Starting phenix.real_space_refine on Mon Nov 18 05:57:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3o_36854/11_2024/8k3o_36854.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3o_36854/11_2024/8k3o_36854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3o_36854/11_2024/8k3o_36854.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3o_36854/11_2024/8k3o_36854.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3o_36854/11_2024/8k3o_36854.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3o_36854/11_2024/8k3o_36854.cif" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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: 5 Type Number sf(0) Gaussians P 1432 5.49 5 S 66 5.16 5 C 25310 2.51 5 N 9192 2.21 5 O 13261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 49261 Number of models: 1 Model: "" Number of chains: 22 Chain: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "G" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1163 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 5, 'TRANS': 143} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "K" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 869 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "L" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "M" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 747 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "O" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 708 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'TRANS': 86} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 545 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "S" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "T" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 664 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "V" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 125 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pyr': 1} Link IDs: {'rna2p': 4, 'rna3p': 1} Chain: "X" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "A" Number of atoms: 30600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1426, 30600 Classifications: {'RNA': 1426} Modifications used: {'rna2p_pur': 114, 'rna2p_pyr': 87, 'rna3p_pur': 699, 'rna3p_pyr': 526} Link IDs: {'rna2p': 201, 'rna3p': 1224} Chain breaks: 1 Chain: "N" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Time building chain proxies: 26.88, per 1000 atoms: 0.55 Number of scatterers: 49261 At special positions: 0 Unit cell: (202.86, 171.12, 234.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 1432 15.00 O 13261 8.00 N 9192 7.00 C 25310 6.00 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 - 3.00 Amino acid : True - 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: 11.55 Conformation dependent library (CDL) restraints added in 3.5 seconds 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4364 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 20 sheets defined 44.5% alpha, 16.8% beta 422 base pairs and 699 stacking pairs defined. Time for finding SS restraints: 24.18 Creating SS restraints... Processing helix chain 'B' and resid 9 through 14 removed outlier: 3.778A pdb=" N VAL B 13 " --> pdb=" O LYS B 10 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS B 14 " --> pdb=" O ALA B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 28 removed outlier: 3.682A pdb=" N MET B 26 " --> pdb=" O ASN B 23 " (cutoff:3.500A) Proline residue: B 28 - end of helix Processing helix chain 'B' and resid 44 through 61 removed outlier: 3.935A pdb=" N MET B 48 " --> pdb=" O LYS B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 76 Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'B' and resid 102 through 122 removed outlier: 3.687A pdb=" N VAL B 106 " --> pdb=" O ASN B 102 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 148 removed outlier: 3.863A pdb=" N ALA B 133 " --> pdb=" O THR B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 179 Processing helix chain 'B' and resid 205 through 223 removed outlier: 3.682A pdb=" N THR B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B 220 " --> pdb=" O VAL B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 10 removed outlier: 3.523A pdb=" N ILE C 9 " --> pdb=" O HIS C 5 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG C 10 " --> pdb=" O PRO C 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 5 through 10' Processing helix chain 'C' and resid 24 through 45 removed outlier: 4.754A pdb=" N ALA C 29 " --> pdb=" O THR C 25 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR C 41 " --> pdb=" O LYS C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 49 