Starting phenix.real_space_refine (version: dev) on Fri May 13 07:06:26 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn1_3236/05_2022/5fn1_3236.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn1_3236/05_2022/5fn1_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_3236/05_2022/5fn1_3236.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn1_3236/05_2022/5fn1_3236.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn1_3236/05_2022/5fn1_3236.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn1_3236/05_2022/5fn1_3236.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: {'rna3p_pyr': 2, 'rna2p_pyr': 3, '3*END': 1} Link IDs: {'rna3p': 2, 'rna2p': 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: {'rna3p_pyr': 2, 'rna2p_pyr': 3, '3*END': 1} Link IDs: {'rna3p': 2, 'rna2p': 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: {'rna3p_pyr': 2, 'rna2p_pyr': 3, '3*END': 1} Link IDs: {'rna3p': 2, 'rna2p': 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: {'rna3p_pyr': 2, 'rna2p_pyr': 3, '3*END': 1} Link IDs: {'rna3p': 2, 'rna2p': 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: {'rna3p_pyr': 2, 'rna2p_pyr': 3, '3*END': 1} Link IDs: {'rna3p': 2, 'rna2p': 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: {'rna3p_pyr': 2, 'rna2p_pyr': 3, '3*END': 1} Link IDs: {'rna3p': 2, 'rna2p': 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: {'rna3p_pyr': 2, 'rna2p_pyr': 3, '3*END': 1} Link IDs: {'rna3p': 2, 'rna2p': 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: {'rna3p_pyr': 2, 'rna2p_pyr': 3, '3*END': 1} Link IDs: {'rna3p': 2, 'rna2p': 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: {'rna3p_pyr': 2, 'rna2p_pyr': 3, '3*END': 1} Link IDs: {'rna3p': 2, 'rna2p': 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: {'rna3p_pyr': 2, 'rna2p_pyr': 3, '3*END': 1} Link IDs: {'rna3p': 2, 'rna2p': 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: {'rna3p_pyr': 2, 'rna2p_pyr': 3, '3*END': 1} Link IDs: {'rna3p': 2, 'rna2p': 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: {'rna3p_pyr': 2, 'rna2p_pyr': 3, '3*END': 1} Link IDs: {'rna3p': 2, 'rna2p': 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: {'rna3p_pyr': 2, 'rna2p_pyr': 3, '3*END': 1} Link IDs: {'rna3p': 2, 'rna2p': 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: {'rna3p_pyr': 2, 'rna2p_pyr': 3, '3*END': 1} Link IDs: {'rna3p': 2, 'rna2p': 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: {'rna3p_pyr': 2, 'rna2p_pyr': 3, '3*END': 1} Link IDs: {'rna3p': 2, 'rna2p': 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: {'rna3p_pyr': 2, 'rna2p_pyr': 3, '3*END': 1} Link IDs: {'rna3p': 2, 'rna2p': 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: {'rna3p_pyr': 2, 'rna2p_pyr': 3, '3*END': 1} Link IDs: {'rna3p': 2, 'rna2p': 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: {'rna3p_pyr': 2, 'rna2p_pyr': 3, '3*END': 1} Link IDs: {'rna3p': 2, 'rna2p': 2} Time building chain proxies: 21.37, per 1000 atoms: 0.35 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: 37.82 Conformation dependent library (CDL) restraints added in 4.3 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: 19.49 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: 16.32 Time building geometry restraints manager: 39.91 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: 23166 17.24 - 34.49: 900 34.49 - 51.73: 342 51.73 - 68.98: 522 68.98 - 86.22: 18 Dihedral angle restraints: 24948 sinusoidal: 11880 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 24945 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.110 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: 0.670 Extract box with map and model: 4.970 Check model and map are aligned: 0.690 Convert atoms to be neutral: 0.390 Process input model: 159.270 Find NCS groups from input model: 2.730 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 171.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2870 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 : 11.466 58.925 11898 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 % 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 *********************** 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 : 3.369 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: symmetry clash outliers start: 0 outliers final: 0 residues processed: 707 average time/residue: 0.8444 time to fit residues: 911.9479 Evaluate side-chains 502 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 502 time to evaluate : 3.367 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2123 ------------------------------------------------------------------------------- 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: 5.9990 chunk 286 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 193 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 296 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 chunk 180 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 343 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 M 120 ASN 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 4 209 ASN 6 209 ASN 8 185 ASN 8 209 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3892 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.118 32076 Z= 0.355 Angle : 0.827 10.969 44010 Z= 0.445 Chirality : 0.041 0.166 5058 Planarity : 0.007 0.080 5472 Dihedral : 8.700 55.083 5184 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 21.01 Ramachandran Plot: Outliers : 1.55 % Allowed : 10.72 % Favored : 87.73 % Rotamer Outliers : 1.81 % 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: -1.94 (0.13), residues: 3870 helix: -0.90 (0.11), residues: 1692 sheet: None (None), residues: 0 loop : -1.61 (0.14), residues: 2178 *********************** 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 661 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 606 time to evaluate : 3.380 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 outliers start: 55 outliers final: 38 residues processed: 647 average time/residue: 0.8384 time to fit residues: 840.3411 Evaluate side-chains 552 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 514 time to evaluate : 3.364 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 4 residues processed: 38 average time/residue: 0.5329 time to fit residues: 41.4827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 285 optimal weight: 20.0000 chunk 233 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 343 optimal weight: 20.0000 chunk 371 optimal weight: 10.0000 chunk 306 optimal weight: 30.0000 chunk 341 optimal weight: 9.9990 chunk 117 optimal weight: 8.9990 chunk 275 optimal weight: 6.9990 overall best weight: 6.7788 ------------------------------------------------------------------------------- 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 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 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** ** 2 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 142 ASN 4 142 ASN ** 4 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 154 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5178 moved from start: 0.8709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.208 32076 Z= 0.403 Angle : 0.850 13.035 44010 Z= 0.449 Chirality : 0.043 0.314 5058 Planarity : 0.007 0.073 5472 Dihedral : 9.421 59.322 5184 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 27.55 Ramachandran Plot: Outliers : 1.19 % Allowed : 13.26 % Favored : 85.56 % Rotamer Outliers : 3.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.13), residues: 3870 helix: -0.54 (0.12), residues: 1584 sheet: None (None), residues: 0 loop : -2.11 (0.13), residues: 2286 *********************** 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 934 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 820 time to evaluate : 3.450 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 outliers start: 114 outliers final: 71 residues processed: 895 average time/residue: 0.8381 time to fit residues: 1160.6795 Evaluate side-chains 737 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 666 time to evaluate : 3.430 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 15 residues processed: 71 average time/residue: 0.5715 time to fit residues: 77.0081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 9.9990 chunk 258 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 164 optimal weight: 9.9990 chunk 230 optimal weight: 20.0000 chunk 345 optimal weight: 4.9990 chunk 365 optimal weight: 7.9990 chunk 180 optimal weight: 7.9990 chunk 327 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 GLN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 ASN ** A 175 GLN ** 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** ** 2 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 142 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5532 moved from start: 1.0379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.088 32076 Z= 0.263 Angle : 0.686 9.717 44010 Z= 0.354 Chirality : 0.037 0.210 5058 Planarity : 0.006 0.117 5472 Dihedral : 9.373 57.746 5184 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 1.19 % Allowed : 10.70 % Favored : 88.11 % Rotamer Outliers : 1.78 % 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: -1.80 (0.13), residues: 3870 helix: -0.34 (0.12), residues: 1710 sheet: None (None), residues: 0 loop : -1.97 (0.13), residues: 2160 *********************** 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 879 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 825 time to evaluate : 3.492 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 outliers start: 54 outliers final: 35 residues processed: 852 average time/residue: 0.8328 time to fit residues: 1091.6881 Evaluate side-chains 789 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 754 time to evaluate : 3.415 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 10 residues processed: 35 average time/residue: 0.5820 time to fit residues: 40.1837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 272 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 311 optimal weight: 20.0000 chunk 252 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 186 optimal weight: 20.0000 chunk 327 optimal weight: 10.0000 chunk 92 optimal weight: 30.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- 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 ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 142 ASN ** O 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN S 170 ASN A 154 GLN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 115 GLN ** U 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 32 ASN 2 73 ASN ** 2 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 142 ASN 8 32 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5920 moved from start: 1.