Starting phenix.real_space_refine on Tue Nov 14 23:57:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn1_3236/11_2023/5fn1_3236.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn1_3236/11_2023/5fn1_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_3236/11_2023/5fn1_3236.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn1_3236/11_2023/5fn1_3236.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn1_3236/11_2023/5fn1_3236.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn1_3236/11_2023/5fn1_3236.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.779 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 90 5.49 5 S 108 5.16 5 C 19476 2.51 5 N 5220 2.21 5 O 6336 1.98 5 H 30078 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 61308 Number of models: 1 Model: "" Number of chains: 36 Chain: "C" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "D" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "E" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "F" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "G" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "H" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "I" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "J" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "K" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "L" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "M" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "N" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "O" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "P" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "Q" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "R" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "S" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "T" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "A" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "B" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "U" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "V" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "W" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "X" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "Y" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "Z" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "0" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "1" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "2" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "3" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "4" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "5" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "6" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "7" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "8" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "9" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Time building chain proxies: 21.07, per 1000 atoms: 0.34 Number of scatterers: 61308 At special positions: 0 Unit cell: (152.32, 152.32, 133.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 108 16.00 P 90 15.00 O 6336 8.00 N 5220 7.00 C 19476 6.00 H 30078 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 41.88 Conformation dependent library (CDL) restraints added in 5.4 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: 19.98 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: 16.57 Time building geometry restraints manager: 43.87 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 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: 0.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.710 Extract box with map and model: 3.510 Check model and map are aligned: 0.710 Set scattering table: 0.450 Process input model: 163.730 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 174.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3004 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.043 32076 Z= 0.553 Angle : 1.180 7.651 44010 Z= 0.771 Chirality : 0.068 0.306 5058 Planarity : 0.005 0.031 5472 Dihedral : 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 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.11), residues: 3870 helix: -2.67 (0.08), residues: 1692 sheet: None (None), residues: 0 loop : -1.85 (0.13), residues: 2178 *********************** 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 : 3.708 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 outliers start: 0 outliers final: 0 residues processed: 707 average time/residue: 0.9070 time to fit residues: 978.6565 Evaluate side-chains 505 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 505 time to evaluate : 3.377 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3087 ------------------------------------------------------------------------------- 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: 20.0000 chunk 114 optimal weight: 8.9990 chunk 180 optimal weight: 0.3980 chunk 220 optimal weight: 7.9990 chunk 343 optimal weight: 20.0000 overall best weight: 5.8788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 209 ASN 6 209 ASN 8 185 ASN 8 209 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3930 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 32076 Z= 0.334 Angle : 0.775 9.535 44010 Z= 0.415 Chirality : 0.040 0.213 5058 Planarity : 0.007 0.073 5472 Dihedral : 8.681 53.652 5184 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 1.65 % Allowed : 10.39 % Favored : 87.96 % Rotamer: Outliers : 1.71 % Allowed : 8.42 % Favored : 89.88 % 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: -1.85 (0.13), residues: 3870 helix: -0.81 (0.11), residues: 1692 sheet: None (None), residues: 0 loop : -1.57 (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 649 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 597 time to evaluate : 4.023 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 