Processing helix chain 'C' and resid 72 through 77 Processing helix chain 'C' and resid 78 through 80 No H-bonds generated for 'chain 'C' and resid 78 through 80' Processing helix chain 'C' and resid 81 through 94 removed outlier: 3.614A pdb=" N LYS C 85 " --> pdb=" O GLU C 81 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL C 89 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA C 94 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 110 Processing helix chain 'C' and resid 111 through 124 Processing helix chain 'C' and resid 128 through 144 removed outlier: 3.715A pdb=" N GLY C 144 " --> pdb=" O ALA C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 180 removed outlier: 3.833A pdb=" N ASP C 180 " --> pdb=" O LEU C 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 removed outlier: 3.900A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 Processing helix chain 'D' and resid 49 through 66 removed outlier: 3.556A pdb=" N GLU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 82 removed outlier: 3.866A pdb=" N LEU D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 95 removed outlier: 3.615A pdb=" N LEU D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 106 Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 147 through 150 removed outlier: 3.547A pdb=" N LYS D 150 " --> pdb=" O GLU D 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 147 through 150' Processing helix chain 'D' and resid 152 through 162 removed outlier: 4.330A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 191 Processing helix chain 'D' and resid 197 through 205 removed outlier: 3.705A pdb=" N VAL D 201 " --> pdb=" O GLU D 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 Processing helix chain 'E' and resid 108 through 119 removed outlier: 3.599A pdb=" N ARG E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 146 removed outlier: 4.418A pdb=" N ARG E 138 " --> pdb=" O ILE E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 160 through 165 removed outlier: 3.645A pdb=" N ILE E 164 " --> pdb=" O SER E 160 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU E 165 " --> pdb=" O VAL E 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 160 through 165' Processing helix chain 'F' and resid 12 through 16 removed outlier: 4.550A pdb=" N GLU F 16 " --> pdb=" O ASP F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 31 Processing helix chain 'F' and resid 67 through 81 Processing helix chain 'F' and resid 100 through 104 Processing helix chain 'G' and resid 22 through 30 Processing helix chain 'G' and resid 34 through 54 Processing helix chain 'G' and resid 56 through 66 removed outlier: 5.371A pdb=" N GLU G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL G 63 " --> pdb=" O GLU G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 69 No H-bonds generated for 'chain 'G' and resid 67 through 69' Processing helix chain 'G' and resid 91 through 109 removed outlier: 3.830A pdb=" N ASN G 96 " --> pdb=" O PRO G 92 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ALA G 97 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU G 98 " --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA G 99 " --> pdb=" O ARG G 95 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET G 100 " --> pdb=" O ASN G 96 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG G 101 " --> pdb=" O ALA G 97 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS G 109 " --> pdb=" O GLU G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 129 Processing helix chain 'G' and resid 131 through 139 removed outlier: 3.601A pdb=" N LYS G 136 " --> pdb=" O THR G 132 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ARG G 137 " --> pdb=" O ALA G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 143 Processing helix chain 'G' and resid 147 through 151 removed outlier: 3.855A pdb=" N PHE G 150 " --> pdb=" O ASN G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 20 removed outlier: 3.839A pdb=" N ASP H 9 " --> pdb=" O ASP H 5 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET H 10 " --> pdb=" O PRO H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 43 Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.802A pdb=" N LEU H 92 " --> pdb=" O LYS H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 99 removed outlier: 3.893A pdb=" N ALA H 97 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 120 removed outlier: 3.782A pdb=" N GLN H 118 " --> pdb=" O ARG H 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 37 No H-bonds generated for 'chain 'I' and resid 35 through 37' Processing helix chain 'I' and resid 43 through 47 removed