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.290 32076 Z= 0.295 Angle : 0.693 23.254 44010 Z= 0.357 Chirality : 0.037 0.249 5058 Planarity : 0.006 0.099 5472 Dihedral : 9.424 58.634 5184 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 1.16 % Allowed : 12.48 % Favored : 86.36 % Rotamer Outliers : 2.07 % 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: -1.37 (0.14), residues: 3870 helix: 0.20 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : -1.84 (0.14), residues: 2232 *********************** 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 942 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 879 time to evaluate : 3.456 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 outliers start: 63 outliers final: 47 residues processed: 914 average time/residue: 0.8630 time to fit residues: 1231.1400 Evaluate side-chains 862 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 815 time to evaluate : 3.447 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 12 residues processed: 47 average time/residue: 0.6426 time to fit residues: 56.6252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 5.9990 chunk 329 optimal weight: 20.0000 chunk 72 optimal weight: 9.9990 chunk 214 optimal weight: 20.0000 chunk 90 optimal weight: 0.9990 chunk 365 optimal weight: 8.9990 chunk 303 optimal weight: 2.9990 chunk 169 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 32 ASN E 120 ASN ** I 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 209 ASN Q 32 ASN S 32 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 32 ASN 8 32 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 1.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.113 32076 Z= 0.259 Angle : 0.697 9.958 44010 Z= 0.357 Chirality : 0.038 0.249 5058 Planarity : 0.006 0.085 5472 Dihedral : 9.759 58.935 5184 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 1.19 % Allowed : 9.97 % Favored : 88.84 % Rotamer Outliers : 2.14 % 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: -1.50 (0.14), residues: 3870 helix: 0.37 (0.13), residues: 1620 sheet: None (None), residues: 0 loop : -2.16 (0.13), residues: 2250 *********************** 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 1015 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 950 time to evaluate : 3.643 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 outliers start: 65 outliers final: 42 residues processed: 981 average time/residue: 0.8630 time to fit residues: 1302.8225 Evaluate side-chains 920 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 878 time to evaluate : 3.452 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 10 residues processed: 42 average time/residue: 0.5965 time to fit residues: 48.8231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 chunk 208 optimal weight: 9.9990 chunk 267 optimal weight: 6.9990 chunk 206 optimal weight: 9.9990 chunk 307 optimal weight: 3.9990 chunk 204 optimal weight: 20.0000 chunk 364 optimal weight: 9.9990 chunk 228 optimal weight: 9.9990 chunk 222 optimal weight: 9.9990 chunk 168 optimal weight: 30.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 30 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 ASN ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN ** S 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 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 32 ASN ** Y 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 32 ASN 6 96 GLN 8 32 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 1.5997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.107 32076 Z= 0.362 Angle : 0.810 12.501 44010 Z= 0.427 Chirality : 0.041 0.204 5058 Planarity : 0.007 0.103 5472 Dihedral : 10.521 62.208 5184 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 25.53 Ramachandran Plot: Outliers : 1.27 % Allowed : 13.46 % Favored : 85.27 % Rotamer Outliers : 2.30 % 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: -1.54 (0.14), residues: 3870 helix: 0.47 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -2.17 (0.13), residues: 2358 *********************** 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 1165 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1095 time to evaluate : 3.517 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 outliers start: 70 outliers final: 45 residues processed: 1126 average time/residue: 0.8460 time to fit residues: 1459.8930 Evaluate side-chains 1039 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 994 time to evaluate : 3.540 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 8 residues processed: 45 average time/residue: 0.5857 time to fit residues: 50.6056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 225 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 217 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 231 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 286 optimal weight: 7.9990 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 120 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 GLN I 32 ASN ** I 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 142 ASN ** 4 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 32 ASN 6 154 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 1.7210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.121 32076 Z= 0.317 Angle : 0.752 13.480 44010 Z= 0.392 Chirality : 0.039 0.321 5058 Planarity : 0.007 0.138 5472 Dihedral : 10.611 67.844 5184 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 1.16 % Allowed : 10.62 % Favored : 88.22 % Rotamer Outliers : 1.68 % 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: -1.48 (0.14), residues: 3870 helix: 0.37 (0.13), residues: 1620 sheet: None (None), residues: 0 loop : -2.13 (0.14), residues: 2250 *********************** 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 1154 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1103 time to evaluate : 3.534 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 outliers start: 51 outliers final: 39 residues processed: 1121 average time/residue: 0.8639 time to fit residues: 1481.1571 Evaluate side-chains 1075 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1036 time to evaluate : 3.479 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 6 residues processed: 39 average time/residue: 0.5547 time to fit residues: 43.7649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 331 optimal weight: 7.9990 chunk 349 optimal weight: 9.9990 chunk 318 optimal weight: 9.9990 chunk 339 optimal weight: 0.7980 chunk 348 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 147 optimal weight: 30.0000 chunk 266 optimal weight: 9.9990 chunk 104 optimal weight: 20.0000 chunk 306 optimal weight: 10.0000 chunk 321 optimal weight: 9.