT: T 263 ARG cc_start: 0.8120 (ptt-90) cc_final: 0.6208 (ptp90) REVERT: T 264 HIS cc_start: 0.4855 (m-70) cc_final: 0.4337 (m-70) REVERT: V 137 ASN cc_start: 0.7990 (OUTLIER) cc_final: 0.7730 (m-40) REVERT: X 198 ARG cc_start: 0.8032 (ttt90) cc_final: 0.7430 (ttm170) REVERT: X 209 GLU cc_start: 0.7413 (mm-30) cc_final: 0.6906 (tm-30) outliers start: 144 outliers final: 115 residues processed: 1028 average time/residue: 0.9434 time to fit residues: 1633.6707 Evaluate side-chains 1039 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 919 time to evaluate : 4.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 84 HIS Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 177 HIS Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 177 HIS Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain D residue 84 HIS Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain E residue 84 HIS Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 84 HIS Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 174 ILE Chi-restraints excluded: chain G residue 245 SER Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 136 ASP Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 232 ILE Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 84 HIS Chi-restraints excluded: chain I residue 135 ILE Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 188 MET Chi-restraints excluded: chain I residue 204 ASN Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 84 HIS Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 245 SER Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 84 HIS Chi-restraints excluded: chain K residue 151 ASP Chi-restraints excluded: chain K residue 204 ASN Chi-restraints excluded: chain K residue 222 SER Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 84 HIS Chi-restraints excluded: chain L residue 128 ASN Chi-restraints excluded: chain L residue 188 MET Chi-restraints excluded: chain M residue 84 HIS Chi-restraints excluded: chain M residue 135 ILE Chi-restraints excluded: chain M residue 151 ASP Chi-restraints excluded: chain M residue 245 SER Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 84 HIS Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 157 GLU Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 204 ASN Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 84 HIS Chi-restraints excluded: chain O residue 128 ASN Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain O residue 210 LEU Chi-restraints excluded: chain O residue 245 SER Chi-restraints excluded: chain P residue 84 HIS Chi-restraints excluded: chain P residue 174 ILE Chi-restraints excluded: chain P residue 188 MET Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 204 ASN Chi-restraints excluded: chain Q residue 84 HIS Chi-restraints excluded: chain Q residue 116 TYR Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain Q residue 135 ILE Chi-restraints excluded: chain Q residue 157 GLU Chi-restraints excluded: chain Q residue 188 MET Chi-restraints excluded: chain Q residue 245 SER Chi-restraints excluded: chain Q residue 251 ASP Chi-restraints excluded: chain R residue 116 TYR Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 188 MET Chi-restraints excluded: chain R residue 222 SER Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain R residue 251 ASP Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 115 GLU Chi-restraints excluded: chain T residue 135 ILE Chi-restraints excluded: chain T residue 177 HIS Chi-restraints excluded: chain T residue 220 VAL Chi-restraints excluded: chain T residue 245 SER Chi-restraints excluded: chain U residue 135 ILE Chi-restraints excluded: chain U residue 148 VAL Chi-restraints excluded: chain U residue 251 ASP Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 137 ASN Chi-restraints excluded: chain V residue 188 MET Chi-restraints excluded: chain V residue 201 LEU Chi-restraints excluded: chain V residue 204 ASN Chi-restraints excluded: chain V residue 245 SER Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 135 ILE Chi-restraints excluded: chain W residue 188 MET Chi-restraints excluded: chain W residue 204 ASN Chi-restraints excluded: chain W residue 219 GLU Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain X residue 84 HIS Chi-restraints excluded: chain X residue 87 GLU Chi-restraints excluded: chain X residue 135 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 8.9990 chunk 455 optimal weight: 7.9990 chunk 278 optimal weight: 8.9990 chunk 216 optimal weight: 0.8980 chunk 316 optimal weight: 0.9980 chunk 478 optimal weight: 9.9990 chunk 440 optimal weight: 10.0000 chunk 380 optimal weight: 0.4980 chunk 39 optimal weight: 4.9990 chunk 294 optimal weight: 6.9990 chunk 233 optimal weight: 1.