Starting phenix.real_space_refine on Tue Mar 12 02:22:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn1_3236/03_2024/5fn1_3236.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn1_3236/03_2024/5fn1_3236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn1_3236/03_2024/5fn1_3236.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn1_3236/03_2024/5fn1_3236.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn1_3236/03_2024/5fn1_3236.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn1_3236/03_2024/5fn1_3236.pdb" } resolution = 3.9 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 ------------------------------------------------------------------------------- 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= 0.008 sd= 0.779 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 90 5.49 5 S 108 5.16 5 C 19476 2.51 5 N 5220 2.21 5 O 6336 1.98 5 H 30078 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 61308 Number of models: 1 Model: "" Number of chains: 36 Chain: "C" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} 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': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "E" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} 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': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "G" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} 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': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "I" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} 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': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "K" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} 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': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "M" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} 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': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "O" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} 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': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "Q" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} 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': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "S" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} 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': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "A" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} 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': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "U" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} 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': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "W" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} 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': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "Y" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "Z" 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': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "0" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "1" 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': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "2" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "3" 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': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "4" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "5" 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': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "6" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "7" 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': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "8" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "9" 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': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Time building chain proxies: 20.55, per 1000 atoms: 0.34 Number of scatterers: 61308 At special positions: 0 Unit cell: (152.32, 152.32, 133.28, 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 108 16.00 P 90 15.00 O 6336 8.00 N 5220 7.00 C 19476 6.00 H 30078 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: 39.20 Conformation dependent library (CDL) restraints added in 4.7 seconds 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7308 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 0 sheets defined 50.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 19.69 Creating SS restraints... Processing helix chain 'A' and resid 24 through 28 removed outlier: 3.729A pdb=" N ASP A 27 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE A 28 " --> pdb=" O PRO A 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 24 through 28' Processing helix chain 'A' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 89 Processing helix chain 'A' and resid 108 through 116 removed outlier: 3.796A pdb=" N LEU A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 120 removed outlier: 3.666A pdb=" N ASN A 120 " --> pdb=" O ASP A 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 117 through 120' Processing helix chain 'A' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 140 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.591A pdb=" N LYS A 158 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP A 232 " --> pdb=" O MET A 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 28 removed outlier: 3.728A pdb=" N ASP C 27 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE C 28 " --> pdb=" O PRO C 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 24 through 28' Processing helix chain 'C' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP C 39 " --> pdb=" O PRO C 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 60 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 89 Processing helix chain 'C' and resid 108 through 116 removed outlier: 3.796A pdb=" N LEU C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 120 removed outlier: 3.667A pdb=" N ASN C 120 " --> pdb=" O ASP C 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 117 through 120' Processing helix chain 'C' and resid 122 through 128 removed outlier: 3.854A pdb=" N MET C 128 " --> pdb=" O ARG C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 140 Processing helix chain 'C' and resid 154 through 158 removed outlier: 3.591A pdb=" N LYS C 158 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER C 206 " --> pdb=" O ARG C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE C 231 " --> pdb=" O THR C 227 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP C 232 " --> pdb=" O MET C 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 28 removed outlier: 3.729A pdb=" N ASP E 27 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE E 28 " --> pdb=" O PRO E 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 24 through 28' Processing helix chain 'E' and resid 33 through 41 removed outlier: 3.560A pdb=" N ASP E 39 " --> pdb=" O PRO E 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE E 58 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA E 60 " --> pdb=" O ALA E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 89 Processing helix chain 'E' and resid 108 through 116 removed outlier: 3.797A pdb=" N LEU E 112 " --> pdb=" O SER E 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 120 removed outlier: 3.667A pdb=" N ASN E 120 " --> pdb=" O ASP E 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 117 through 120' Processing helix chain 'E' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET E 128 " --> pdb=" O ARG E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 140 Processing helix chain 'E' and resid 154 through 158 removed outlier: 3.591A pdb=" N LYS E 158 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU E 189 " --> pdb=" O ASN E 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER E 206 " --> pdb=" O ARG E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE E 231 " --> pdb=" O THR E 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP E 232 " --> pdb=" O MET E 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 28 removed outlier: 3.729A pdb=" N ASP G 27 " --> pdb=" O ALA G 24 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE G 28 " --> pdb=" O PRO G 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 24 through 28' Processing helix chain 'G' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP G 39 " --> pdb=" O PRO G 35 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE G 58 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 89 Processing helix chain 'G' and resid 108 through 116 removed outlier: 3.796A pdb=" N LEU G 112 " --> pdb=" O SER G 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE G 116 " --> pdb=" O LEU G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 120 removed outlier: 3.667A pdb=" N ASN G 120 " --> pdb=" O ASP G 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 117 through 120' Processing helix chain 'G' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET G 128 " --> pdb=" O ARG G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 140 Processing helix chain 'G' and resid 154 through 158 removed outlier: 3.591A pdb=" N LYS G 158 " --> pdb=" O GLU G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU G 189 " --> pdb=" O ASN G 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER G 206 " --> pdb=" O ARG G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE G 231 " --> pdb=" O THR G 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP G 232 " --> pdb=" O MET G 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 28 removed outlier: 3.728A pdb=" N ASP I 27 " --> pdb=" O ALA I 24 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE I 28 " --> pdb=" O PRO I 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 24 through 28' Processing helix chain 'I' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP I 39 " --> pdb=" O PRO I 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS I 41 " --> pdb=" O LEU I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE I 58 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA I 60 " --> pdb=" O ALA I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 89 Processing helix chain 'I' and resid 108 through 116 removed outlier: 3.796A pdb=" N LEU I 112 " --> pdb=" O SER I 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE I 116 " --> pdb=" O LEU I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 120 removed outlier: 3.667A pdb=" N ASN I 120 " --> pdb=" O ASP I 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 117 through 120' Processing helix chain 'I' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET I 128 " --> pdb=" O ARG I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 140 Processing helix chain 'I' and resid 154 through 158 removed outlier: 3.592A pdb=" N LYS I 158 " --> pdb=" O GLU I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU I 189 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER I 206 " --> pdb=" O ARG I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE I 231 " --> pdb=" O THR I 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 28 removed outlier: 3.729A pdb=" N ASP K 27 " --> pdb=" O ALA K 24 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE K 28 " --> pdb=" O PRO K 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 24 through 28' Processing helix chain 'K' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP K 39 " --> pdb=" O PRO K 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS K 41 " --> pdb=" O LEU K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE K 58 " --> pdb=" O THR K 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA K 60 " --> pdb=" O ALA K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 89 Processing helix chain 'K' and resid 108 through 116 removed outlier: 3.796A pdb=" N LEU K 112 " --> pdb=" O SER K 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE K 116 " --> pdb=" O LEU K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 120 removed outlier: 3.666A pdb=" N ASN K 120 " --> pdb=" O ASP K 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 117 through 120' Processing helix chain 'K' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET K 128 " --> pdb=" O ARG K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 140 Processing helix chain 'K' and resid 154 through 158 removed outlier: 3.591A pdb=" N LYS K 158 " --> pdb=" O GLU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU K 189 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER K 206 " --> pdb=" O ARG K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE K 231 " --> pdb=" O THR K 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP K 232 " --> pdb=" O MET K 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 24 through 28 removed outlier: 3.728A pdb=" N ASP M 27 " --> pdb=" O ALA M 24 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE M 28 " --> pdb=" O PRO M 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 