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- 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** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 203 GLN ** S 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 32 ASN 8 32 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 1.7937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.266 32076 Z= 0.331 Angle : 0.752 16.311 44010 Z= 0.392 Chirality : 0.038 0.178 5058 Planarity : 0.007 0.108 5472 Dihedral : 10.606 69.406 5184 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 1.11 % Allowed : 12.22 % Favored : 86.67 % Rotamer Outliers : 1.28 % 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: -1.29 (0.14), residues: 3870 helix: 0.58 (0.13), residues: 1620 sheet: None (None), residues: 0 loop : -2.06 (0.14), residues: 2250 *********************** 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 1163 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1124 time to evaluate : 3.541 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 outliers start: 39 outliers final: 31 residues processed: 1137 average time/residue: 0.9041 time to fit residues: 1581.3488 Evaluate side-chains 1115 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1084 time to evaluate : 3.633 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 5 residues processed: 31 average time/residue: 0.6252 time to fit residues: 38.7407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 6.9990 chunk 222 optimal weight: 7.9990 chunk 359 optimal weight: 10.0000 chunk 219 optimal weight: 6.9990 chunk 170 optimal weight: 9.9990 chunk 249 optimal weight: 20.0000 chunk 376 optimal weight: 5.9990 chunk 346 optimal weight: 9.9990 chunk 299 optimal weight: 0.0770 chunk 31 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 overall best weight: 4.4146 ------------------------------------------------------------------------------- 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 120 ASN E 209 ASN Q 203 GLN S 32 ASN ** S 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** 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** ** W 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 1.8486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.372 32076 Z= 0.347 Angle : 0.756 21.425 44010 Z= 0.389 Chirality : 0.038 0.204 5058 Planarity : 0.007 0.092 5472 Dihedral : 10.596 69.225 5184 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 1.09 % Allowed : 11.03 % Favored : 87.88 % Rotamer Outliers : 0.59 % 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: -1.15 (0.14), residues: 3870 helix: 0.70 (0.13), residues: 1620 sheet: None (None), residues: 0 loop : -2.00 (0.14), residues: 2250 ********************** 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 1133 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1115 time to evaluate : 3.657 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 outliers start: 18 outliers final: 12 residues processed: 1122 average time/residue: 0.8568 time to fit residues: 1463.1474 Evaluate side-chains 1096 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1084 time to evaluate : 3.505 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 12 average time/residue: 0.5706 time to fit residues: 16.6347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 183 optimal weight: 7.9990 chunk 238 optimal weight: 20.0000 chunk 319 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 276 optimal weight: 0.1980 chunk 44 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 300 optimal weight: 10.0000 chunk 125 optimal weight: 20.0000 chunk 308 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 overall best weight: 5.4388 ------------------------------------------------------------------------------- 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 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 GLN O 96 GLN S 32 ASN ** S 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 154 GLN 2 203 GLN ** 4 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 147 ASN ** 8 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.171218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.152338 restraints weight = 149495.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.158314 restraints weight = 66731.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.161971 restraints weight = 36636.690| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 1.9127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.517 32076 Z= 0.430 Angle : 0.767 21.788 44010 Z= 0.400 Chirality : 0.038 0.198 5058 Planarity : 0.007 0.096 5472 Dihedral : 10.775 70.777 5184 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 1.06 % Allowed : 12.53 % Favored : 86.41 % Rotamer Outliers : 0.95 % 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: -1.11 (0.14), residues: 3870 helix: 0.74 (0.13), residues: 1620 sheet: None (None), residues: 0 loop : -1.97 (0.14), residues: 2250 =============================================================================== Job complete usr+sys time: 17003.58 seconds wall clock time: 293 minutes 5.75 seconds (17585.75 seconds total)