outlier: 3.536A pdb=" N VAL I 47 " --> pdb=" O ARG I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 54 Processing helix chain 'I' and resid 70 through 90 removed outlier: 3.648A pdb=" N GLU I 88 " --> pdb=" O ARG I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 99 removed outlier: 4.430A pdb=" N LYS I 99 " --> pdb=" O SER I 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 30 removed outlier: 3.502A pdb=" N ILE J 18 " --> pdb=" O ASP J 14 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL J 26 " --> pdb=" O THR J 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 59 removed outlier: 3.777A pdb=" N SER K 58 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR K 59 " --> pdb=" O SER K 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 54 through 59' Processing helix chain 'K' and resid 59 through 70 removed outlier: 4.178A pdb=" N ALA K 63 " --> pdb=" O THR K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 75 Processing helix chain 'K' and resid 76 through 78 No H-bonds generated for 'chain 'K' and resid 76 through 78' Processing helix chain 'K' and resid 92 through 94 No H-bonds generated for 'chain 'K' and resid 92 through 94' Processing helix chain 'K' and resid 95 through 103 removed outlier: 3.882A pdb=" N ALA K 99 " --> pdb=" O SER K 95 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU K 100 " --> pdb=" O THR K 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 21 through 25 Processing helix chain 'L' and resid 113 through 117 removed outlier: 3.691A pdb=" N LYS L 116 " --> pdb=" O ALA L 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 20 Processing helix chain 'M' and resid 25 through 37 removed outlier: 3.554A pdb=" N LEU M 33 " --> pdb=" O SER M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 60 removed outlier: 4.595A pdb=" N THR M 54 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU M 55 " --> pdb=" O GLN M 51 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG M 56 " --> pdb=" O ILE M 52 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP M 57 " --> pdb=" O ASP M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 82 removed outlier: 4.149A pdb=" N LEU M 82 " --> pdb=" O ARG M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 92 removed outlier: 3.880A pdb=" N ARG M 92 " --> pdb=" O LEU M 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 16 removed outlier: 4.036A pdb=" N SER O 13 " --> pdb=" O ALA O 9 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU O 14 " --> pdb=" O LYS O 10 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE O 15 " --> pdb=" O ILE O 11 " (cutoff:3.500A) Processing helix chain 'O' and resid 24 through 44 removed outlier: 4.825A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE O 43 " --> pdb=" O LEU O 39 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA O 44 " --> pdb=" O GLN O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 74 removed outlier: 4.075A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG O 72 " --> pdb=" O ASP O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'P' and resid 53 through 64 Processing helix chain 'P' and resid 68 through 81 Processing helix chain 'R' and resid 12 through 17 Processing helix chain 'R' and resid 26 through 31 removed outlier: 3.887A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 removed outlier: 3.865A pdb=" N THR R 45 " --> pdb=" O PRO R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 65 removed outlier: 3.727A pdb=" N LEU R 65 " --> pdb=" O ARG R 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 11 through 24 removed outlier: 4.448A pdb=" N LYS S 17 " --> pdb=" O HIS S 13 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 44 removed outlier: 4.021A pdb=" N ILE S 44 " --> pdb=" O PRO S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 68 removed outlier: 4.286A pdb=" N VAL S 66 " --> pdb=" O ASP S 63 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY S 67 " --> pdb=" O GLU S 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 74 removed outlier: 3.567A pdb=" N PHE S 73 " --> pdb=" O LEU S 70 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 42 removed outlier: 3.716A pdb=" N ILE T 12 " --> pdb=" O LYS T 8 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG T 24 " --> pdb=" O HIS T 20 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 65 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 86 removed outlier: 3.681A pdb=" N ALA T 72 " --> pdb=" O HIS T 68 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU T 86 " --> pdb=" O GLN T 82 " (cutoff:3.500A) Processing helix chain 'X' and resid 18 through 23 removed outlier: 