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN D 144 ASN ** I 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 264 HIS V 137 ASN ** V 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.8318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 43344 Z= 0.185 Angle : 0.525 5.567 59064 Z= 0.282 Chirality : 0.039 0.226 6552 Planarity : 0.004 0.052 7320 Dihedral : 13.100 70.460 7320 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.04 % Allowed : 18.84 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.12), residues: 4920 helix: 0.09 (0.13), residues: 1896 sheet: None (None), residues: 0 loop : -2.60 (0.11), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 147 HIS 0.008 0.001 HIS Q 264 PHE 0.012 0.001 PHE N 215 TYR 0.018 0.001 TYR F 199 ARG 0.006 0.000 ARG M 212 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1050 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 962 time to evaluate : 4.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7914 (ppp) cc_final: 0.7529 (ttp) REVERT: B 61 ARG cc_start: 0.7064 (mtm-85) cc_final: 0.5495 (mmt180) REVERT: B 94 ASP cc_start: 0.8415 (t0) cc_final: 0.7915 (t0) REVERT: B 204 ASN cc_start: 0.8716 (m-40) cc_final: 0.8266 (p0) REVERT: C 61 ARG cc_start: 0.7160 (mtm-85) cc_final: 0.5615 (mmt180) REVERT: C 177 HIS cc_start: 0.8894 (OUTLIER) cc_final: 0.8398 (m170) REVERT: C 204 ASN cc_start: 0.7150 (p0) cc_final: 0.6712 (p0) REVERT: E 89 LYS cc_start: 0.8602 (mttt) cc_final: 0.8351 (mttp) REVERT: E 117 ASP cc_start: 0.7497 (t0) cc_final: 0.6624 (p0) REVERT: E 188 MET cc_start: 0.8374 (ptm) cc_final: 0.8070 (ptm) REVERT: E 201 LEU cc_start: 0.8833 (mm) cc_final: 0.8394 (tp) REVERT: F 150 MET cc_start: 0.7713 (ttp) cc_final: 0.7436 (ttp) REVERT: F 173 GLN cc_start: 0.7700 (tp-100) cc_final: 0.7415 (tp-100) REVERT: G 123 MET cc_start: 0.7046 (mmm) cc_final: 0.6679 (ttm) REVERT: H 118 LEU cc_start: 0.8694 (mt) cc_final: 0.7987 (mt) REVERT: H 120 ASP cc_start: 0.7524 (m-30) cc_final: 0.7052 (m-30) REVERT: H 136 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8206 (t0) REVERT: H 196 MET cc_start: 0.8890 (mmm) cc_final: 0.8597 (mmm) REVERT: H 201 LEU cc_start: 0.8686 (mm) cc_final: 0.8360 (tp) REVERT: H 251 ASP cc_start: 0.8521 (t0) cc_final: 0.8282 (m-30) REVERT: I 201 LEU cc_start: 0.8498 (mm) cc_final: 0.8200 (tp) REVERT: J 61 ARG cc_start: 0.7025 (mtm-85) cc_final: 0.6048 (mmt180) REVERT: J 117 ASP cc_start: 0.8037 (t0) cc_final: 0.7746 (t70) REVERT: J 148 VAL cc_start: 0.9153 (OUTLIER) cc_final: 0.8906 (p) REVERT: J 196 MET cc_start: 0.8986 (mmm) cc_final: 0.8659 (mmm) REVERT: J 251 ASP cc_start: 0.8314 (t70) cc_final: 0.7994 (t70) REVERT: K 127 MET cc_start: 0.8554 (mmp) cc_final: 0.8331 (mmp) REVERT: K 201 LEU cc_start: 0.8597 (mm) cc_final: 0.8348 (tp) REVERT: L 251 ASP cc_start: 0.8608 (t70) cc_final: 0.8238 (t70) REVERT: M 148 VAL cc_start: 0.9279 (OUTLIER) cc_final: 0.9027 (p) REVERT: M 151 ASP cc_start: 0.8795 (OUTLIER) cc_final: 0.8064 (p0) REVERT: M 196 MET cc_start: 0.8891 (mmm) cc_final: 0.8512 (ttm) REVERT: O 131 MET cc_start: 0.7799 (ttt) cc_final: 0.7129 (ttt) REVERT: Q 116 TYR cc_start: 0.7971 (OUTLIER) cc_final: 0.6195 (t80) REVERT: T 106 GLU cc_start: 0.8440 (tp30) cc_final: 0.7887 (tp30) REVERT: T 127 MET cc_start: 0.8875 (mmp) cc_final: 0.8669 (mmt) REVERT: T 263 ARG cc_start: 0.8144 (ptt-90) cc_final: 0.6266 (ptp90) REVERT: T 264 HIS cc_start: 0.4862 (m-70) cc_final: 0.4348 (m-70) REVERT: U 89 LYS cc_start: 0.8002 (mttt) cc_final: 0.7746 (mttt) REVERT: V 196 MET cc_start: 0.9247 (mmm) cc_final: 0.8906 (mmm) REVERT: X 201 LEU cc_start: 0.8604 (mm) cc_final: 0.8398 (tp) outliers start: 88 outliers final: 75 residues processed: 998 average time/residue: 0.9437 time to fit residues: 1592.2840 Evaluate side-chains 996 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 915 time to evaluate : 4.