24 through 28' Processing helix chain 'M' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP M 39 " --> pdb=" O PRO M 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS M 41 " --> pdb=" O LEU M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 69 removed outlier: 3.680A pdb=" N ILE M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA M 60 " --> pdb=" O ALA M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 89 Processing helix chain 'M' and resid 108 through 116 removed outlier: 3.797A pdb=" N LEU M 112 " --> pdb=" O SER M 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE M 116 " --> pdb=" O LEU M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 117 through 120 removed outlier: 3.667A pdb=" N ASN M 120 " --> pdb=" O ASP M 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 117 through 120' Processing helix chain 'M' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET M 128 " --> pdb=" O ARG M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 140 Processing helix chain 'M' and resid 154 through 158 removed outlier: 3.592A pdb=" N LYS M 158 " --> pdb=" O GLU M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU M 189 " --> pdb=" O ASN M 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER M 206 " --> pdb=" O ARG M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 227 through 233 removed outlier: 4.173A pdb=" N ILE M 231 " --> pdb=" O THR M 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP M 232 " --> pdb=" O MET M 228 " (cutoff:3.500A) Processing helix chain 'O' and resid 24 through 28 removed outlier: 3.729A pdb=" N ASP O 27 " --> pdb=" O ALA O 24 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE O 28 " --> pdb=" O PRO O 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 24 through 28' Processing helix chain 'O' and resid 33 through 41 removed outlier: 3.560A pdb=" N ASP O 39 " --> pdb=" O PRO O 35 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS O 41 " --> pdb=" O LEU O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE O 58 " --> pdb=" O THR O 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA O 60 " --> pdb=" O ALA O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 89 Processing helix chain 'O' and resid 108 through 116 removed outlier: 3.796A pdb=" N LEU O 112 " --> pdb=" O SER O 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE O 116 " --> pdb=" O LEU O 112 " (cutoff:3.500A) Processing helix chain 'O' and resid 117 through 120 removed outlier: 3.666A pdb=" N ASN O 120 " --> pdb=" O ASP O 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 117 through 120' Processing helix chain 'O' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET O 128 " --> pdb=" O ARG O 124 " (cutoff:3.500A) Processing helix chain 'O' and resid 130 through 140 Processing helix chain 'O' and resid 154 through 158 removed outlier: 3.591A pdb=" N LYS O 158 " --> pdb=" O GLU O 155 " (cutoff:3.500A) Processing helix chain 'O' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU O 189 " --> pdb=" O ASN O 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER O 206 " --> pdb=" O ARG O 202 " (cutoff:3.500A) Processing helix chain 'O' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE O 231 " --> pdb=" O THR O 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP O 232 " --> pdb=" O MET O 228 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 28 removed outlier: 3.729A pdb=" N ASP Q 27 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE Q 28 " --> pdb=" O PRO Q 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 24 through 28' Processing helix chain 'Q' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP Q 39 " --> pdb=" O PRO Q 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS Q 41 " --> pdb=" O LEU Q 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE Q 58 " --> pdb=" O THR Q 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA Q 60 " --> pdb=" O ALA Q 56 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 89 Processing helix chain 'Q' and resid 108 through 116 removed outlier: 3.795A pdb=" N LEU Q 112 " --> pdb=" O SER Q 108 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE Q 116 " --> pdb=" O LEU Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 120 removed outlier: 3.667A pdb=" N ASN Q 120 " --> pdb=" O ASP Q 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 117 through 120' Processing helix chain 'Q' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET Q 128 " --> pdb=" O ARG Q 124 " (cutoff:3.500A) Processing helix chain 'Q' and resid 130 through 140 Processing helix chain 'Q' and resid 154 through 158 removed outlier: 3.591A pdb=" N LYS Q 158 " --> pdb=" O GLU Q 155 " (cutoff:3.500A) Processing helix chain 'Q' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU Q 189 " --> pdb=" O ASN Q 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER Q 206 " --> pdb=" O ARG Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE Q 231 " --> pdb=" O THR Q 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP Q 232 " --> pdb=" O MET Q 228 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 28 removed outlier: 3.728A pdb=" N ASP S 27 " --> pdb=" O ALA S 24 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE S 28 " --> pdb=" O PRO S 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 24 through 28' Processing helix chain 'S' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP S 39 " --> pdb=" O PRO S 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS S 41 " --> pdb=" O LEU S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE S 58 " --> pdb=" O THR S 54 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA S 60 " --> pdb=" O ALA S 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 89 Processing helix chain 'S' and resid 108 through 116 removed outlier: 3.796A pdb=" N LEU S 112 " --> pdb=" O SER S 108 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE S 116 " --> pdb=" O LEU S 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 117 through 120 removed outlier: 3.666A pdb=" N ASN S 120 " --> pdb=" O ASP S 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 117 through 120' Processing helix chain 'S' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET S 128 " --> pdb=" O ARG S 124 " (cutoff:3.500A) Processing helix chain 'S' and resid 130 through 140 Processing helix chain 'S' and resid 154 through 158 removed outlier: 3.591A pdb=" N LYS S 158 " --> pdb=" O GLU S 155 " (cutoff:3.500A) Processing helix chain 'S' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU S 189 " --> pdb=" O ASN S 185 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER S 206 " --> pdb=" O ARG S 202 " (cutoff:3.500A) Processing helix chain 'S' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE S 231 " --> pdb=" O THR S 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP S 232 " --> pdb=" O MET S 228 " (cutoff:3.500A) Processing helix chain 'U' and resid 24 through 28 removed outlier: 3.729A pdb=" N ASP U 27 " --> pdb=" O ALA U 24 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE U 28 " --> pdb=" O PRO U 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 24 through 28' Processing helix chain 'U' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP U 39 " --> pdb=" O PRO U 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS U 41 " --> pdb=" O LEU U 37 " (cutoff:3.500A) Processing helix chain 'U' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE U 58 " --> pdb=" O THR U 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA U 60 " --> pdb=" O ALA U 56 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 89 Processing helix chain 'U' and resid 108 through 116 removed outlier: 3.797A pdb=" N LEU U 112 " --> pdb=" O SER U 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE U 116 " --> pdb=" O LEU U 112 " (cutoff:3.500A) Processing helix chain 'U' and resid 117 through 120 removed outlier: 3.667A pdb=" N ASN U 120 " --> pdb=" O ASP U 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 117 through 120' Processing helix chain 'U' and resid 122 through 128 removed outlier: 3.854A pdb=" N MET U 128 " --> pdb=" O ARG U 124 " (cutoff:3.500A) Processing helix chain 'U' and resid 130 through 140 Processing helix chain 'U' and resid 154 through 158 removed outlier: 3.592A pdb=" N LYS U 158 " --> pdb=" O GLU U 155 " (cutoff:3.500A) Processing helix chain 'U' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU U 189 " --> pdb=" O ASN U 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER U 206 " --> pdb=" O ARG U 202 " (cutoff:3.500A) Processing helix chain 'U' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE U 231 " --> pdb=" O THR U 227 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP U 232 " --> pdb=" O MET U 228 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 28 removed outlier: 3.729A pdb=" N ASP W 27 " --> pdb=" O ALA W 24 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE W 28 " --> pdb=" O PRO W 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 24 through 28' Processing helix chain 'W' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP W 39 " --> pdb=" O PRO W 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS W 41 " --> pdb=" O LEU W 37 " (cutoff:3.500A) Processing helix chain 'W' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE W 58 " --> pdb=" O THR W 54 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA W 60 " --> pdb=" O ALA W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 75 through 89 Processing helix chain 'W' and resid 108 through 116 removed outlier: 3.796A pdb=" N LEU W 112 " --> pdb=" O SER W 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE W 116 " --> pdb=" O LEU W 112 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 120 removed outlier: 3.667A pdb=" N ASN W 120 " --> pdb=" O ASP W 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 117 through 120' Processing helix chain 'W' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET W 128 " --> pdb=" O ARG W 124 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 140 Processing helix chain 'W' and resid 154 through 158 removed outlier: 3.591A pdb=" N LYS W 158 " --> pdb=" O GLU W 155 " (cutoff:3.500A) Processing helix chain 'W' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU W 189 " --> pdb=" O ASN W 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER W 206 " --> pdb=" O ARG W 202 " (cutoff:3.500A) Processing helix chain 'W' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE W 231 " --> pdb=" O THR W 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP W 232 " --> pdb=" O MET W 228 " (cutoff:3.500A) Processing helix chain 'Y' and resid 24 through 28 removed outlier: 3.728A pdb=" N ASP Y 27 " --> pdb=" O ALA Y 24 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE Y 28 " --> pdb=" O PRO Y 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 24 through 28' Processing helix chain 'Y' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP Y 39 " --> pdb=" O PRO Y 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS Y 41 " --> pdb=" O LEU Y 37 " (cutoff:3.500A) Processing helix chain 'Y' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE Y 58 " --> pdb=" O THR Y 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA Y 60 " --> pdb=" O ALA Y 56 " (cutoff:3.500A) Processing helix chain 'Y' and resid 75 through 89 Processing helix chain 'Y' and resid 108 through 116 removed outlier: 3.796A pdb=" N LEU Y 112 " --> pdb=" O SER Y 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE Y 116 " --> pdb=" O LEU Y 112 " (cutoff:3.500A) Processing helix chain 'Y' and resid 117 through 120 removed outlier: 3.666A pdb=" N ASN Y 120 " --> pdb=" O ASP Y 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 117 through 120' Processing helix chain 'Y' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET Y 128 " --> pdb=" O ARG Y 124 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 140 Processing helix chain 'Y' and resid 154 through 158 removed outlier: 3.590A pdb=" N LYS Y 158 " --> pdb=" O GLU Y 155 " (cutoff:3.500A) Processing helix chain 'Y' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU Y 189 " --> pdb=" O ASN Y 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER Y 206 " --> pdb=" O ARG Y 202 " (cutoff:3.500A) Processing helix chain 'Y' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE Y 231 " --> pdb=" O THR Y 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP Y 232 " --> pdb=" O MET Y 228 " (cutoff:3.500A) Processing helix chain '0' and resid 24 through 28 removed outlier: 3.728A pdb=" N ASP 0 27 " --> pdb=" O ALA 0 24 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE 0 28 " --> pdb=" O PRO 0 25 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 24 through 28' Processing helix chain '0' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP 0 39 " --> pdb=" O PRO 0 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS 0 41 " --> pdb=" O LEU 0 37 " (cutoff:3.500A) Processing helix chain '0' and resid 54 through 69 removed outlier: 3.680A pdb=" N ILE 0 58 " --> pdb=" O THR 0 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA 0 60 " --> pdb=" O ALA 0 56 " (cutoff:3.500A) Processing helix chain '0' and resid 75 through 89 Processing helix chain '0' and resid 108 through 116 removed outlier: 3.796A pdb=" N LEU 0 112 " --> pdb=" O SER 0 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE 0 116 " --> pdb=" O LEU 0 112 " (cutoff:3.500A) Processing helix chain '0' and resid 117 through 120 removed outlier: 3.666A pdb=" N ASN 0 120 " --> pdb=" O ASP 0 117 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 117 through 120' Processing helix chain '0' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET 0 128 " --> pdb=" O ARG 0 124 " (cutoff:3.500A) Processing helix chain '0' and resid 130 through 140 Processing helix chain '0' and resid 154 through 158 removed outlier: 3.591A pdb=" N LYS 0 158 " --> pdb=" O GLU 0 155 " (cutoff:3.500A) Processing helix chain '0' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU 0 189 " --> pdb=" O ASN 0 185 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER 0 206 " --> pdb=" O ARG 0 202 " (cutoff:3.500A) Processing helix chain '0' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE 0 231 " --> pdb=" O THR 0 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP 0 232 " --> pdb=" O MET 0 228 " (cutoff:3.500A) Processing helix chain '2' and resid 24 through 28 removed outlier: 3.728A pdb=" N ASP 2 27 " --> pdb=" O ALA 2 24 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE 2 28 " --> pdb=" O PRO 2 25 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 24 through 28' Processing helix chain '2' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP 2 39 " --> pdb=" O PRO 2 35 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS 2 41 " --> pdb=" O LEU 2 37 " (cutoff:3.500A) Processing helix chain '2' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE 2 58 " --> pdb=" O THR 2 54 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA 2 60 " --> pdb=" O ALA 2 56 " (cutoff:3.500A) Processing helix chain '2' and resid 75 through 89 Processing helix chain '2' and resid 108 through 116 removed outlier: 3.796A pdb=" N LEU 2 112 " --> pdb=" O SER 2 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE 2 116 " --> pdb=" O LEU 2 112 " (cutoff:3.500A) Processing helix chain '2' and resid 117 through 120 removed outlier: 3.666A pdb=" N ASN 2 120 " --> pdb=" O ASP 2 117 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 117 through 120' Processing helix chain '2' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET 2 128 " --> pdb=" O ARG 2 124 " (cutoff:3.500A) Processing helix chain '2' and resid 130 through 140 Processing helix chain '2' and resid 154 through 158 removed outlier: 3.591A pdb=" N LYS 2 158 " --> pdb=" O GLU 2 155 " (cutoff:3.500A) Processing helix chain '2' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU 2 189 " --> pdb=" O ASN 2 185 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER 2 206 " --> pdb=" O ARG 2 202 " (cutoff:3.500A) Processing helix chain '2' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE 2 231 " --> pdb=" O THR 2 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP 2 232 " --> pdb=" O MET 2 228 " (cutoff:3.500A) Processing helix chain '4' and resid 24 through 28 removed outlier: 3.728A pdb=" N ASP 4 27 " --> pdb=" O ALA 4 24 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE 4 28 " --> pdb=" O PRO 4 25 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 24 through 28' Processing helix chain '4' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP 4 39 " --> pdb=" O PRO 4 35 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS 4 41 " --> pdb=" O LEU 4 37 " (cutoff:3.500A) Processing helix chain '4' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE 4 58 " --> pdb=" O THR 4 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA 4 60 " --> pdb=" O ALA 4 56 " (cutoff:3.500A) Processing helix chain '4' and resid 75 through 89 Processing helix chain '4' and resid 108 through 116 removed outlier: 3.796A pdb=" N LEU 4 112 " --> pdb=" O SER 4 108 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE 4 116 " --> pdb=" O LEU 4 112 " (cutoff:3.500A) Processing helix chain '4' and resid 117 through 120 removed outlier: 3.667A pdb=" N ASN 4 120 " --> pdb=" O ASP 4 117 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 117 through 120' Processing helix chain '4' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET 4 128 " --> pdb=" O ARG 4 124 " (cutoff:3.500A) Processing helix chain '4' and resid 130 through 140 Processing helix chain '4' and resid 154 through 158 removed outlier: 3.591A pdb=" N LYS 4 158 " --> pdb=" O GLU 4 155 " (cutoff:3.500A) Processing helix chain '4' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU 4 189 " --> pdb=" O ASN 4 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER 4 206 " --> pdb=" O ARG 4 202 " (cutoff:3.500A) Processing helix chain '4' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE 4 231 " --> pdb=" O THR 4 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP 4 232 " --> pdb=" O MET 4 228 " (cutoff:3.500A) Processing helix chain '6' and resid 24 through 28 removed outlier: 3.729A pdb=" N ASP 6 27 " --> pdb=" O ALA 6 24 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE 6 28 " --> pdb=" O PRO 6 25 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 24 through 28' Processing helix chain '6' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP 6 39 " --> pdb=" O PRO 6 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS 6 41 " --> pdb=" O LEU 6 37 " (cutoff:3.500A) Processing helix chain '6' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE 6 58 " --> pdb=" O THR 6 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA 6 60 " --> pdb=" O ALA 6 56 " (cutoff:3.500A) Processing helix chain '6' and resid 75 through 89 Processing helix chain '6' and resid 108 through 116 removed outlier: 3.797A pdb=" N LEU 6 112 " --> pdb=" O SER 6 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE 6 116 " --> pdb=" O LEU 6 112 " (cutoff:3.500A) Processing helix chain '6' and resid 117 through 120 removed outlier: 3.666A pdb=" N ASN 6 120 " --> pdb=" O ASP 6 117 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 117 through 120' Processing helix chain '6' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET 6 128 " --> pdb=" O ARG 6 124 " (cutoff:3.500A) Processing helix chain '6' and resid 130 through 140 Processing helix chain '6' and resid 154 through 158 removed outlier: 3.591A pdb=" N LYS 6 158 " --> pdb=" O GLU 6 155 " (cutoff:3.500A) Processing helix chain '6' and resid 185 through 206 removed outlier: 3.541A pdb=" N LEU 6 189 " --> pdb=" O ASN 6 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER 6 206 " --> pdb=" O ARG 6 202 " (cutoff:3.500A) Processing helix chain '6' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE 6 231 " --> pdb=" O THR 6 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP 6 232 " --> pdb=" O MET 6 228 " (cutoff:3.500A) Processing helix chain '8' and resid 24 through 28 removed outlier: 3.729A pdb=" N ASP 8 27 " --> pdb=" O ALA 8 24 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE 8 28 " --> pdb=" O PRO 8 25 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 24 through 28' Processing helix chain '8' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP 8 39 " --> pdb=" O PRO 8 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS 8 41 " --> pdb=" O LEU 8 37 " (cutoff:3.500A) Processing helix chain '8' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE 8 58 " --> pdb=" O THR 8 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA 8 60 " --> pdb=" O ALA 8 56 " (cutoff:3.500A) Processing helix chain '8' and resid 75 through 89 Processing helix chain '8' and resid 108 through 116 removed outlier: 3.796A pdb=" N LEU 8 112 " --> pdb=" O SER 8 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE 8 116 " --> pdb=" O LEU 8 112 " (cutoff:3.500A) Processing helix chain '8' and resid 117 through 120 removed outlier: 3.667A pdb=" N ASN 8 120 " --> pdb=" O ASP 8 117 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 117 through 120' Processing helix chain '8' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET 8 128 " --> pdb=" O ARG 8 124 " (cutoff:3.500A) Processing helix chain '8' and resid 130 through 140 Processing helix chain '8' and resid 154 through 158 removed outlier: 3.591A pdb=" N LYS 8 158 " --> pdb=" O GLU 8 155 " (cutoff:3.500A) Processing helix chain '8' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU 8 189 " --> pdb=" O ASN 8 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER 8 206 " --> pdb=" O ARG 8 202 " (cutoff:3.500A) Processing helix chain '8' and resid 227 through 233 removed outlier: 4.173A pdb=" N ILE 8 231 " --> pdb=" O THR 8 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP 8 232 " --> pdb=" O MET 8 228 " (cutoff:3.500A) 972 hydrogen bonds defined for protein. 2862 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 16.43 Time building geometry restraints manager: 41.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 30060 1.03 - 1.23: 108 1.23 - 1.42: 13070 1.42 - 1.61: 18718 1.61 - 1.80: 198 Bond restraints: 62154 Sorted by residual: bond pdb=" CA PRO Q 234 " pdb=" C PRO Q 234 " ideal model delta sigma weight residual 1.517 1.548 -0.031 9.30e-03 1.16e+04 1.10e+01 bond pdb=" CA PRO 2 234 " pdb=" C PRO 2 234 " ideal model delta sigma weight residual 1.517 1.548 -0.031 9.30e-03 1.16e+04 1.10e+01 bond pdb=" CA PRO K 234 " pdb=" C PRO K 234 " ideal model delta sigma weight residual 1.517 1.548 -0.031 9.30e-03 1.16e+04 1.10e+01 bond pdb=" CA PRO C 234 " pdb=" C PRO C 234 " ideal model delta sigma weight residual 1.517 1.548 -0.031 9.30e-03 1.16e+04 1.10e+01 bond pdb=" CA PRO U 234 " pdb=" C PRO U 234 " ideal model delta sigma weight residual 1.517 1.548 -0.031 9.30e-03 1.16e+04 1.09e+01 ... (remaining 62149 not shown) Histogram of bond angle deviations from ideal: 100.58 - 107.26: 11803 107.26 - 113.94: 62768 113.94 - 120.62: 21628 120.62 - 127.31: 15915 127.31 - 133.99: 368 Bond angle restraints: 112482 Sorted by residual: angle pdb=" N PRO C 234 " pdb=" CA PRO C 234 " pdb=" C PRO C 234 " ideal model delta sigma weight residual 110.70 117.67 -6.97 1.22e+00 6.72e-01 3.26e+01 angle pdb=" N PRO M 234 " pdb=" CA PRO M 234 " pdb=" C PRO M 234 " ideal model delta sigma weight residual 110.70 117.66 -6.96 1.22e+00 6.72e-01 3.25e+01 angle pdb=" N PRO K 234 " pdb=" CA PRO K 234 " pdb=" C PRO K 234 " ideal model delta sigma weight residual 110.70 117.65 -6.95 1.22e+00 6.72e-01 3.25e+01 angle pdb=" N PRO 0 234 " pdb=" CA PRO 0 234 " pdb=" C PRO 0 234 " ideal model delta sigma weight residual 110.70 117.65 -6.95 1.22e+00 6.72e-01 3.25e+01 angle pdb=" N PRO Q 234 " pdb=" CA PRO Q 234 " pdb=" C PRO Q 234 " ideal model delta sigma weight residual 110.70 117.65 -6.95 1.22e+00 6.72e-01 3.25e+01 ... (remaining 112477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 26946 17.24 - 34.49: 1440 34.49 - 51.73: 666 51.73 - 68.98: 864 68.98 - 86.22: 18 Dihedral angle restraints: 29934 sinusoidal: 16866 harmonic: 13068 Sorted by residual: dihedral pdb=" CA TYR E 45 " pdb=" C TYR E 45 " pdb=" N VAL E 46 " pdb=" CA VAL E 46 " ideal model delta harmonic sigma weight residual 180.00 155.81 24.19 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA TYR G 45 " pdb=" C TYR G 45 " pdb=" N VAL G 46 " pdb=" CA VAL G 46 " ideal model delta harmonic sigma weight residual 180.00 155.82 24.18 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA TYR C 45 " pdb=" C TYR C 45 " pdb=" N VAL C 46 " pdb=" CA VAL C 46 " ideal model delta harmonic sigma weight residual 180.00 155.82 24.18 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 29931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3743 0.061 - 0.122: 833 0.122 - 0.184: 334 0.184 - 0.245: 130 0.245 - 0.306: 18 Chirality restraints: 5058 Sorted by residual: chirality pdb=" CA ASN W 209 " pdb=" N ASN W 209 " pdb=" C ASN W 209 " pdb=" CB ASN W 209 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA ASN 2 209 " pdb=" N ASN 2 209 " pdb=" C ASN 2 209 " pdb=" CB ASN 2 209 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA ASN Y 209 " pdb=" N ASN Y 209 " pdb=" C ASN Y 209 " pdb=" CB ASN Y 209 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 5055 not shown) Planarity restraints: 9090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS 2 93 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.48e+00 pdb=" C LYS 2 93 " 0.027 2.00e-02 2.50e+03 pdb=" O LYS 2 93 " -0.010 2.00e-02 2.50e+03 pdb=" N SER 2 94 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS 8 93 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.46e+00 pdb=" C LYS 8 93 " 0.027 2.00e-02 2.50e+03 pdb=" O LYS 8 93 " -0.010 2.00e-02 2.50e+03 pdb=" N SER 8 94 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS K 93 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.45e+00 pdb=" C LYS K 93 " 0.027 2.00e-02 2.50e+03 pdb=" O LYS K 93 " -0.010 2.00e-02 2.50e+03 pdb=" N SER K 94 " -0.009 2.00e-02 2.50e+03 ... (remaining 9087 not shown) Histogram of nonbonded interaction distances: 0.26 - 1.13: 670 1.13 - 1.99: 3628 1.99 - 2.86: 151678 2.86 - 3.73: 253909 3.73 - 4.60: 430391 Warning: very small nonbonded interaction distances. Nonbonded interactions: 840276 Sorted by model distance: nonbonded pdb=" O ALA U 72 " pdb=" HB3 SER W 26 " model vdw 0.258 2.620 nonbonded pdb=" O ALA Q 72 " pdb=" HB3 SER S 26 " model vdw 0.258 2.620 nonbonded pdb=" O ALA E 72 " pdb=" HB3 SER G 26 " model vdw 0.259 2.620 nonbonded pdb=" O ALA 4 72 " pdb=" HB3 SER 6 26 " model vdw 0.259 2.620 nonbonded pdb=" O ALA K 72 " pdb=" HB3 SER M 26 " model vdw 0.259 2.620 ... (remaining 840271 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 '0' selection = chain '2' selection = chain '4' selection = chain '6' selection = chain '8' selection = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain '1' selection = chain '3' selection = chain '5' selection = chain '7' selection = chain '9' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' } 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: 0.010 Normalize map: mean=0, sd=1: 0.090 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: 0.710 Extract box with map and model: 3.490 Check model and map are aligned: 0.680 Set scattering table: 0.440 Process input model: 157.270 Find NCS groups from input model: 2.340 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 167.