3.768A pdb=" N CYS X 22 " --> pdb=" O PHE X 18 " (cutoff:3.500A) Processing helix chain 'X' and resid 39 through 50 removed outlier: 4.209A pdb=" N GLU X 43 " --> pdb=" O LYS X 39 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG X 46 " --> pdb=" O THR X 42 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA X 47 " --> pdb=" O GLU X 43 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS X 48 " --> pdb=" O ARG X 44 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER X 50 " --> pdb=" O ARG X 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 17 removed outlier: 3.792A pdb=" N GLU N 9 " --> pdb=" O MET N 5 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL N 10 " --> pdb=" O LYS N 6 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU N 15 " --> pdb=" O LYS N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 30 removed outlier: 4.493A pdb=" N LEU N 26 " --> pdb=" O LYS N 22 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS N 27 " --> pdb=" O ARG N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 49 removed outlier: 3.750A pdb=" N GLN N 48 " --> pdb=" O VAL N 44 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR N 49 " --> pdb=" O LEU N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 90 Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 34 removed outlier: 3.581A pdb=" N GLY B 32 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 89 through 91 removed outlier: 6.324A pdb=" N ILE B 66 " --> pdb=" O PHE B 89 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N VAL B 91 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE B 68 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B 67 " --> pdb=" O PHE B 161 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 185 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL B 182 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ILE B 199 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA B 184 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 19 through 20 removed outlier: 3.608A pdb=" N THR C 20 " --> pdb=" O ILE C 56 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C 53 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE C 63 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N ASN C 101 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL C 65 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ALA C 103 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE C 67 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 147 through 152 removed outlier: 3.733A pdb=" N GLY C 147 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN C 184 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 128 through 130 removed outlier: 4.770A pdb=" N ILE D 123 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 12 through 22 removed outlier: 6.909A pdb=" N LEU E 36 " --> pdb=" O ILE E 16 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL E 18 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR E 34 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG E 20 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N SER E 32 " --> pdb=" O ARG E 20 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 85 through 89 removed outlier: 6.587A pdb=" N ILE E 106 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ALA E 127 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 35 through 51 removed outlier: 6.431A pdb=" N ASN F 63 " --> pdb=" O HIS F 37 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU F 39 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU F 61 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ASP F 41 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N TYR F 59 " --> pdb=" O ASP F 41 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLY F 43 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA F 57 " --> pdb=" O GLY F 43 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ARG F 45 " --> pdb=" O HIS F 55 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N HIS F 55 " --> pdb=" O ARG F 45 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG F 2 " --> pdb=" O ALA F 66 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLU F 5 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL F 89 " --> pdb=" O GLU F 5 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL F 7 " --> pdb=" O SER F 87 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N SER F 87 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N MET F 9 " --> pdb=" O ILE F 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 24 through 28 removed outlier: 4.467A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 65 through 66 