outliers start: 52 outliers final: 36 residues processed: 636 average time/residue: 0.9233 time to fit residues: 916.6953 Evaluate side-chains 554 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 518 time to evaluate : 3.467 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 2 residues processed: 36 average time/residue: 0.5886 time to fit residues: 43.4080 ------------------------------------------------------------------------------- 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: 10.0000 chunk 106 optimal weight: 5.9990 chunk 285 optimal weight: 30.0000 chunk 233 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 343 optimal weight: 30.0000 chunk 371 optimal weight: 8.9990 chunk 306 optimal weight: 4.9990 chunk 341 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 275 optimal weight: 20.0000 overall best weight: 3.5186 ------------------------------------------------------------------------------- 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 209 ASN ** K 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 209 ASN W 209 ASN Y 209 ASN ** 0 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4377 moved from start: 0.6130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 32076 Z= 0.240 Angle : 0.639 8.949 44010 Z= 0.326 Chirality : 0.035 0.152 5058 Planarity : 0.005 0.049 5472 Dihedral : 8.368 55.200 5184 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 1.19 % Allowed : 11.24 % Favored : 87.57 % Rotamer: Outliers : 2.33 % Allowed : 11.83 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.13), residues: 3870 helix: -0.13 (0.12), residues: 1638 sheet: None (None), residues: 0 loop : -1.50 (0.14), residues: 2232 *********************** 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 692 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 621 time to evaluate : 3.470 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 outliers start: 71 outliers final: 45 residues processed: 667 average time/residue: 0.9102 time to fit residues: 941.6827 Evaluate side-chains 611 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 566 time to evaluate : 3.455 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 outliers start: 45 outliers final: 11 residues processed: 45 average time/residue: 0.6642 time to fit residues: 55.7391 ------------------------------------------------------------------------------- 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: 5.9990 chunk 258 optimal weight: 20.0000 chunk 178 optimal weight: 0.4980 chunk 38 optimal weight: 9.9990 chunk 164 optimal weight: 9.9990 chunk 230 optimal weight: 9.9990 chunk 345 optimal weight: 10.0000 chunk 365 optimal weight: 0.0970 chunk 180 optimal weight: 4.9990 chunk 327 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 overall best weight: 3.7184 ------------------------------------------------------------------------------- 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** C 209 ASN ** K 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 209 ASN ** 2 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 209 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4918 moved from start: 0.7860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 32076 Z= 0.238 Angle : 0.650 9.905 44010 Z= 0.329 Chirality : 0.036 0.156 5058 Planarity : 0.005 0.085 5472 Dihedral : 8.597 56.290 5184 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 1.21 % Allowed : 10.41 % Favored : 88.37 % Rotamer: Outliers : 2.01 % Allowed : 13.51 % Favored : 84.48 % 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: -1.18 (0.14), residues: 3870 helix: 0.03 (0.13), residues: 1710 sheet: None (None), residues: 0 loop : -1.50 (0.14), 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 771 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 710 time to evaluate : 3.569 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 outliers start: 61 outliers final: 30 residues processed: 751 average time/residue: 0.9152 time to fit residues: 1064.9369 Evaluate side-chains 659 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 629 time to evaluate : 3.518 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 5 residues processed: 30 average time/residue: 0.6758 time to fit residues: 39.3624 ------------------------------------------------------------------------------- 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: 6.9990 chunk 207 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 272 optimal weight: 7.9990 chunk 150 optimal weight: 0.8980 chunk 311 optimal weight: 20.0000 chunk 252 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 186 optimal weight: 20.0000 chunk 327 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- 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 115 GLN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN S 170 ASN A 30 ASN A 32 ASN A 120 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5887 moved from start: 1.