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3004 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 : 0.009 0.043 32076 Z= 0.553 Angle : 1.180 7.651 44010 Z= 0.771 Chirality : 0.068 0.306 5058 Planarity : 0.005 0.031 5472 Dihedral : 12.984 58.925 12258 Min Nonbonded Distance : 0.877 Molprobity Statistics. All-atom Clashscore : 53.81 Ramachandran Plot: Outliers : 2.79 % Allowed : 8.84 % Favored : 88.37 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.11), residues: 3870 helix: -2.67 (0.08), residues: 1692 sheet: None (None), residues: 0 loop : -1.85 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 80 HIS 0.002 0.001 HIS 4 192 PHE 0.010 0.002 PHE O 65 TYR 0.014 0.002 TYR E 210 ARG 0.002 0.000 ARG O 109 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 707 time to evaluate : 3.439 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 PHE cc_start: 0.7531 (m-80) cc_final: 0.7191 (m-80) REVERT: C 120 ASN cc_start: 0.7718 (m110) cc_final: 0.7514 (m-40) REVERT: E 183 GLN cc_start: 0.7219 (tp-100) cc_final: 0.5853 (pt0) REVERT: E 196 LYS cc_start: 0.7830 (ttpt) cc_final: 0.7363 (tptt) outliers start: 0 outliers final: 0 residues processed: 707 average time/residue: 0.9240 time to fit residues: 999.6723 Evaluate side-chains 507 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 507 time to evaluate : 3.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 8.9990 chunk 286 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 296 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 chunk 180 optimal weight: 0.8980 chunk 220 optimal weight: 8.9990 chunk 343 optimal weight: 20.0000 overall best weight: 6.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 209 ASN I 120 ASN ** I 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 ASN ** K 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 120 ASN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 120 ASN O 209 ASN Q 120 ASN Q 209 ASN S 115 GLN S 120 ASN S 209 ASN A 115 GLN A 120 ASN A 209 ASN ** U 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 209 ASN ** Y 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 209 ASN 6 209 ASN 8 185 ASN 8 209 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4130 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 32076 Z= 0.381 Angle : 0.840 10.394 44010 Z= 0.455 Chirality : 0.042 0.220 5058 Planarity : 0.007 0.069 5472 Dihedral : 12.713 59.629 5544 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 1.71 % Allowed : 10.78 % Favored : 87.52 % Rotamer: Outliers : 1.78 % Allowed : 8.42 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.13), residues: 3870 helix: -0.94 (0.11), residues: 1692 sheet: None (None), residues: 0 loop : -1.62 (0.14), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.005 TRP W 80 HIS 0.009 0.002 HIS W 192 PHE 0.027 0.002 PHE A 164 TYR 0.029 0.004 TYR Y 229 ARG 0.006 0.001 ARG 2 202 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 614 time to evaluate : 3.415 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 185 ASN cc_start: 0.7925 (t0) cc_final: 0.7626 (t0) REVERT: O 211 ILE cc_start: 0.6021 (pt) cc_final: 0.5627 (pt) REVERT: Q 126 PHE cc_start: 0.5684 (OUTLIER) cc_final: 0.5157 (t80) REVERT: S 27 ASP cc_start: 0.7699 (m-30) cc_final: 0.7484 (m-30) REVERT: S 139 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.7025 (tt) REVERT: U 58 ILE cc_start: 0.6669 (tt) cc_final: 0.5793 (tt) REVERT: U 185 ASN cc_start: 0.7607 (t0) cc_final: 0.7258 (t0) outliers start: 54 outliers final: 36 residues processed: 653 average time/residue: 0.9207 time to fit residues: 931.2858 Evaluate side-chains 567 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 529 time to evaluate : 3.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 226 ASN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 226 ASN Chi-restraints excluded: chain K residue 226 ASN Chi-restraints excluded: chain M residue 226 ASN Chi-restraints excluded: chain O residue 163 ASP Chi-restraints excluded: chain Q residue 126 PHE Chi-restraints excluded: chain Q residue 226 ASN Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 139 LEU Chi-restraints excluded: chain S residue 226 ASN Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain U residue 226 ASN Chi-restraints excluded: chain W residue 89 VAL Chi-restraints excluded: chain W residue 226 ASN Chi-restraints excluded: chain Y residue 51 SER Chi-restraints excluded: chain Y residue 141 SER Chi-restraints excluded: chain 0 residue 226 ASN Chi-restraints excluded: chain 2 residue 222 MET Chi-restraints excluded: chain 2 residue 226 ASN Chi-restraints excluded: chain 4 residue 126 PHE Chi-restraints excluded: chain 4 residue 226 ASN Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 226 ASN Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 147 ASN Chi-restraints excluded: chain 8 residue 214 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 20.0000 chunk 106 optimal weight: 7.9990 chunk 285 optimal weight: 0.9990 chunk 233 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 343 optimal weight: 10.0000 chunk 371 optimal weight: 10.0000 chunk 306 optimal weight: 5.9990 chunk 341 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 275 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 ASN I 90 GLN ** I 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 209 ASN A 115 GLN Y 90 GLN ** Y 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 142 ASN 4 142 ASN ** 8 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5241 moved from start: 0.8445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.134 32076 Z= 0.386 Angle : 0.814 11.389 44010 Z= 0.423 Chirality : 0.041 0.270 5058 Planarity : 0.007 0.074 5472 Dihedral : 12.785 59.391 5544 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 24.48 Ramachandran Plot: Outliers : 1.21 % Allowed : 12.27 % Favored : 86.51 % Rotamer: Outliers : 3.35 % Allowed : 11.24 % Favored : 85.40 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.13), residues: 3870 helix: -0.39 (0.12), residues: 1566 sheet: None (None), residues: 0 loop : -1.90 (0.13), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 135 HIS 0.007 0.002 HIS O 221 PHE 0.032 0.003 PHE W 28 TYR 0.030 0.003 TYR S 45 ARG 0.009 0.001 ARG S 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 798 time to evaluate : 3.411 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: C 37 LEU cc_start: 0.8368 (mt) cc_final: 0.8125 (mt) REVERT: C 39 ASP cc_start: 0.7165 (p0) cc_final: 0.6790 (p0) REVERT: C 137 ILE cc_start: 0.8789 (pp) cc_final: 0.8553 (pt) REVERT: C 214 LEU cc_start: 0.8509 (tp) cc_final: 0.8262 (tp) REVERT: E 166 ASP cc_start: 0.7516 (p0) cc_final: 0.7117 (p0) REVERT: G 58 ILE cc_start: 0.8104 (mm) cc_final: 0.7474 (mt) REVERT: K 205 ILE cc_start: 0.4095 (mm) cc_final: 0.3577 (mm) REVERT: Q 188 GLU cc_start: 0.5603 (mm-30) cc_final: 0.5379 (mm-30) REVERT: S 61 LEU cc_start: 0.9211 (tp) cc_final: 0.8405 (tp) REVERT: S 65 PHE cc_start: 0.8446 (m-10) cc_final: 0.8134 (m-10) REVERT: S 121 ILE cc_start: 0.8930 (mm) cc_final: 0.8612 (tt) REVERT: A 166 ASP cc_start: 0.8367 (p0) cc_final: 0.7652 (p0) REVERT: U 50 THR cc_start: 0.8769 (p) cc_final: 0.8459 (p) REVERT: U 77 PRO cc_start: 0.8957 (Cg_exo) cc_final: 0.8751 (Cg_endo) REVERT: U 196 LYS cc_start: 0.8705 (tptt) cc_final: 0.8484 (tttm) REVERT: 0 79 MET cc_start: 0.5684 (mmp) cc_final: 0.5445 (mmp) REVERT: 6 204 LYS cc_start: 0.6700 (tttt) cc_final: 0.6475 (mmmt) REVERT: 8 30 ASN cc_start: 0.7452 (p0) cc_final: 0.7217 (p0) REVERT: 8 143 ILE cc_start: 0.8037 (mt) cc_final: 0.7814 (tt) REVERT: 8 175 GLN cc_start: 0.8153 (pp30) cc_final: 0.7833 (pp30) REVERT: 8 204 LYS cc_start: 0.8966 (tptm) cc_final: 0.8725 (tppp) outliers start: 102 outliers final: 62 residues processed: 863 average time/residue: 0.8933 time to fit residues: 1193.4633 Evaluate side-chains 733 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 671 time to evaluate : 3.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 229 TYR Chi-restraints excluded: chain G residue 32 ASN Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 229 TYR Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 229 TYR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 32 ASN Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 32 ASN Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 194 VAL Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 32 ASN Chi-restraints excluded: chain O residue 194 VAL Chi-restraints excluded: chain O residue 228 MET Chi-restraints excluded: chain Q residue 126 PHE Chi-restraints excluded: chain Q residue 229 TYR Chi-restraints excluded: chain S residue 54 THR Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 81 ASP Chi-restraints excluded: chain S residue 139 LEU Chi-restraints excluded: chain S residue 229 TYR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 229 TYR Chi-restraints excluded: chain U residue 229 TYR Chi-restraints excluded: chain W residue 32 ASN Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 166 ASP Chi-restraints excluded: chain W residue 229 TYR Chi-restraints excluded: chain Y residue 26 SER Chi-restraints excluded: chain Y residue 32 ASN Chi-restraints excluded: chain Y residue 47 SER Chi-restraints excluded: chain Y residue 141 SER Chi-restraints excluded: chain Y residue 166 ASP Chi-restraints excluded: chain Y residue 226 ASN Chi-restraints excluded: chain Y residue 229 TYR Chi-restraints excluded: chain 0 residue 26 SER Chi-restraints excluded: chain 0 residue 32 ASN Chi-restraints excluded: chain 0 residue 138 LEU Chi-restraints excluded: chain 2 residue 26 SER Chi-restraints excluded: chain 2 residue 66 THR Chi-restraints excluded: chain 2 residue 229 TYR Chi-restraints excluded: chain 4 residue 116 PHE Chi-restraints excluded: chain 4 residue 126 PHE Chi-restraints excluded: chain 4 residue 142 ASN Chi-restraints excluded: chain 4 residue 163 ASP Chi-restraints excluded: chain 6 residue 32 ASN Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 8 residue 50 THR Chi-restraints excluded: chain 8 residue 64 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 10.0000 chunk 258 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 164 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 345 optimal weight: 9.9990 chunk 365 optimal weight: 6.9990 chunk 180 optimal weight: 8.9990 chunk 327 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 GLN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN S 170 ASN ** U 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6107 moved from start: 1.