Processing sheet with id=AB2, first strand: chain 'H' and resid 74 through 77 removed outlier: 3.913A pdb=" N GLN H 76 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 74 through 77 removed outlier: 3.913A pdb=" N GLN H 76 " --> pdb=" O TYR H 128 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 5 through 9 removed outlier: 3.613A pdb=" N GLY I 7 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL I 18 " --> pdb=" O GLY I 7 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY I 9 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR I 63 " --> pdb=" O PHE I 19 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL I 28 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N VAL I 66 " --> pdb=" O VAL I 28 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 72 through 73 removed outlier: 3.552A pdb=" N LEU J 10 " --> pdb=" O ARG J 72 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS J 11 " --> pdb=" O ASP J 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 45 through 49 Processing sheet with id=AB7, first strand: chain 'K' and resid 41 through 46 removed outlier: 4.032A pdb=" N GLY K 43 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL K 84 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE K 110 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL K 86 " --> pdb=" O ILE K 110 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASP K 112 " --> pdb=" O VAL K 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 30 through 40 removed outlier: 6.372A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR L 39 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG L 50 " --> pdb=" O THR L 39 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LYS L 51 " --> pdb=" O ILE L 67 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYR L 95 " --> pdb=" O THR L 64 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N HIS L 96 " --> pdb=" O ARG L 83 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 50 through 52 removed outlier: 3.562A pdb=" N ARG P 51 " --> pdb=" O PHE P 38 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL P 2 " --> pdb=" O THR P 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Q' and resid 7 through 17 removed outlier: 16.576A pdb=" N THR Q 7 " --> pdb=" O PHE Q 28 " (cutoff:3.500A) removed outlier: 12.928A pdb=" N PHE Q 28 " --> pdb=" O THR Q 7 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLN Q 9 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLU Q 26 " --> pdb=" O GLN Q 9 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASP Q 15 " --> pdb=" O SER Q 20 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N SER Q 20 " --> pdb=" O ASP Q 15 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TRP Q 73 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU Q 75 " --> pdb=" O HIS Q 47 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N VAL Q 78 " --> pdb=" O VAL Q 58 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL Q 58 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'S' and resid 30 through 32 removed outlier: 5.970A pdb=" N LEU S 30 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N HIS S 51 " --> pdb=" O LEU S 30 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N THR S 32 " --> pdb=" O HIS S 51 " (cutoff:3.500A) 777 hydrogen bonds defined for protein. 2172 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1075 hydrogen bonds 1756 hydrogen bond angles 0 basepair planarities 422 basepair parallelities 699 stacking parallelities Total time for adding SS restraints: 46.50 Time building geometry restraints manager: 13.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7874 1.33 - 1.45: 21447 1.45 - 1.58: 20904 1.58 - 1.70: 2862 1.70 - 1.82: 117 Bond restraints: 53204 Sorted by residual: bond pdb=" CG PRO B 200 " pdb=" CD PRO B 200 " ideal model delta sigma weight residual 1.503 1.262 0.241 3.40e-02 8.65e+02 5.03e+01 bond pdb=" N LYS L 44 " pdb=" CA LYS L 44 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.41e-02 5.03e+03 9.16e+00 bond pdb=" N LYS L 43 " pdb=" CA LYS L 43 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.27e-02 6.20e+03 6.40e+00 bond pdb=" C LYS X 39 " pdb=" O LYS X 39 " ideal model delta sigma weight residual 1.235 1.224 0.011 4.70e-03 4.53e+04 5.81e+00 bond pdb=" CA ASP D 174 " pdb=" CB ASP D 174 " ideal model delta sigma weight residual 1.525 1.559 -0.034 1.47e-02 4.63e+03 5.37e+00 ... (remaining 53199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 78383 3.36 - 6.71: 443 6.71 - 10.07: 63 10.07 - 13.42: 9 13.42 - 16.78: 1 Bond angle restraints: 78899 Sorted by residual: angle pdb=" N PRO B 200 " pdb=" CD PRO