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 32076 Z= 0.348 Angle : 0.792 12.312 44010 Z= 0.411 Chirality : 0.041 0.266 5058 Planarity : 0.006 0.103 5472 Dihedral : 9.489 59.757 5184 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 22.49 Ramachandran Plot: Outliers : 1.19 % Allowed : 12.07 % Favored : 86.74 % Rotamer: Outliers : 2.83 % Allowed : 15.29 % Favored : 81.89 % 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: -1.44 (0.14), residues: 3870 helix: -0.06 (0.13), residues: 1620 sheet: None (None), residues: 0 loop : -1.69 (0.14), residues: 2250 *********************** 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 982 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 896 time to evaluate : 3.479 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: 86 outliers final: 52 residues processed: 945 average time/residue: 0.9096 time to fit residues: 1331.6526 Evaluate side-chains 836 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 784 time to evaluate : 3.465 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: 52 outliers final: 6 residues processed: 52 average time/residue: 0.6749 time to fit residues: 65.2113 ------------------------------------------------------------------------------- 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: 2.9990 chunk 329 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 214 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 365 optimal weight: 20.0000 chunk 303 optimal weight: 0.9980 chunk 169 optimal weight: 0.9990 chunk 30 optimal weight: 20.0000 chunk 120 optimal weight: 0.2980 chunk 192 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN E 120 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 154 GLN ** U 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5841 moved from start: 1.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32076 Z= 0.177 Angle : 0.610 7.827 44010 Z= 0.306 Chirality : 0.035 0.175 5058 Planarity : 0.004 0.070 5472 Dihedral : 9.209 57.599 5184 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 1.19 % Allowed : 9.12 % Favored : 89.69 % Rotamer: Outliers : 1.18 % Allowed : 19.56 % Favored : 79.26 % 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: -0.97 (0.14), residues: 3870 helix: 0.39 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : -1.49 (0.14), residues: 2232 *********************** 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 858 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 822 time to evaluate : 3.488 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 outliers start: 36 outliers final: 27 residues processed: 838 average time/residue: 0.8852 time to fit residues: 1135.0407 Evaluate side-chains 808 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 781 time to evaluate : 3.528 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 outliers start: 27 outliers final: 7 residues processed: 27 average time/residue: 0.6098 time to fit residues: 33.3286 ------------------------------------------------------------------------------- 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: 20.0000 chunk 41 optimal weight: 10.0000 chunk 208 optimal weight: 10.0000 chunk 267 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 307 optimal weight: 3.9990 chunk 204 optimal weight: 9.9990 chunk 364 optimal weight: 9.9990 chunk 228 optimal weight: 9.9990 chunk 222 optimal weight: 9.9990 chunk 168 optimal weight: 40.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- 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** ** I 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 32 ASN ** S 32 ASN ** 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 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 154 GLN 2 73 ASN ** 2 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 1.5953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 32076 Z= 0.458 Angle : 0.964 11.195 44010 Z= 0.510 Chirality : 0.048 0.347 5058 Planarity : 0.007 0.110 5472 Dihedral : 11.208 66.377 5184 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 34.53 Ramachandran Plot: Outliers : 1.27 % Allowed : 14.70 % Favored : 84.03 % Rotamer: Outliers : 2.56 % Allowed : 19.86 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.13), residues: 3870 helix: -0.56 (0.12), residues: 1674 sheet: None (None), residues: 0 loop : -2.37 (0.14), residues: 2196 *********************** 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 1234 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1156 time to evaluate : 3.515 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 outliers start: 78 outliers final: 41 residues processed: 1187 average time/residue: 0.9258 time to fit residues: 1681.9930 Evaluate side-chains 1079 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 1038 time to evaluate : 3.559 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 outliers start: 41 outliers final: 7 residues processed: 41 average time/residue: 0.6248 time to fit residues: 49.7859 ------------------------------------------------------------------------------- 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: 3.9990 chunk 145 optimal weight: 10.0000 chunk 217 optimal weight: 8.9990 chunk 109 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 231 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 180 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 286 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** 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 30 ASN G 90 GLN I 32 ASN ** I 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN A 32 ASN ** U 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 32 ASN 6 203 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 1.6912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 32076 Z= 0.260 Angle : 0.698 8.993 44010 Z= 0.355 Chirality : 0.038 0.188 5058 Planarity : 0.005 0.108 5472 Dihedral : 10.562 65.688 5184 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 1.11 % Allowed : 10.16 % Favored : 88.73 % Rotamer: Outliers : 1.41 % Allowed : 24.62 % Favored : 73.96 % 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: -1.47 (0.14), residues: 3870 helix: 0.36 (0.13), residues: 1548 sheet: None (None), residues: 0 loop : -2.04 (0.14), residues: 2322 *********************** 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 1155 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1112 time to evaluate : 3.558 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 outliers start: 43 outliers final: 26 residues processed: 1128 average time/residue: 0.8876 time to fit residues: 1530.6768 Evaluate side-chains 1067 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1041 time to evaluate : 3.565 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 26 outliers final: 1 residues processed: 26 average time/residue: 0.5682 time to fit residues: 31.1080 ------------------------------------------------------------------------------- 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: 10.0000 chunk 349 optimal weight: 8.9990 chunk 318 optimal weight: 10.0000 chunk 339 optimal weight: 0.6980 chunk 348 optimal weight: 9.9990 chunk 204 optimal weight: 10.0000 chunk 147 optimal weight: 40.0000 chunk 266 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 306 optimal weight: 9.9990 chunk 321 optimal weight: 9.9990 overall best weight: 7.