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 32076 Z= 0.405 Angle : 0.820 12.584 44010 Z= 0.427 Chirality : 0.041 0.214 5058 Planarity : 0.006 0.089 5472 Dihedral : 13.091 60.063 5544 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 26.18 Ramachandran Plot: Outliers : 1.21 % Allowed : 11.96 % Favored : 86.82 % Rotamer: Outliers : 3.19 % Allowed : 16.57 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.13), residues: 3870 helix: -0.23 (0.13), residues: 1584 sheet: None (None), residues: 0 loop : -1.97 (0.13), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP 6 80 HIS 0.015 0.003 HIS 8 221 PHE 0.047 0.003 PHE G 164 TYR 0.028 0.003 TYR S 45 ARG 0.046 0.001 ARG 4 182 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 994 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 897 time to evaluate : 3.472 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 ARG cc_start: 0.7492 (tpp80) cc_final: 0.7259 (ttp80) REVERT: C 121 ILE cc_start: 0.9251 (mm) cc_final: 0.8743 (tt) REVERT: E 86 TYR cc_start: 0.9015 (OUTLIER) cc_final: 0.8698 (m-10) REVERT: E 122 THR cc_start: 0.9068 (m) cc_final: 0.8815 (p) REVERT: G 50 THR cc_start: 0.8797 (p) cc_final: 0.8408 (t) REVERT: G 151 LEU cc_start: 0.8789 (mt) cc_final: 0.8553 (mp) REVERT: G 153 TYR cc_start: 0.8864 (m-80) cc_final: 0.8577 (m-80) REVERT: G 183 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.6332 (pt0) REVERT: G 187 LYS cc_start: 0.8674 (tppt) cc_final: 0.8294 (tptt) REVERT: Q 57 GLU cc_start: 0.7731 (pm20) cc_final: 0.7464 (pm20) REVERT: Q 204 LYS cc_start: 0.7428 (tttt) cc_final: 0.6925 (mmtt) REVERT: S 61 LEU cc_start: 0.9225 (tp) cc_final: 0.8742 (tp) REVERT: S 65 PHE cc_start: 0.8123 (m-10) cc_final: 0.7893 (m-10) REVERT: S 121 ILE cc_start: 0.9344 (mm) cc_final: 0.8965 (tt) REVERT: S 165 PHE cc_start: 0.9262 (t80) cc_final: 0.9019 (t80) REVERT: S 204 LYS cc_start: 0.9036 (tptm) cc_final: 0.8756 (tppt) REVERT: A 30 ASN cc_start: 0.7241 (p0) cc_final: 0.7039 (p0) REVERT: A 86 TYR cc_start: 0.9080 (m-80) cc_final: 0.8823 (m-80) REVERT: U 33 THR cc_start: 0.8105 (t) cc_final: 0.7721 (m) REVERT: U 122 THR cc_start: 0.8643 (m) cc_final: 0.8312 (p) REVERT: U 187 LYS cc_start: 0.8264 (mmmm) cc_final: 0.7960 (tptt) REVERT: U 218 THR cc_start: 0.7885 (p) cc_final: 0.7610 (p) REVERT: W 110 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7850 (ttp-110) REVERT: 0 79 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.6607 (mmp) REVERT: 0 187 LYS cc_start: 0.4770 (OUTLIER) cc_final: 0.3195 (tptp) REVERT: 2 202 ARG cc_start: 0.4836 (ttp-110) cc_final: 0.4628 (ttp-110) REVERT: 4 202 ARG cc_start: 0.7342 (ttp-170) cc_final: 0.7075 (ttp-110) REVERT: 6 30 ASN cc_start: 0.5337 (p0) cc_final: 0.4862 (p0) REVERT: 6 91 SER cc_start: 0.8457 (t) cc_final: 0.7524 (p) REVERT: 8 30 ASN cc_start: 0.8160 (p0) cc_final: 0.7793 (p0) REVERT: 8 170 ASN cc_start: 0.8993 (p0) cc_final: 0.8729 (p0) outliers start: 97 outliers final: 66 residues processed: 949 average time/residue: 0.8971 time to fit residues: 1309.4566 Evaluate side-chains 886 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 815 time to evaluate : 3.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 226 ASN Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 183 GLN Chi-restraints excluded: chain G residue 222 MET Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 229 TYR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 104 ASN Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 128 MET Chi-restraints excluded: chain O residue 126 PHE Chi-restraints excluded: chain O residue 194 VAL Chi-restraints excluded: chain O residue 229 TYR Chi-restraints excluded: chain Q residue 126 PHE Chi-restraints excluded: chain Q residue 194 VAL Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain S residue 54 THR Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 81 ASP Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain S residue 92 SER Chi-restraints excluded: chain S residue 154 GLN Chi-restraints excluded: chain S residue 170 ASN Chi-restraints excluded: chain S residue 219 ARG Chi-restraints excluded: chain S residue 228 MET Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain U residue 58 ILE Chi-restraints excluded: chain U residue 150 LYS Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 110 ARG Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain W residue 166 ASP Chi-restraints excluded: chain W residue 229 TYR Chi-restraints excluded: chain Y residue 47 SER Chi-restraints excluded: chain Y residue 141 SER Chi-restraints excluded: chain Y residue 166 ASP Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain 0 residue 26 SER Chi-restraints excluded: chain 0 residue 79 MET Chi-restraints excluded: chain 0 residue 138 LEU Chi-restraints excluded: chain 0 residue 187 LYS Chi-restraints excluded: chain 2 residue 79 MET Chi-restraints excluded: chain 2 residue 117 ASP Chi-restraints excluded: chain 2 residue 163 ASP Chi-restraints excluded: chain 4 residue 80 TRP Chi-restraints excluded: chain 4 residue 116 PHE Chi-restraints excluded: chain 4 residue 126 PHE Chi-restraints excluded: chain 4 residue 140 ASP Chi-restraints excluded: chain 4 residue 163 ASP Chi-restraints excluded: chain 4 residue 229 TYR Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 137 ILE Chi-restraints excluded: chain 6 residue 140 ASP Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 103 SER Chi-restraints excluded: chain 8 residue 138 LEU Chi-restraints excluded: chain 8 residue 154 GLN Chi-restraints excluded: chain 8 residue 228 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 272 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 311 optimal weight: 20.0000 chunk 252 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 186 optimal weight: 10.0000 chunk 327 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN E 120 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 170 ASN ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 ASN ** U 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 154 GLN ** U 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 142 ASN 6 104 ASN 8 154 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 1.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.206 32076 Z= 0.351 Angle : 0.783 15.956 44010 Z= 0.408 Chirality : 0.041 0.444 5058 Planarity : 0.007 0.099 5472 Dihedral : 13.321 61.122 5544 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 22.75 Ramachandran Plot: Outliers : 1.19 % Allowed : 12.25 % Favored : 86.56 % Rotamer: Outliers : 3.91 % Allowed : 19.63 % Favored : 76.46 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.13), residues: 3870 helix: -0.37 (0.12), residues: 1710 sheet: None (None), residues: 0 loop : -2.09 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP W 148 HIS 0.009 0.002 HIS 4 221 PHE 0.068 0.003 PHE S 162 TYR 0.035 0.003 TYR Y 197 ARG 0.019 0.001 ARG W 109 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1168 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1049 time to evaluate : 3.484 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 ARG cc_start: 0.7686 (tpp80) cc_final: 0.7347 (ttp80) REVERT: C 121 ILE cc_start: 0.9226 (mm) cc_final: 0.8693 (tt) REVERT: C 137 ILE cc_start: 0.9373 (pp) cc_final: 0.9114 (pt) REVERT: E 33 THR cc_start: 0.8257 (t) cc_final: 0.8006 (m) REVERT: E 84 ARG cc_start: 0.8165 (tpt90) cc_final: 0.7864 (tpt90) REVERT: E 166 ASP cc_start: 0.7962 (p0) cc_final: 0.7589 (p0) REVERT: G 50 THR cc_start: 0.9232 (p) cc_final: 0.8988 (t) REVERT: G 59 GLU cc_start: 0.6093 (tm-30) cc_final: 0.5589 (tm-30) REVERT: G 151 LEU cc_start: 0.8917 (mt) cc_final: 0.8704 (mp) REVERT: G 183 GLN cc_start: 0.8182 (tp40) cc_final: 0.6436 (pt0) REVERT: G 229 TYR cc_start: 0.4084 (OUTLIER) cc_final: 0.3621 (m-10) REVERT: I 77 PRO cc_start: 0.7968 (Cg_exo) cc_final: 0.7730 (Cg_endo) REVERT: M 128 MET cc_start: 0.4007 (mtp) cc_final: 0.3370 (mtp) REVERT: O 75 THR cc_start: 0.7018 (OUTLIER) cc_final: 0.6661 (p) REVERT: O 142 ASN cc_start: 0.7771 (t0) cc_final: 0.7261 (m-40) REVERT: O 159 PHE cc_start: 0.8740 (m-10) cc_final: 0.8421 (m-80) REVERT: O 182 ARG cc_start: 0.6578 (ptt180) cc_final: 0.5450 (tpt170) REVERT: O 204 LYS cc_start: 0.7514 (tttt) cc_final: 0.7037 (tttt) REVERT: Q 30 ASN cc_start: 0.5153 (p0) cc_final: 0.4901 (p0) REVERT: Q 38 SER cc_start: 0.8903 (m) cc_final: 0.8662 (t) REVERT: Q 94 SER cc_start: 0.9095 (m) cc_final: 0.8648 (p) REVERT: Q 216 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7152 (mm-30) REVERT: S 61 LEU cc_start: 0.9201 (tp) cc_final: 0.8873 (tp) REVERT: S 65 PHE cc_start: 0.8483 (m-10) cc_final: 0.8260 (m-10) REVERT: S 121 ILE cc_start: 0.9372 (mm) cc_final: 0.9025 (tt) REVERT: A 79 MET cc_start: 0.8079 (mmp) cc_final: 0.7773 (mmp) REVERT: U 202 ARG cc_start: 0.8779 (ttp-110) cc_final: 0.8502 (mtm-85) REVERT: W 68 MET cc_start: 0.6061 (mmm) cc_final: 0.5515 (tmm) REVERT: Y 77 PRO cc_start: 0.8002 (Cg_exo) cc_final: 0.7783 (Cg_endo) REVERT: 4 159 PHE cc_start: 0.8968 (m-10) cc_final: 0.8597 (m-80) REVERT: 4 209 ASN cc_start: 0.7621 (m-40) cc_final: 0.7305 (m-40) REVERT: 6 30 ASN cc_start: 0.6354 (p0) cc_final: 0.5906 (p0) REVERT: 6 91 SER cc_start: 0.8802 (t) cc_final: 0.8008 (p) REVERT: 6 154 GLN cc_start: 0.7202 (tp-100) cc_final: 0.6859 (mm-40) REVERT: 6 203 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.8035 (tt0) REVERT: 8 30 ASN cc_start: 0.7890 (p0) cc_final: 0.7524 (p0) REVERT: 8 159 PHE cc_start: 0.8953 (m-80) cc_final: 0.8690 (m-80) REVERT: 8 175 GLN cc_start: 0.8453 (pp30) cc_final: 0.7930 (pp30) outliers start: 119 outliers final: 74 residues processed: 1101 average time/residue: 0.9076 time to fit residues: 1533.3593 Evaluate side-chains 1017 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 940 time to evaluate : 3.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain G residue 32 ASN Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 222 MET Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain G residue 228 MET Chi-restraints excluded: chain G residue 229 TYR Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 120 ASN Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 229 TYR Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain K residue 226 ASN Chi-restraints excluded: chain M residue 104 ASN Chi-restraints excluded: chain M residue 194 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 120 ASN Chi-restraints excluded: chain O residue 126 PHE Chi-restraints excluded: chain O residue 229 TYR Chi-restraints excluded: chain Q residue 126 PHE Chi-restraints excluded: chain Q residue 140 ASP Chi-restraints excluded: chain S residue 54 THR Chi-restraints excluded: chain S residue 81 ASP Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain S residue 170 ASN Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain S residue 226 ASN Chi-restraints excluded: chain S residue 229 TYR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain U residue 115 GLN Chi-restraints excluded: chain U residue 139 LEU Chi-restraints excluded: chain U residue 236 GLU Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain W residue 90 GLN Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain W residue 166 ASP Chi-restraints excluded: chain W residue 228 MET Chi-restraints excluded: chain W residue 229 TYR Chi-restraints excluded: chain Y residue 32 ASN Chi-restraints excluded: chain Y residue 79 MET Chi-restraints excluded: chain Y residue 141 SER Chi-restraints excluded: chain Y residue 166 ASP Chi-restraints excluded: chain 0 residue 202 ARG Chi-restraints excluded: chain 2 residue 68 MET Chi-restraints excluded: chain 2 residue 163 ASP Chi-restraints excluded: chain 2 residue 194 VAL Chi-restraints excluded: chain 4 residue 116 PHE Chi-restraints excluded: chain 4 residue 126 PHE Chi-restraints excluded: chain 4 residue 137 ILE Chi-restraints excluded: chain 4 residue 163 ASP Chi-restraints excluded: chain 4 residue 229 TYR Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 6 residue 203 GLN Chi-restraints excluded: chain 6 residue 228 MET Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 8 residue 57 GLU Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 140 ASP Chi-restraints excluded: chain 8 residue 228 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 10.0000 chunk 329 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 214 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 365 optimal weight: 2.9990 chunk 303 optimal weight: 1.9990 chunk 169 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 192 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 203 GLN ** S 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 ASN A 154 GLN A 209 ASN ** U 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 142 ASN 8 32 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 1.