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 84 HIS Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 177 HIS Chi-restraints excluded: chain D residue 84 HIS Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain E residue 84 HIS Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain F residue 84 HIS Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 245 SER Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain H residue 136 ASP Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 84 HIS Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 188 MET Chi-restraints excluded: chain J residue 84 HIS Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 84 HIS Chi-restraints excluded: chain K residue 151 ASP Chi-restraints excluded: chain K residue 204 ASN Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 84 HIS Chi-restraints excluded: chain L residue 128 ASN Chi-restraints excluded: chain L residue 188 MET Chi-restraints excluded: chain M residue 84 HIS Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 151 ASP Chi-restraints excluded: chain M residue 245 SER Chi-restraints excluded: chain N residue 84 HIS Chi-restraints excluded: chain N residue 157 GLU Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 204 ASN Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 84 HIS Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain O residue 245 SER Chi-restraints excluded: chain P residue 84 HIS Chi-restraints excluded: chain P residue 174 ILE Chi-restraints excluded: chain P residue 188 MET Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 204 ASN Chi-restraints excluded: chain Q residue 84 HIS Chi-restraints excluded: chain Q residue 116 TYR Chi-restraints excluded: chain Q residue 149 MET Chi-restraints excluded: chain Q residue 188 MET Chi-restraints excluded: chain Q residue 245 SER Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 116 TYR Chi-restraints excluded: chain R residue 188 MET Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain R residue 251 ASP Chi-restraints excluded: chain S residue 116 TYR Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 135 ILE Chi-restraints excluded: chain T residue 245 SER Chi-restraints excluded: chain U residue 148 VAL Chi-restraints excluded: chain U residue 251 ASP Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 135 ILE Chi-restraints excluded: chain V residue 188 MET Chi-restraints excluded: chain V residue 201 LEU Chi-restraints excluded: chain W residue 188 MET Chi-restraints excluded: chain W residue 204 ASN Chi-restraints excluded: chain W residue 219 GLU Chi-restraints excluded: chain X residue 84 HIS Chi-restraints excluded: chain X residue 148 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 6.9990 chunk 405 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 351 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 105 optimal weight: 8.9990 chunk 381 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 chunk 391 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 70 optimal weight: 0.5980 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN E 144 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 137 ASN ** W 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.130559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.108006 restraints weight = 199468.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.111896 restraints weight = 109370.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.114455 restraints weight = 72736.169| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.8522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 43344 Z= 0.249 Angle : 0.557 6.144 59064 Z= 0.301 Chirality : 0.041 0.235 6552 Planarity : 0.004 0.054 7320 Dihedral : 13.116 71.690 7320 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 2.45 % Allowed : 19.00 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.12), residues: 4920 helix: 0.05 (0.13), residues: 1896 sheet: None (None), residues: 0 loop : -2.59 (0.11), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP M 147 HIS 0.003 0.001 HIS M 84 PHE 0.018 0.001 PHE N 215 TYR 0.027 0.001 TYR V 109 ARG 0.010 0.001 ARG Q 189 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23041.75 seconds wall clock time: 397 minutes 21.61 seconds (23841.61 seconds total)