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 ASN ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 32 ASN U 115 GLN ** 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** ** 0 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 1.8464 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= 0.344 Angle : 0.787 14.199 44010 Z= 0.410 Chirality : 0.041 0.202 5058 Planarity : 0.006 0.113 5472 Dihedral : 11.062 68.694 5184 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 25.38 Ramachandran Plot: Outliers : 1.14 % Allowed : 14.19 % Favored : 84.68 % Rotamer: Outliers : 1.41 % Allowed : 27.12 % Favored : 71.47 % 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: 0.45 (0.13), residues: 1548 sheet: None (None), residues: 0 loop : -2.14 (0.14), residues: 2322 *********************** 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 1243 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1200 time to evaluate : 3.570 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 outliers start: 43 outliers final: 25 residues processed: 1213 average time/residue: 0.9656 time to fit residues: 1781.8053 Evaluate side-chains 1147 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1122 time to evaluate : 3.532 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 25 outliers final: 1 residues processed: 25 average time/residue: 0.5729 time to fit residues: 31.1303 ------------------------------------------------------------------------------- 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: 5.9990 chunk 222 optimal weight: 0.8980 chunk 359 optimal weight: 9.9990 chunk 219 optimal weight: 9.9990 chunk 170 optimal weight: 0.0770 chunk 249 optimal weight: 10.0000 chunk 376 optimal weight: 0.0170 chunk 346 optimal weight: 1.9990 chunk 299 optimal weight: 20.0000 chunk 31 optimal weight: 0.8980 chunk 231 optimal weight: 10.0000 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 30 ASN E 32 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 142 ASN M 203 GLN S 115 GLN S 142 ASN U 32 ASN ** U 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 154 GLN 2 203 GLN 4 32 ASN 8 32 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 1.8634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32076 Z= 0.199 Angle : 0.681 11.739 44010 Z= 0.343 Chirality : 0.036 0.176 5058 Planarity : 0.005 0.082 5472 Dihedral : 10.684 68.364 5184 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 1.09 % Allowed : 9.79 % Favored : 89.12 % Rotamer: Outliers : 0.56 % Allowed : 29.26 % Favored : 70.18 % 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: -1.08 (0.14), residues: 3870 helix: 0.74 (0.13), residues: 1548 sheet: None (None), residues: 0 loop : -1.86 (0.14), residues: 2322 ********************** 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 1143 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 1126 time to evaluate : 3.547 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 outliers start: 17 outliers final: 13 residues processed: 1132 average time/residue: 0.9060 time to fit residues: 1551.8863 Evaluate side-chains 1089 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1076 time to evaluate : 3.554 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 2 residues processed: 13 average time/residue: 0.5870 time to fit residues: 17.8017 ------------------------------------------------------------------------------- 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: 5.9990 chunk 238 optimal weight: 20.0000 chunk 319 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 276 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 300 optimal weight: 10.0000 chunk 125 optimal weight: 20.0000 chunk 308 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 overall best weight: 7.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 125 GLN Q 147 ASN ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 203 GLN ** 6 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 32 ASN ** 8 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.173141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.153803 restraints weight = 149264.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.159947 restraints weight = 64429.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.163519 restraints weight = 34740.115| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 1.9497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 32076 Z= 0.315 Angle : 0.745 10.026 44010 Z= 0.386 Chirality : 0.040 0.168 5058 Planarity : 0.006 0.085 5472 Dihedral : 11.036 69.077 5184 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 24.11 Ramachandran Plot: Outliers : 1.03 % Allowed : 13.26 % Favored : 85.71 % Rotamer: Outliers : 0.95 % Allowed : 29.55 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.14), residues: 3870 helix: 0.45 (0.13), residues: 1656 sheet: None (None), residues: 0 loop : -2.04 (0.14), residues: 2214 =============================================================================== Job complete usr+sys time: 17657.75 seconds wall clock time: 304 minutes 57.11 seconds (18297.11 seconds total)