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 32076 Z= 0.260 Angle : 0.678 10.804 44010 Z= 0.347 Chirality : 0.037 0.192 5058 Planarity : 0.005 0.067 5472 Dihedral : 13.336 73.565 5544 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 1.11 % Allowed : 11.29 % Favored : 87.60 % Rotamer: Outliers : 3.39 % Allowed : 23.04 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.14), residues: 3870 helix: 0.38 (0.13), residues: 1602 sheet: None (None), residues: 0 loop : -2.16 (0.14), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP 6 148 HIS 0.007 0.002 HIS 6 192 PHE 0.022 0.002 PHE O 130 TYR 0.018 0.002 TYR S 86 ARG 0.012 0.001 ARG Q 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1152 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 1049 time to evaluate : 3.519 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: C 33 THR cc_start: 0.7981 (t) cc_final: 0.7713 (t) REVERT: C 61 LEU cc_start: 0.8743 (tt) cc_final: 0.7792 (tt) REVERT: C 118 ARG cc_start: 0.7668 (tpp80) cc_final: 0.7288 (ttp80) REVERT: C 121 ILE cc_start: 0.9229 (mm) cc_final: 0.8794 (tt) REVERT: C 137 ILE cc_start: 0.9306 (pp) cc_final: 0.9082 (pt) REVERT: C 138 LEU cc_start: 0.9331 (mt) cc_final: 0.9106 (mt) REVERT: E 50 THR cc_start: 0.9430 (p) cc_final: 0.9047 (t) REVERT: E 84 ARG cc_start: 0.8112 (tpt90) cc_final: 0.7607 (tpt90) REVERT: G 50 THR cc_start: 0.9236 (p) cc_final: 0.8997 (t) REVERT: G 59 GLU cc_start: 0.6073 (tm-30) cc_final: 0.5557 (tm-30) REVERT: G 93 LYS cc_start: 0.9069 (mmtp) cc_final: 0.8806 (mmtp) REVERT: G 128 MET cc_start: 0.8145 (mmm) cc_final: 0.7932 (mmm) REVERT: G 151 LEU cc_start: 0.8975 (mt) cc_final: 0.8710 (mp) REVERT: G 182 ARG cc_start: 0.6623 (tpt170) cc_final: 0.5267 (tmm-80) REVERT: G 183 GLN cc_start: 0.8201 (tp40) cc_final: 0.6757 (pt0) REVERT: G 216 GLU cc_start: 0.7833 (tp30) cc_final: 0.7521 (tp30) REVERT: I 189 LEU cc_start: 0.8707 (tt) cc_final: 0.8448 (tt) REVERT: I 229 TYR cc_start: 0.2996 (OUTLIER) cc_final: 0.2549 (m-10) REVERT: O 79 MET cc_start: 0.8105 (mmp) cc_final: 0.7690 (mmp) REVERT: O 159 PHE cc_start: 0.8897 (m-10) cc_final: 0.8591 (m-80) REVERT: O 178 ASP cc_start: 0.6727 (p0) cc_final: 0.5029 (t0) REVERT: O 182 ARG cc_start: 0.7141 (ptt180) cc_final: 0.5905 (tpt170) REVERT: O 204 LYS cc_start: 0.7846 (tttt) cc_final: 0.7599 (tttt) REVERT: Q 30 ASN cc_start: 0.5253 (p0) cc_final: 0.5031 (p0) REVERT: Q 74 GLU cc_start: 0.6826 (pm20) cc_final: 0.6586 (pm20) REVERT: Q 227 THR cc_start: 0.8961 (p) cc_final: 0.8657 (t) REVERT: S 61 LEU cc_start: 0.9207 (tp) cc_final: 0.8992 (tp) REVERT: S 65 PHE cc_start: 0.8281 (m-10) cc_final: 0.8074 (m-10) REVERT: S 121 ILE cc_start: 0.9324 (mm) cc_final: 0.9102 (tt) REVERT: S 125 GLN cc_start: 0.8634 (mt0) cc_final: 0.8212 (mt0) REVERT: S 128 MET cc_start: 0.8394 (mmm) cc_final: 0.8094 (mmm) REVERT: A 65 PHE cc_start: 0.8628 (m-10) cc_final: 0.8407 (m-10) REVERT: A 128 MET cc_start: 0.7844 (tpt) cc_final: 0.7491 (tpt) REVERT: A 166 ASP cc_start: 0.8137 (p0) cc_final: 0.7555 (p0) REVERT: A 174 LEU cc_start: 0.7714 (mt) cc_final: 0.7173 (mt) REVERT: U 32 ASN cc_start: 0.7557 (m-40) cc_final: 0.7195 (m-40) REVERT: U 33 THR cc_start: 0.8499 (t) cc_final: 0.8198 (p) REVERT: U 54 THR cc_start: 0.8407 (m) cc_final: 0.8029 (p) REVERT: U 58 ILE cc_start: 0.8849 (mt) cc_final: 0.8642 (mt) REVERT: U 129 TYR cc_start: 0.8658 (t80) cc_final: 0.8442 (t80) REVERT: W 32 ASN cc_start: 0.7452 (m-40) cc_final: 0.7203 (m-40) REVERT: W 59 GLU cc_start: 0.6371 (tm-30) cc_final: 0.5785 (tm-30) REVERT: W 68 MET cc_start: 0.6850 (mmm) cc_final: 0.6429 (tmm) REVERT: Y 77 PRO cc_start: 0.8373 (Cg_exo) cc_final: 0.8143 (Cg_endo) REVERT: Y 82 LEU cc_start: 0.7834 (tp) cc_final: 0.7634 (tp) REVERT: 0 90 GLN cc_start: 0.7310 (mm-40) cc_final: 0.6709 (mp10) REVERT: 0 162 PHE cc_start: 0.7406 (p90) cc_final: 0.6937 (p90) REVERT: 0 163 ASP cc_start: 0.5764 (m-30) cc_final: 0.5555 (m-30) REVERT: 4 159 PHE cc_start: 0.9059 (m-80) cc_final: 0.8735 (m-80) REVERT: 4 210 TYR cc_start: 0.6845 (p90) cc_final: 0.6511 (p90) REVERT: 6 30 ASN cc_start: 0.6541 (p0) cc_final: 0.5978 (p0) REVERT: 6 91 SER cc_start: 0.8950 (t) cc_final: 0.8418 (p) REVERT: 6 203 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7959 (tt0) REVERT: 8 30 ASN cc_start: 0.7740 (p0) cc_final: 0.7309 (p0) outliers start: 103 outliers final: 80 residues processed: 1091 average time/residue: 0.8982 time to fit residues: 1503.4659 Evaluate side-chains 1076 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 994 time to evaluate : 3.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 222 MET Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain G residue 228 MET Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 120 ASN Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 194 VAL Chi-restraints excluded: chain I residue 229 TYR Chi-restraints excluded: chain K residue 163 ASP Chi-restraints excluded: chain M residue 194 VAL Chi-restraints excluded: chain M residue 236 GLU Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain O residue 126 PHE Chi-restraints excluded: chain O residue 194 VAL Chi-restraints excluded: chain Q residue 126 PHE Chi-restraints excluded: chain Q residue 140 ASP Chi-restraints excluded: chain Q residue 194 VAL Chi-restraints excluded: chain Q residue 203 GLN Chi-restraints excluded: chain Q residue 211 ILE Chi-restraints excluded: chain Q residue 226 ASN Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain S residue 54 THR Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 81 ASP Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain S residue 92 SER Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain S residue 138 LEU Chi-restraints excluded: chain S residue 163 ASP Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain S residue 228 MET Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain U residue 41 LYS Chi-restraints excluded: chain U residue 91 SER Chi-restraints excluded: chain U residue 122 THR Chi-restraints excluded: chain U residue 194 VAL Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain W residue 73 ASN Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain W residue 90 GLN Chi-restraints excluded: chain W residue 122 THR Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain W residue 186 GLU Chi-restraints excluded: chain W residue 194 VAL Chi-restraints excluded: chain W residue 228 MET Chi-restraints excluded: chain W residue 229 TYR Chi-restraints excluded: chain Y residue 141 SER Chi-restraints excluded: chain 0 residue 79 MET Chi-restraints excluded: chain 0 residue 194 VAL Chi-restraints excluded: chain 2 residue 142 ASN Chi-restraints excluded: chain 2 residue 163 ASP Chi-restraints excluded: chain 4 residue 126 PHE Chi-restraints excluded: chain 4 residue 194 VAL Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 6 residue 203 GLN Chi-restraints excluded: chain 6 residue 228 MET Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 8 residue 57 GLU Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 92 SER Chi-restraints excluded: chain 8 residue 228 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 208 optimal weight: 8.9990 chunk 267 optimal weight: 20.0000 chunk 206 optimal weight: 9.9990 chunk 307 optimal weight: 9.9990 chunk 204 optimal weight: 10.0000 chunk 364 optimal weight: 10.0000 chunk 228 optimal weight: 6.9990 chunk 222 optimal weight: 9.9990 chunk 168 optimal weight: 20.0000 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 30 ASN E 32 ASN E 120 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 203 GLN ** S 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 154 GLN ** 2 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 32 ASN 6 32 ASN 8 32 ASN 8 154 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 1.7691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 32076 Z= 0.384 Angle : 0.806 11.725 44010 Z= 0.428 Chirality : 0.042 0.316 5058 Planarity : 0.006 0.081 5472 Dihedral : 14.003 69.286 5544 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 26.96 Ramachandran Plot: Outliers : 1.16 % Allowed : 13.72 % Favored : 85.12 % Rotamer: Outliers : 4.60 % Allowed : 23.73 % Favored : 71.66 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.14), residues: 3870 helix: 0.19 (0.13), residues: 1620 sheet: None (None), residues: 0 loop : -2.35 (0.14), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Y 148 HIS 0.014 0.003 HIS O 192 PHE 0.033 0.003 PHE K 65 TYR 0.042 0.003 TYR S 229 ARG 0.011 0.001 ARG Q 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1344 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1204 time to evaluate : 3.564 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: C 118 ARG cc_start: 0.7870 (tpp80) cc_final: 0.7459 (ttp80) REVERT: C 121 ILE cc_start: 0.9044 (mm) cc_final: 0.8735 (tt) REVERT: E 50 THR cc_start: 0.9482 (p) cc_final: 0.9275 (t) REVERT: E 84 ARG cc_start: 0.8304 (tpt90) cc_final: 0.7909 (tpt90) REVERT: E 153 TYR cc_start: 0.9054 (m-80) cc_final: 0.8846 (m-80) REVERT: G 51 SER cc_start: 0.9098 (m) cc_final: 0.8694 (t) REVERT: G 58 ILE cc_start: 0.8767 (mm) cc_final: 0.8262 (mt) REVERT: G 59 GLU cc_start: 0.6184 (tm-30) cc_final: 0.5727 (tm-30) REVERT: G 93 LYS cc_start: 0.9130 (mmtp) cc_final: 0.8800 (mmtp) REVERT: G 128 MET cc_start: 0.8568 (mmm) cc_final: 0.8360 (mmm) REVERT: G 142 ASN cc_start: 0.8635 (t0) cc_final: 0.8182 (t0) REVERT: G 182 ARG cc_start: 0.7094 (tpt170) cc_final: 0.5298 (tmm160) REVERT: G 216 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7687 (tp30) REVERT: I 59 GLU cc_start: 0.6220 (tm-30) cc_final: 0.5556 (tm-30) REVERT: I 153 TYR cc_start: 0.8976 (m-80) cc_final: 0.8578 (m-10) REVERT: I 189 LEU cc_start: 0.8912 (tt) cc_final: 0.8553 (tt) REVERT: M 121 ILE cc_start: 0.5827 (mm) cc_final: 0.5605 (mm) REVERT: M 187 LYS cc_start: 0.8166 (ttpp) cc_final: 0.7602 (tttt) REVERT: O 55 PRO cc_start: 0.8623 (Cg_exo) cc_final: 0.8420 (Cg_endo) REVERT: O 139 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8638 (tt) REVERT: O 178 ASP cc_start: 0.7222 (p0) cc_final: 0.6387 (t0) REVERT: O 183 GLN cc_start: 0.6331 (OUTLIER) cc_final: 0.5895 (tp-100) REVERT: Q 30 ASN cc_start: 0.6689 (p0) cc_final: 0.6475 (p0) REVERT: Q 74 GLU cc_start: 0.7083 (pm20) cc_final: 0.6541 (pm20) REVERT: Q 129 TYR cc_start: 0.9086 (t80) cc_final: 0.8870 (t80) REVERT: Q 174 LEU cc_start: 0.7785 (mp) cc_final: 0.7451 (mp) REVERT: S 65 PHE cc_start: 0.8586 (m-10) cc_final: 0.8344 (m-10) REVERT: S 121 ILE cc_start: 0.9313 (mm) cc_final: 0.9069 (tt) REVERT: S 128 MET cc_start: 0.8491 (mmm) cc_final: 0.8106 (mmm) REVERT: A 79 MET cc_start: 0.8340 (mmp) cc_final: 0.8125 (mmp) REVERT: U 32 ASN cc_start: 0.8041 (m-40) cc_final: 0.7689 (m-40) REVERT: U 41 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6866 (mmmt) REVERT: U 57 GLU cc_start: 0.8375 (pm20) cc_final: 0.8150 (pm20) REVERT: U 58 ILE cc_start: 0.9028 (mt) cc_final: 0.8746 (mt) REVERT: U 68 MET cc_start: 0.7570 (mmm) cc_final: 0.7240 (mtm) REVERT: W 59 GLU cc_start: 0.6419 (tm-30) cc_final: 0.5784 (tm-30) REVERT: W 93 LYS cc_start: 0.8819 (mmtp) cc_final: 0.8575 (mmtm) REVERT: W 128 MET cc_start: 0.8230 (mmt) cc_final: 0.7766 (mmt) REVERT: W 150 LYS cc_start: 0.8821 (mtpp) cc_final: 0.8544 (mtmm) REVERT: Y 59 GLU cc_start: 0.6233 (tm-30) cc_final: 0.6023 (tm-30) REVERT: 0 121 ILE cc_start: 0.7406 (mm) cc_final: 0.7135 (mm) REVERT: 0 159 PHE cc_start: 0.8689 (m-10) cc_final: 0.8470 (m-80) REVERT: 0 202 ARG cc_start: 0.7861 (tpp80) cc_final: 0.7499 (tpp80) REVERT: 2 79 MET cc_start: 0.7888 (mmp) cc_final: 0.7678 (mmp) REVERT: 4 159 PHE cc_start: 0.9229 (m-80) cc_final: 0.8874 (m-80) REVERT: 6 30 ASN cc_start: 0.7167 (p0) cc_final: 0.6747 (p0) REVERT: 6 74 GLU cc_start: 0.6897 (pm20) cc_final: 0.6648 (pm20) REVERT: 6 91 SER cc_start: 0.9231 (t) cc_final: 0.8407 (p) REVERT: 6 182 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8003 (ptm160) REVERT: 6 188 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7719 (mt-10) REVERT: 8 30 ASN cc_start: 0.7879 (p0) cc_final: 0.7523 (p0) REVERT: 8 50 THR cc_start: 0.9438 (m) cc_final: 0.9181 (t) REVERT: 8 84 ARG cc_start: 0.7968 (tpt170) cc_final: 0.6919 (tmm160) REVERT: 8 170 ASN cc_start: 0.8711 (p0) cc_final: 0.8494 (p0) outliers start: 140 outliers final: 102 residues processed: 1258 average time/residue: 0.9286 time to fit residues: 1783.9399 Evaluate side-chains 1224 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1117 time to evaluate : 3.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 154 GLN Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain G residue 32 ASN Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain G residue 222 MET Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain G residue 229 TYR Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 120 ASN Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain I residue 229 TYR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 163 ASP Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain M residue 236 GLU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 98 ILE Chi-restraints excluded: chain O residue 119 ILE Chi-restraints excluded: chain O residue 126 PHE Chi-restraints excluded: chain O residue 139 LEU Chi-restraints excluded: chain O residue 183 GLN Chi-restraints excluded: chain Q residue 92 SER Chi-restraints excluded: chain Q residue 126 PHE Chi-restraints excluded: chain Q residue 140 ASP Chi-restraints excluded: chain Q residue 211 ILE Chi-restraints excluded: chain S residue 54 THR Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 81 ASP Chi-restraints excluded: chain S residue 86 TYR Chi-restraints excluded: chain S residue 92 SER Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain S residue 138 LEU Chi-restraints excluded: chain S residue 139 LEU Chi-restraints excluded: chain S residue 194 VAL Chi-restraints excluded: chain S residue 228 MET Chi-restraints excluded: chain S residue 229 TYR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 229 TYR Chi-restraints excluded: chain U residue 41 LYS Chi-restraints excluded: chain U residue 91 SER Chi-restraints excluded: chain U residue 194 VAL Chi-restraints excluded: chain U residue 205 ILE Chi-restraints excluded: chain U residue 227 THR Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain W residue 73 ASN Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain W residue 90 GLN Chi-restraints excluded: chain W residue 151 LEU Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain W residue 166 ASP Chi-restraints excluded: chain W residue 186 GLU Chi-restraints excluded: chain W residue 194 VAL Chi-restraints excluded: chain W residue 228 MET Chi-restraints excluded: chain W residue 229 TYR Chi-restraints excluded: chain W residue 236 GLU Chi-restraints excluded: chain Y residue 32 ASN Chi-restraints excluded: chain Y residue 81 ASP Chi-restraints excluded: chain Y residue 120 ASN Chi-restraints excluded: chain Y residue 141 SER Chi-restraints excluded: chain Y residue 157 THR Chi-restraints excluded: chain 0 residue 47 SER Chi-restraints excluded: chain 0 residue 79 MET Chi-restraints excluded: chain 2 residue 68 MET Chi-restraints excluded: chain 2 residue 163 ASP Chi-restraints excluded: chain 2 residue 194 VAL Chi-restraints excluded: chain 4 residue 47 SER Chi-restraints excluded: chain 4 residue 126 PHE Chi-restraints excluded: chain 4 residue 137 ILE Chi-restraints excluded: chain 4 residue 194 VAL Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 92 SER Chi-restraints excluded: chain 6 residue 104 ASN Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 6 residue 228 MET Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 8 residue 57 GLU Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 92 SER Chi-restraints excluded: chain 8 residue 151 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 225 optimal weight: 8.9990 chunk 145 optimal weight: 9.9990 chunk 217 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 231 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 180 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 286 optimal weight: 1.