B 200 " pdb=" CG PRO B 200 " ideal model delta sigma weight residual 103.20 86.42 16.78 1.50e+00 4.44e-01 1.25e+02 angle pdb=" N VAL X 13 " pdb=" CA VAL X 13 " pdb=" C VAL X 13 " ideal model delta sigma weight residual 111.91 104.44 7.47 8.90e-01 1.26e+00 7.05e+01 angle pdb=" CA PRO B 200 " pdb=" CB PRO B 200 " pdb=" CG PRO B 200 " ideal model delta sigma weight residual 104.50 91.92 12.58 1.90e+00 2.77e-01 4.38e+01 angle pdb=" N PRO L 45 " pdb=" CA PRO L 45 " pdb=" C PRO L 45 " ideal model delta sigma weight residual 113.81 104.51 9.30 1.45e+00 4.76e-01 4.12e+01 angle pdb=" CA PRO B 200 " pdb=" N PRO B 200 " pdb=" CD PRO B 200 " ideal model delta sigma weight residual 112.00 103.40 8.60 1.40e+00 5.10e-01 3.77e+01 ... (remaining 78894 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 30366 35.97 - 71.95: 3264 71.95 - 107.92: 392 107.92 - 143.89: 13 143.89 - 179.87: 13 Dihedral angle restraints: 34048 sinusoidal: 27301 harmonic: 6747 Sorted by residual: dihedral pdb=" O4' U A 439 " pdb=" C1' U A 439 " pdb=" N1 U A 439 " pdb=" C2 U A 439 " ideal model delta sinusoidal sigma weight residual 200.00 32.96 167.04 1 1.50e+01 4.44e-03 8.42e+01 dihedral pdb=" O4' U A 467 " pdb=" C1' U A 467 " pdb=" N1 U A 467 " pdb=" C2 U A 467 " ideal model delta sinusoidal sigma weight residual 200.00 47.00 153.00 1 1.50e+01 4.44e-03 8.07e+01 dihedral pdb=" O4' U A 4 " pdb=" C1' U A 4 " pdb=" N1 U A 4 " pdb=" C2 U A 4 " ideal model delta sinusoidal sigma weight residual 200.00 49.57 150.43 1 1.50e+01 4.44e-03 7.98e+01 ... (remaining 34045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 8809 0.055 - 0.109: 967 0.109 - 0.164: 173 0.164 - 0.218: 31 0.218 - 0.273: 4 Chirality restraints: 9984 Sorted by residual: chirality pdb=" C1' C A1303 " pdb=" O4' C A1303 " pdb=" C2' C A1303 " pdb=" N1 C A1303 " both_signs ideal model delta sigma weight residual False 2.47 2.19 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CG LEU O 32 " pdb=" CB LEU O 32 " pdb=" CD1 LEU O 32 " pdb=" CD2 LEU O 32 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB THR F 76 " pdb=" CA THR F 76 " pdb=" OG1 THR F 76 " pdb=" CG2 THR F 76 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 9981 not shown) Planarity restraints: 4693 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS L 44 " -0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C LYS L 44 " 0.072 2.00e-02 2.50e+03 pdb=" O LYS L 44 " -0.025 2.00e-02 2.50e+03 pdb=" N PRO L 45 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 79 " -0.318 9.50e-02 1.11e+02 1.43e-01 1.41e+01 pdb=" NE ARG I 79 " 0.026 2.00e-02 2.50e+03 pdb=" CZ ARG I 79 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG I 79 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG I 79 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP L 109 " 0.019 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" CG ASP L 109 " -0.065 2.00e-02 2.50e+03 pdb=" OD1 ASP L 109 " 0.024 2.00e-02 2.50e+03 pdb=" OD2 ASP L 109 " 0.022 2.00e-02 2.50e+03 ... (remaining 4690 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 1032 2.62 - 3.19: 40718 3.19 - 3.76: 93156 3.76 - 4.33: 118926 4.33 - 4.90: 167230 Nonbonded interactions: 421062 Sorted by model distance: nonbonded pdb=" OD1 ASN E 43 " pdb=" N GLY E 44 " model vdw 2.054 3.120 nonbonded pdb=" OP2 G A 976 " pdb=" O2' U A1358 " model vdw 2.081 3.040 nonbonded pdb=" O ARG S 36 " pdb=" NZ LYS S 69 " model vdw 2.086 3.120 nonbonded pdb=" OD1 ASP R 25 " pdb=" OG1 THR R 28 " model vdw 2.087 3.040 nonbonded pdb=" OG1 THR E 80 " pdb=" OD1 ASN E 122 " model vdw 2.095 3.040 ... (remaining 421057 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.810 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: 0.040 Extract box with map and model: 1.970 Check model and map are aligned: 0.390 Set scattering table: 0.500 Process input model: 139.980 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 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 : 0.003 0.241 53204 Z= 0.189 Angle : 0.712 16.777 78899 Z= 0.372 Chirality : 0.037 0.273 9984 Planarity : 0.006 0.143 4693 Dihedral : 22.924 179.868 29684 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.19 % Favored : 93.68 % Rotamer: Outliers : 1.13 % Allowed : 30.18 % Favored : 68.69 % 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: -1.14 (0.17), residues: 2311 helix: -0.42 (0.17), residues: 868 sheet: -0.36 (0.26), residues: 379 loop : -1.08 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP K 44 HIS 0.012 0.001 HIS G 141 PHE 0.030 0.002 PHE N 72 TYR 0.029 0.002 TYR D 75 ARG 0.022 0.001 ARG I 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 