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 ASN E 120 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 203 GLN Q 125 GLN ** S 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 170 ASN ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 32 ASN ** U 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 203 GLN 2 203 GLN 6 32 ASN 8 32 ASN 8 147 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 1.8491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 32076 Z= 0.274 Angle : 0.687 10.019 44010 Z= 0.352 Chirality : 0.038 0.232 5058 Planarity : 0.005 0.065 5472 Dihedral : 13.837 68.469 5544 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 1.11 % Allowed : 11.60 % Favored : 87.29 % Rotamer: Outliers : 4.11 % Allowed : 25.64 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.14), residues: 3870 helix: 0.41 (0.13), residues: 1602 sheet: None (None), residues: 0 loop : -2.12 (0.14), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP K 80 HIS 0.012 0.002 HIS 8 221 PHE 0.017 0.002 PHE Y 162 TYR 0.019 0.002 TYR S 229 ARG 0.010 0.001 ARG 6 124 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1299 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1174 time to evaluate : 3.609 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: C 65 PHE cc_start: 0.8503 (m-10) cc_final: 0.8250 (m-10) REVERT: C 118 ARG cc_start: 0.7889 (tpp80) cc_final: 0.7460 (ttp80) REVERT: C 136 ASN cc_start: 0.9164 (m-40) cc_final: 0.8853 (m-40) REVERT: G 51 SER cc_start: 0.9028 (m) cc_final: 0.8803 (t) REVERT: G 58 ILE cc_start: 0.8889 (mm) cc_final: 0.8381 (mt) REVERT: G 59 GLU cc_start: 0.6365 (tm-30) cc_final: 0.5682 (tm-30) REVERT: G 63 LYS cc_start: 0.7235 (mtpt) cc_final: 0.6379 (mtmm) REVERT: G 182 ARG cc_start: 0.7150 (tpt170) cc_final: 0.5590 (ptt-90) REVERT: G 216 GLU cc_start: 0.7386 (tp30) cc_final: 0.6923 (tp30) REVERT: I 59 GLU cc_start: 0.6444 (tm-30) cc_final: 0.5817 (tm-30) REVERT: I 150 LYS cc_start: 0.8791 (mmmm) cc_final: 0.8563 (mmmm) REVERT: I 153 TYR cc_start: 0.9003 (m-80) cc_final: 0.8698 (m-10) REVERT: K 153 TYR cc_start: 0.8355 (m-80) cc_final: 0.8024 (m-80) REVERT: M 121 ILE cc_start: 0.6104 (mm) cc_final: 0.5841 (mm) REVERT: M 187 LYS cc_start: 0.8196 (ttpp) cc_final: 0.7968 (tttt) REVERT: O 139 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8607 (tt) REVERT: O 158 LYS cc_start: 0.9131 (pttt) cc_final: 0.8875 (pttp) REVERT: O 178 ASP cc_start: 0.7191 (p0) cc_final: 0.6638 (t0) REVERT: O 222 MET cc_start: 0.8342 (tmm) cc_final: 0.8019 (tmm) REVERT: Q 30 ASN cc_start: 0.6760 (p0) cc_final: 0.6560 (p0) REVERT: Q 74 GLU cc_start: 0.7090 (pm20) cc_final: 0.6510 (pm20) REVERT: Q 79 MET cc_start: 0.8151 (mmp) cc_final: 0.7864 (mmt) REVERT: Q 108 SER cc_start: 0.7940 (OUTLIER) cc_final: 0.7403 (p) REVERT: Q 163 ASP cc_start: 0.8309 (p0) cc_final: 0.8063 (p0) REVERT: Q 188 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6628 (mm-30) REVERT: Q 204 LYS cc_start: 0.9192 (mmtt) cc_final: 0.8886 (tptm) REVERT: A 228 MET cc_start: 0.5733 (OUTLIER) cc_final: 0.5444 (ttm) REVERT: U 32 ASN cc_start: 0.7952 (OUTLIER) cc_final: 0.7664 (m-40) REVERT: U 33 THR cc_start: 0.8267 (t) cc_final: 0.7964 (p) REVERT: U 41 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.6872 (mmmt) REVERT: W 32 ASN cc_start: 0.8026 (m-40) cc_final: 0.7781 (m-40) REVERT: W 59 GLU cc_start: 0.6308 (tm-30) cc_final: 0.5727 (tm-30) REVERT: W 93 LYS cc_start: 0.8734 (mmtp) cc_final: 0.8500 (mmtm) REVERT: W 128 MET cc_start: 0.8284 (mmt) cc_final: 0.7933 (mmt) REVERT: W 129 TYR cc_start: 0.8643 (t80) cc_final: 0.8068 (t80) REVERT: W 150 LYS cc_start: 0.8827 (mtpp) cc_final: 0.8624 (mtmm) REVERT: 0 159 PHE cc_start: 0.8709 (m-10) cc_final: 0.8354 (m-80) REVERT: 0 170 ASN cc_start: 0.7951 (p0) cc_final: 0.7561 (p0) REVERT: 2 68 MET cc_start: 0.5566 (mtp) cc_final: 0.5205 (ttp) REVERT: 2 79 MET cc_start: 0.8214 (mmp) cc_final: 0.7938 (mmp) REVERT: 2 121 ILE cc_start: 0.7294 (mm) cc_final: 0.7082 (mm) REVERT: 4 74 GLU cc_start: 0.6094 (pm20) cc_final: 0.5550 (pm20) REVERT: 4 159 PHE cc_start: 0.9156 (m-80) cc_final: 0.8864 (m-80) REVERT: 4 178 ASP cc_start: 0.7630 (p0) cc_final: 0.7167 (m-30) REVERT: 6 30 ASN cc_start: 0.7151 (p0) cc_final: 0.6761 (p0) REVERT: 6 74 GLU cc_start: 0.6677 (pm20) cc_final: 0.6391 (pm20) REVERT: 6 91 SER cc_start: 0.9309 (t) cc_final: 0.8593 (p) REVERT: 6 108 SER cc_start: 0.8147 (OUTLIER) cc_final: 0.7718 (p) REVERT: 6 203 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.8018 (tt0) REVERT: 8 30 ASN cc_start: 0.7966 (p0) cc_final: 0.7567 (p0) REVERT: 8 50 THR cc_start: 0.9436 (m) cc_final: 0.9158 (t) REVERT: 8 84 ARG cc_start: 0.7728 (tpt170) cc_final: 0.7002 (tmm160) outliers start: 125 outliers final: 100 residues processed: 1223 average time/residue: 0.8849 time to fit residues: 1651.1278 Evaluate side-chains 1236 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1129 time to evaluate : 3.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 154 GLN Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 222 MET Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 120 ASN Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain I residue 229 TYR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 120 ASN Chi-restraints excluded: chain K residue 163 ASP Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 203 GLN Chi-restraints excluded: chain M residue 222 MET Chi-restraints excluded: chain M residue 226 ASN Chi-restraints excluded: chain M residue 236 GLU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 98 ILE Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain O residue 126 PHE Chi-restraints excluded: chain O residue 139 LEU Chi-restraints excluded: chain Q residue 92 SER Chi-restraints excluded: chain Q residue 108 SER Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 140 ASP Chi-restraints excluded: chain Q residue 194 VAL Chi-restraints excluded: chain Q residue 211 ILE Chi-restraints excluded: chain Q residue 228 MET Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 81 ASP Chi-restraints excluded: chain S residue 86 TYR Chi-restraints excluded: chain S residue 92 SER Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain S residue 138 LEU Chi-restraints excluded: chain S residue 139 LEU Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain S residue 194 VAL Chi-restraints excluded: chain S residue 228 MET Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain U residue 32 ASN Chi-restraints excluded: chain U residue 41 LYS Chi-restraints excluded: chain U residue 92 SER Chi-restraints excluded: chain U residue 122 THR Chi-restraints excluded: chain U residue 194 VAL Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain W residue 90 GLN Chi-restraints excluded: chain W residue 166 ASP Chi-restraints excluded: chain W residue 186 GLU Chi-restraints excluded: chain W residue 194 VAL Chi-restraints excluded: chain W residue 228 MET Chi-restraints excluded: chain W residue 229 TYR Chi-restraints excluded: chain W residue 232 ASP Chi-restraints excluded: chain W residue 236 GLU Chi-restraints excluded: chain Y residue 32 ASN Chi-restraints excluded: chain Y residue 47 SER Chi-restraints excluded: chain Y residue 86 TYR Chi-restraints excluded: chain Y residue 141 SER Chi-restraints excluded: chain 0 residue 47 SER Chi-restraints excluded: chain 0 residue 79 MET Chi-restraints excluded: chain 0 residue 203 GLN Chi-restraints excluded: chain 2 residue 126 PHE Chi-restraints excluded: chain 2 residue 163 ASP Chi-restraints excluded: chain 4 residue 47 SER Chi-restraints excluded: chain 4 residue 126 PHE Chi-restraints excluded: chain 4 residue 194 VAL Chi-restraints excluded: chain 4 residue 228 MET Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 92 SER Chi-restraints excluded: chain 6 residue 108 SER Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 6 residue 203 GLN Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 81 ASP Chi-restraints excluded: chain 8 residue 92 SER Chi-restraints excluded: chain 8 residue 139 LEU Chi-restraints excluded: chain 8 residue 147 ASN Chi-restraints excluded: chain 8 residue 188 GLU Chi-restraints excluded: chain 8 residue 228 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 331 optimal weight: 10.0000 chunk 349 optimal weight: 10.0000 chunk 318 optimal weight: 0.9980 chunk 339 optimal weight: 0.3980 chunk 348 optimal weight: 8.9990 chunk 204 optimal weight: 10.0000 chunk 147 optimal weight: 30.0000 chunk 266 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 306 optimal weight: 10.0000 chunk 321 optimal weight: 5.9990 overall best weight: 4.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 32 ASN ** U 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 1.8841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 32076 Z= 0.223 Angle : 0.672 9.490 44010 Z= 0.341 Chirality : 0.037 0.158 5058 Planarity : 0.005 0.066 5472 Dihedral : 13.675 68.131 5544 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 1.09 % Allowed : 11.52 % Favored : 87.39 % Rotamer: Outliers : 3.48 % Allowed : 27.88 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.14), residues: 3870 helix: 0.58 (0.13), residues: 1620 sheet: None (None), residues: 0 loop : -2.03 (0.14), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP K 80 HIS 0.008 0.002 HIS 6 192 PHE 0.017 0.002 PHE M 126 TYR 0.016 0.002 TYR 6 153 ARG 0.012 0.001 ARG G 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1262 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1156 time to evaluate : 3.476 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: C 118 ARG cc_start: 0.7954 (tpp80) cc_final: 0.7655 (ttp80) REVERT: C 136 ASN cc_start: 0.9174 (m-40) cc_final: 0.8859 (m-40) REVERT: G 58 ILE cc_start: 0.8907 (mm) cc_final: 0.8422 (mt) REVERT: G 59 GLU cc_start: 0.6354 (tm-30) cc_final: 0.5893 (tm-30) REVERT: G 182 ARG cc_start: 0.7067 (tpt170) cc_final: 0.5505 (ptt-90) REVERT: G 216 GLU cc_start: 0.7636 (tp30) cc_final: 0.7278 (tp30) REVERT: I 59 GLU cc_start: 0.6366 (tm-30) cc_final: 0.5751 (tm-30) REVERT: I 153 TYR cc_start: 0.9008 (m-80) cc_final: 0.8686 (m-10) REVERT: K 153 TYR cc_start: 0.8472 (m-80) cc_final: 0.8182 (m-80) REVERT: O 84 ARG cc_start: 0.8576 (tpt170) cc_final: 0.8320 (tpt170) REVERT: O 158 LYS cc_start: 0.9211 (pttt) cc_final: 0.8951 (pttp) REVERT: O 178 ASP cc_start: 0.7141 (p0) cc_final: 0.6847 (t0) REVERT: O 222 MET cc_start: 0.8420 (tmm) cc_final: 0.8162 (tmm) REVERT: Q 30 ASN cc_start: 0.6835 (p0) cc_final: 0.6614 (p0) REVERT: Q 74 GLU cc_start: 0.7068 (pm20) cc_final: 0.6620 (pm20) REVERT: Q 79 MET cc_start: 0.8103 (mmp) cc_final: 0.7875 (mmt) REVERT: Q 108 SER cc_start: 0.7889 (p) cc_final: 0.7430 (p) REVERT: Q 163 ASP cc_start: 0.8181 (p0) cc_final: 0.7947 (p0) REVERT: Q 188 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6802 (mm-30) REVERT: Q 204 LYS cc_start: 0.9247 (mmtt) cc_final: 0.9001 (tptm) REVERT: S 88 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7416 (t0) REVERT: U 41 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6866 (mmmt) REVERT: W 32 ASN cc_start: 0.8106 (m-40) cc_final: 0.7865 (m-40) REVERT: W 59 GLU cc_start: 0.6338 (tm-30) cc_final: 0.5712 (tm-30) REVERT: W 90 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8260 (mp10) REVERT: W 93 LYS cc_start: 0.8720 (mmtp) cc_final: 0.8497 (mmtm) REVERT: W 128 MET cc_start: 0.8326 (mmt) cc_final: 0.7964 (mmt) REVERT: W 129 TYR cc_start: 0.8648 (t80) cc_final: 0.8096 (t80) REVERT: 0 159 PHE cc_start: 0.8703 (m-10) cc_final: 0.8433 (m-80) REVERT: 2 64 ILE cc_start: 0.8064 (tp) cc_final: 0.7674 (tt) REVERT: 2 121 ILE cc_start: 0.7455 (mm) cc_final: 0.6917 (mm) REVERT: 4 74 GLU cc_start: 0.6229 (pm20) cc_final: 0.5465 (pm20) REVERT: 4 204 LYS cc_start: 0.9123 (tppt) cc_final: 0.8919 (tppt) REVERT: 6 30 ASN cc_start: 0.7145 (p0) cc_final: 0.6766 (p0) REVERT: 6 74 GLU cc_start: 0.6797 (pm20) cc_final: 0.6475 (pm20) REVERT: 6 108 SER cc_start: 0.8070 (OUTLIER) cc_final: 0.7649 (p) REVERT: 6 128 MET cc_start: 0.8360 (mmm) cc_final: 0.8078 (mmm) REVERT: 6 203 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7847 (tt0) REVERT: 8 30 ASN cc_start: 0.7846 (p0) cc_final: 0.7408 (p0) REVERT: 8 50 THR cc_start: 0.9427 (m) cc_final: 0.9184 (t) REVERT: 8 84 ARG cc_start: 0.7467 (tpt170) cc_final: 0.6875 (tmm160) REVERT: 8 138 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8831 (mt) REVERT: 8 147 ASN cc_start: 0.8068 (OUTLIER) cc_final: 0.7683 (p0) REVERT: 8 187 LYS cc_start: 0.8822 (mttt) cc_final: 0.8404 (mtpp) outliers start: 106 outliers final: 86 residues processed: 1200 average time/residue: 0.9043 time to fit residues: 1658.4358 Evaluate side-chains 1221 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1128 time to evaluate : 3.