415 time to evaluate : 3.158 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: B 26 MET cc_start: 0.4036 (ptm) cc_final: 0.3245 (ppp) REVERT: B 57 ASN cc_start: 0.7818 (m110) cc_final: 0.7593 (m110) REVERT: B 89 PHE cc_start: 0.5242 (m-80) cc_final: 0.4482 (m-80) REVERT: B 141 GLU cc_start: 0.7590 (tp30) cc_final: 0.7356 (tp30) REVERT: B 144 GLU cc_start: 0.6445 (mm-30) cc_final: 0.6110 (pp20) REVERT: C 2 GLN cc_start: 0.8078 (pm20) cc_final: 0.7759 (mm-40) REVERT: C 28 PHE cc_start: 0.8166 (t80) cc_final: 0.7735 (m-80) REVERT: C 30 ASP cc_start: 0.9208 (t0) cc_final: 0.8938 (p0) REVERT: C 35 ASP cc_start: 0.5734 (m-30) cc_final: 0.5455 (m-30) REVERT: D 70 ARG cc_start: 0.8313 (mtp85) cc_final: 0.8034 (mmm-85) REVERT: D 75 TYR cc_start: 0.7586 (m-10) cc_final: 0.7188 (m-80) REVERT: D 88 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8253 (tm-30) REVERT: E 20 ARG cc_start: 0.8850 (tmm-80) cc_final: 0.8545 (tmm-80) REVERT: E 31 PHE cc_start: 0.7812 (m-10) cc_final: 0.7507 (m-10) REVERT: E 64 MET cc_start: 0.8320 (tmm) cc_final: 0.7837 (tmm) REVERT: E 100 SER cc_start: 0.8988 (t) cc_final: 0.8771 (p) REVERT: F 17 GLN cc_start: 0.8176 (pp30) cc_final: 0.7610 (pm20) REVERT: F 90 MET cc_start: 0.8628 (mtm) cc_final: 0.8204 (mmm) REVERT: F 91 ARG cc_start: 0.7887 (ttm-80) cc_final: 0.7568 (mtt180) REVERT: G 102 TRP cc_start: 0.6750 (m-10) cc_final: 0.6302 (m-10) REVERT: H 42 GLU cc_start: 0.8135 (tp30) cc_final: 0.7811 (tm-30) REVERT: H 43 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8516 (mm-30) REVERT: H 89 LYS cc_start: 0.6765 (ptpp) cc_final: 0.6551 (pttm) REVERT: H 111 MET cc_start: 0.8087 (pmm) cc_final: 0.7443 (pmm) REVERT: H 113 ASP cc_start: 0.8188 (p0) cc_final: 0.7627 (p0) REVERT: H 125 ILE cc_start: 0.8826 (pt) cc_final: 0.8402 (mt) REVERT: I 38 PHE cc_start: 0.6749 (m-10) cc_final: 0.5750 (m-10) REVERT: I 56 MET cc_start: 0.3222 (ttt) cc_final: 0.2778 (tmm) REVERT: I 126 PHE cc_start: 0.5951 (t80) cc_final: 0.5683 (t80) REVERT: J 68 ARG cc_start: 0.6507 (mmt180) cc_final: 0.6038 (mmt180) REVERT: K 40 ASN cc_start: 0.4876 (t0) cc_final: 0.4302 (t0) REVERT: L 56 ARG cc_start: 0.8369 (tmm-80) cc_final: 0.8116 (tmm-80) REVERT: L 57 LEU cc_start: 0.8314 (mt) cc_final: 0.6966 (mp) REVERT: L 70 GLU cc_start: 0.6211 (pm20) cc_final: 0.5920 (pm20) REVERT: M 55 LEU cc_start: 0.6846 (tp) cc_final: 0.6435 (mm) REVERT: M 70 ARG cc_start: 0.8194 (ppt170) cc_final: 0.7577 (ppt170) REVERT: O 10 LYS cc_start: 0.8693 (ptmm) cc_final: 0.8312 (pptt) REVERT: Q 49 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6987 (pm20) REVERT: R 19 GLN cc_start: 0.7885 (mt0) cc_final: 0.7468 (mp10) REVERT: R 33 ILE cc_start: 0.8561 (mm) cc_final: 0.8319 (tp) REVERT: S 9 PHE cc_start: 0.1786 (t80) cc_final: 0.1293 (m-10) REVERT: T 78 ASN cc_start: 0.8199 (m-40) cc_final: 0.7510 (t0) REVERT: N 32 ASP cc_start: 0.4709 (m-30) cc_final: 0.4147 (t0) REVERT: N 88 MET cc_start: 0.7041 (mmp) cc_final: 0.6265 (mmm) outliers start: 22 outliers final: 11 residues processed: 426 average time/residue: 0.6853 time to fit residues: 462.5682 Evaluate side-chains 363 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 351 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 49 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 309 optimal weight: 30.0000 chunk 277 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 chunk 94 optimal weight: 40.0000 chunk 187 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 286 optimal weight: 9.9990 chunk 111 optimal weight: 0.0470 chunk 174 optimal weight: 0.9990 chunk 213 optimal weight: 0.9980 chunk 332 optimal weight: 30.0000 overall best weight: 4.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN B 119 GLN C 18 ASN E 122 ASN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 GLN K 22 HIS ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 HIS L 96 HIS O 38 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 53204 Z= 0.279 Angle : 0.742 11.642 78899 Z= 0.378 Chirality : 0.040 0.298 9984 Planarity : 0.006 0.091 4693 Dihedral : 23.446 178.509 25027 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.40 % Favored : 93.42 % Rotamer: Outliers : 6.16 % Allowed : 23.46 % Favored : 70.38 % 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: -1.00 (0.17), residues: 2311 helix: -0.21 (0.17), residues: 852 sheet: -0.39 (0.25), residues: 391 loop : -1.05 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP K 44 HIS 0.007 0.002 HIS Q 47 PHE 0.028 0.003 PHE F 80 TYR 0.030 0.002 TYR D 75 ARG 0.043 0.001 ARG I 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 394 time to evaluate : 3.068 