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 222 MET Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 120 ASN Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 229 TYR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 120 ASN Chi-restraints excluded: chain K residue 128 MET Chi-restraints excluded: chain K residue 163 ASP Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain M residue 194 VAL Chi-restraints excluded: chain M residue 222 MET Chi-restraints excluded: chain M residue 236 GLU Chi-restraints excluded: chain O residue 98 ILE Chi-restraints excluded: chain O residue 126 PHE Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain Q residue 92 SER Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 193 SER Chi-restraints excluded: chain Q residue 194 VAL Chi-restraints excluded: chain Q residue 211 ILE Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 81 ASP Chi-restraints excluded: chain S residue 86 TYR Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain S residue 92 SER Chi-restraints excluded: chain S residue 120 ASN Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain S residue 138 LEU Chi-restraints excluded: chain S residue 139 LEU Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain S residue 194 VAL Chi-restraints excluded: chain S residue 228 MET Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain U residue 41 LYS Chi-restraints excluded: chain U residue 92 SER Chi-restraints excluded: chain U residue 122 THR Chi-restraints excluded: chain U residue 194 VAL Chi-restraints excluded: chain U residue 227 THR Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain W residue 90 GLN Chi-restraints excluded: chain W residue 166 ASP Chi-restraints excluded: chain W residue 186 GLU Chi-restraints excluded: chain W residue 194 VAL Chi-restraints excluded: chain W residue 229 TYR Chi-restraints excluded: chain Y residue 32 ASN Chi-restraints excluded: chain Y residue 47 SER Chi-restraints excluded: chain Y residue 86 TYR Chi-restraints excluded: chain Y residue 120 ASN Chi-restraints excluded: chain Y residue 166 ASP Chi-restraints excluded: chain 2 residue 122 THR Chi-restraints excluded: chain 2 residue 126 PHE Chi-restraints excluded: chain 2 residue 163 ASP Chi-restraints excluded: chain 4 residue 47 SER Chi-restraints excluded: chain 4 residue 126 PHE Chi-restraints excluded: chain 4 residue 189 LEU Chi-restraints excluded: chain 4 residue 194 VAL Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 92 SER Chi-restraints excluded: chain 6 residue 108 SER Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 6 residue 189 LEU Chi-restraints excluded: chain 6 residue 203 GLN Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 81 ASP Chi-restraints excluded: chain 8 residue 92 SER Chi-restraints excluded: chain 8 residue 138 LEU Chi-restraints excluded: chain 8 residue 147 ASN Chi-restraints excluded: chain 8 residue 188 GLU Chi-restraints excluded: chain 8 residue 228 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 9.9990 chunk 222 optimal weight: 0.7980 chunk 359 optimal weight: 4.9990 chunk 219 optimal weight: 9.9990 chunk 170 optimal weight: 7.9990 chunk 249 optimal weight: 20.0000 chunk 376 optimal weight: 0.5980 chunk 346 optimal weight: 3.9990 chunk 299 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 231 optimal weight: 20.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 ASN K 203 GLN O 96 GLN ** Q 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN S 154 GLN ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 203 GLN 6 32 ASN 6 203 GLN ** 8 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 125 GLN 8 147 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 1.9088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32076 Z= 0.195 Angle : 0.658 10.099 44010 Z= 0.331 Chirality : 0.036 0.152 5058 Planarity : 0.005 0.065 5472 Dihedral : 13.457 67.732 5544 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 1.11 % Allowed : 10.83 % Favored : 88.06 % Rotamer: Outliers : 2.83 % Allowed : 29.06 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.14), residues: 3870 helix: 0.79 (0.13), residues: 1620 sheet: None (None), residues: 0 loop : -1.87 (0.14), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP K 80 HIS 0.008 0.001 HIS 6 192 PHE 0.020 0.002 PHE E 28 TYR 0.022 0.002 TYR 2 197 ARG 0.009 0.001 ARG G 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1261 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1175 time to evaluate : 4.311 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: C 118 ARG cc_start: 0.8058 (tpp80) cc_final: 0.7806 (ttp80) REVERT: C 136 ASN cc_start: 0.9168 (m-40) cc_final: 0.8835 (m-40) REVERT: G 58 ILE cc_start: 0.8942 (mm) cc_final: 0.8458 (mt) REVERT: G 59 GLU cc_start: 0.6468 (tm-30) cc_final: 0.5688 (tm-30) REVERT: G 63 LYS cc_start: 0.7436 (mtpt) cc_final: 0.6775 (mttt) REVERT: G 182 ARG cc_start: 0.6900 (tpt170) cc_final: 0.5466 (ptt-90) REVERT: G 216 GLU cc_start: 0.7697 (tp30) cc_final: 0.7380 (tp30) REVERT: I 59 GLU cc_start: 0.6477 (tm-30) cc_final: 0.5845 (tm-30) REVERT: I 153 TYR cc_start: 0.8988 (m-80) cc_final: 0.8647 (m-10) REVERT: K 153 TYR cc_start: 0.8613 (m-80) cc_final: 0.8355 (m-80) REVERT: M 79 MET cc_start: 0.8286 (mmp) cc_final: 0.7904 (mmt) REVERT: M 128 MET cc_start: 0.6701 (mmm) cc_final: 0.5580 (mmm) REVERT: O 84 ARG cc_start: 0.8711 (tpt170) cc_final: 0.8486 (tpt170) REVERT: O 158 LYS cc_start: 0.9219 (pttt) cc_final: 0.8955 (pttp) REVERT: O 222 MET cc_start: 0.8389 (tmm) cc_final: 0.8020 (tmm) REVERT: Q 74 GLU cc_start: 0.7019 (pm20) cc_final: 0.6637 (pm20) REVERT: Q 79 MET cc_start: 0.8161 (mmp) cc_final: 0.7901 (mmt) REVERT: Q 108 SER cc_start: 0.7810 (p) cc_final: 0.7360 (p) REVERT: Q 163 ASP cc_start: 0.7838 (p0) cc_final: 0.7491 (p0) REVERT: Q 188 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6970 (mm-30) REVERT: Q 204 LYS cc_start: 0.9296 (mmtt) cc_final: 0.8938 (tptm) REVERT: A 128 MET cc_start: 0.7994 (tpt) cc_final: 0.7640 (tpt) REVERT: W 32 ASN cc_start: 0.8023 (m-40) cc_final: 0.7740 (m-40) REVERT: W 59 GLU cc_start: 0.6455 (tm-30) cc_final: 0.5914 (tm-30) REVERT: W 81 ASP cc_start: 0.7988 (t70) cc_final: 0.7515 (t0) REVERT: W 90 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8157 (mp10) REVERT: W 93 LYS cc_start: 0.8549 (mmtp) cc_final: 0.8289 (mmtm) REVERT: W 128 MET cc_start: 0.8347 (mmt) cc_final: 0.8009 (mmt) REVERT: W 129 TYR cc_start: 0.8778 (t80) cc_final: 0.8129 (t80) REVERT: 0 59 GLU cc_start: 0.6556 (tm-30) cc_final: 0.6111 (tm-30) REVERT: 2 68 MET cc_start: 0.5815 (tmm) cc_final: 0.5401 (tmm) REVERT: 2 136 ASN cc_start: 0.8477 (t0) cc_final: 0.8221 (t0) REVERT: 2 153 TYR cc_start: 0.8362 (m-80) cc_final: 0.8142 (m-80) REVERT: 4 74 GLU cc_start: 0.6140 (pm20) cc_final: 0.5479 (pm20) REVERT: 6 30 ASN cc_start: 0.6988 (p0) cc_final: 0.6755 (p0) REVERT: 6 86 TYR cc_start: 0.8958 (m-80) cc_final: 0.8498 (m-80) REVERT: 6 108 SER cc_start: 0.7982 (OUTLIER) cc_final: 0.7548 (p) REVERT: 6 128 MET cc_start: 0.8350 (mmm) cc_final: 0.8086 (mmm) REVERT: 6 182 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8233 (ptm160) REVERT: 8 30 ASN cc_start: 0.7616 (p0) cc_final: 0.7250 (p0) REVERT: 8 50 THR cc_start: 0.9411 (m) cc_final: 0.9169 (t) REVERT: 8 84 ARG cc_start: 0.7490 (tpt170) cc_final: 0.6903 (tmm160) REVERT: 8 138 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8791 (mt) REVERT: 8 187 LYS cc_start: 0.8835 (mttt) cc_final: 0.8401 (mtpp) outliers start: 86 outliers final: 75 residues processed: 1207 average time/residue: 0.9290 time to fit residues: 1714.0925 Evaluate side-chains 1223 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1144 time to evaluate : 3.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 222 MET Chi-restraints excluded: chain G residue 228 MET Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 120 ASN Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 120 ASN Chi-restraints excluded: chain K residue 128 MET Chi-restraints excluded: chain K residue 163 ASP Chi-restraints excluded: chain M residue 194 VAL Chi-restraints excluded: chain M residue 236 GLU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain Q residue 92 SER Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 193 SER Chi-restraints excluded: chain Q residue 194 VAL Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 81 ASP Chi-restraints excluded: chain S residue 86 TYR Chi-restraints excluded: chain S residue 120 ASN Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain S residue 138 LEU Chi-restraints excluded: chain S residue 139 LEU Chi-restraints excluded: chain S residue 194 VAL Chi-restraints excluded: chain S residue 228 MET Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain U residue 92 SER Chi-restraints excluded: chain U residue 122 THR Chi-restraints excluded: chain U residue 194 VAL Chi-restraints excluded: chain U residue 227 THR Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 90 GLN Chi-restraints excluded: chain W residue 166 ASP Chi-restraints excluded: chain W residue 186 GLU Chi-restraints excluded: chain W residue 194 VAL Chi-restraints excluded: chain W residue 236 GLU Chi-restraints excluded: chain Y residue 32 ASN Chi-restraints excluded: chain Y residue 47 SER Chi-restraints excluded: chain Y residue 86 TYR Chi-restraints excluded: chain Y residue 166 ASP Chi-restraints excluded: chain 0 residue 203 GLN Chi-restraints excluded: chain 2 residue 122 THR Chi-restraints excluded: chain 2 residue 126 PHE Chi-restraints excluded: chain 2 residue 163 ASP Chi-restraints excluded: chain 4 residue 189 LEU Chi-restraints excluded: chain 4 residue 194 VAL Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 92 SER Chi-restraints excluded: chain 6 residue 108 SER Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 6 residue 189 LEU Chi-restraints excluded: chain 6 residue 203 GLN Chi-restraints excluded: chain 8 residue 81 ASP Chi-restraints excluded: chain 8 residue 92 SER Chi-restraints excluded: chain 8 residue 138 LEU Chi-restraints excluded: chain 8 residue 147 ASN Chi-restraints excluded: chain 8 residue 188 GLU Chi-restraints excluded: chain 8 residue 228 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 183 optimal weight: 3.9990 chunk 238 optimal weight: 20.0000 chunk 319 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 276 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 300 optimal weight: 7.9990 chunk 125 optimal weight: 20.0000 chunk 308 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 ASN E 120 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 ASN ** G 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 209 ASN ** Q 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 115 GLN S 154 GLN ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 32 ASN 0 203 GLN 6 32 ASN 6 203 GLN ** 8 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.175193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.155003 restraints weight = 148658.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.161386 restraints weight = 65908.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.165263 restraints weight = 35800.837| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 1.9119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.289 32076 Z= 0.325 Angle : 0.857 59.200 44010 Z= 0.503 Chirality : 0.037 0.246 5058 Planarity : 0.006 0.158 5472 Dihedral : 13.456 67.590 5544 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 1.09 % Allowed : 10.75 % Favored : 88.17 % Rotamer: Outliers : 2.86 % Allowed : 29.52 % Favored : 67.62 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3870 helix: 0.79 (0.13), residues: 1620 sheet: None (None), residues: 0 loop : -1.86 (0.14), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP K 80 HIS 0.007 0.001 HIS 6 192 PHE 0.039 0.002 PHE 0 28 TYR 0.019 0.002 TYR S 45 ARG 0.011 0.001 ARG O 84 =============================================================================== Job complete usr+sys time: 18800.49 seconds wall clock time: 324 minutes 39.97 seconds (19479.97 seconds total)