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: B 8 MET cc_start: 0.6889 (mmm) cc_final: 0.6045 (ppp) REVERT: B 174 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7435 (tp30) REVERT: B 197 PHE cc_start: 0.7862 (m-80) cc_final: 0.7083 (m-80) REVERT: B 202 ASN cc_start: 0.6853 (t0) cc_final: 0.6200 (t0) REVERT: C 30 ASP cc_start: 0.9330 (t0) cc_final: 0.8985 (p0) REVERT: C 131 ARG cc_start: 0.5282 (ptt180) cc_final: 0.4985 (ptt180) REVERT: D 70 ARG cc_start: 0.8499 (mtp85) cc_final: 0.7865 (mmm-85) REVERT: D 75 TYR cc_start: 0.8130 (m-80) cc_final: 0.7667 (m-80) REVERT: D 88 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8315 (tm-30) REVERT: D 124 MET cc_start: 0.7979 (mtp) cc_final: 0.7679 (ttm) REVERT: E 37 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8304 (p) REVERT: E 64 MET cc_start: 0.8594 (tmm) cc_final: 0.8155 (tmm) REVERT: E 100 SER cc_start: 0.9126 (t) cc_final: 0.8784 (p) REVERT: E 120 VAL cc_start: 0.7205 (OUTLIER) cc_final: 0.6761 (p) REVERT: E 147 MET cc_start: 0.7942 (ttt) cc_final: 0.7721 (ttt) REVERT: F 5 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8166 (tm-30) REVERT: F 14 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8215 (tm-30) REVERT: F 65 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6092 (pp20) REVERT: F 88 MET cc_start: 0.8748 (tpp) cc_final: 0.8313 (tmm) REVERT: G 102 TRP cc_start: 0.6823 (m-10) cc_final: 0.6533 (m-10) REVERT: G 135 LYS cc_start: 0.7403 (ttmt) cc_final: 0.7019 (mmmt) REVERT: H 3 MET cc_start: 0.8026 (tpt) cc_final: 0.7462 (tpt) REVERT: H 5 ASP cc_start: 0.7942 (p0) cc_final: 0.7691 (p0) REVERT: H 43 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8488 (mm-30) REVERT: H 66 PHE cc_start: 0.8446 (t80) cc_final: 0.8075 (t80) REVERT: H 72 VAL cc_start: 0.7069 (OUTLIER) cc_final: 0.6689 (p) REVERT: H 111 MET cc_start: 0.8014 (pmm) cc_final: 0.7235 (pmm) REVERT: H 113 ASP cc_start: 0.8469 (p0) cc_final: 0.8078 (p0) REVERT: H 125 ILE cc_start: 0.8913 (pt) cc_final: 0.8565 (mt) REVERT: I 91 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7214 (pm20) REVERT: J 28 THR cc_start: 0.7997 (p) cc_final: 0.7673 (t) REVERT: K 40 ASN cc_start: 0.5779 (m-40) cc_final: 0.5302 (t0) REVERT: L 25 GLU cc_start: 0.8920 (pt0) cc_final: 0.8545 (pm20) REVERT: L 57 LEU cc_start: 0.9044 (mt) cc_final: 0.8804 (mt) REVERT: L 75 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8449 (tm-30) REVERT: O 24 SER cc_start: 0.8015 (t) cc_final: 0.7716 (p) REVERT: P 52 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7783 (mp) REVERT: Q 17 MET cc_start: 0.7868 (pmm) cc_final: 0.6687 (pmm) REVERT: Q 26 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7428 (tt0) REVERT: Q 49 GLU cc_start: 0.7585 (mp0) cc_final: 0.7062 (pm20) REVERT: R 19 GLN cc_start: 0.7971 (mt0) cc_final: 0.7426 (mp10) REVERT: S 10 ILE cc_start: 0.4286 (OUTLIER) cc_final: 0.3461 (mm) REVERT: T 59 ASP cc_start: 0.8720 (t70) cc_final: 0.7985 (t70) REVERT: N 6 LYS cc_start: 0.6847 (mtpt) cc_final: 0.6415 (ttmm) REVERT: N 32 ASP cc_start: 0.5047 (m-30) cc_final: 0.3997 (t0) REVERT: N 88 MET cc_start: 0.7121 (mmp) cc_final: 0.6629 (mmm) outliers start: 120 outliers final: 63 residues processed: 475 average time/residue: 0.6482 time to fit residues: 500.8296 Evaluate side-chains 409 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 336 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 58 HIS Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 91 GLU Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 77 TYR Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain M residue 20 SER Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 38 HIS Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 26 GLU Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 53 CYS Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain X residue 18 PHE Chi-restraints excluded: chain X residue 28 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 184 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 276 optimal weight: 10.0000 chunk 226 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 332 optimal weight: 30.0000 chunk 359 optimal weight: 10.0000 chunk 296 optimal weight: 8.9990 chunk 330 optimal weight: 30.0000 chunk 113 optimal weight: 8.9990 chunk 267 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 HIS ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 53204 Z= 0.339 Angle : 0.771 12.840 78899 Z= 0.392 Chirality : 0.042 0.245 9984 Planarity : 0.006 0.099 4693 Dihedral : 23.691 179.973 25005 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.88 % Favored : 92.99 % Rotamer: Outliers : 6.67 % Allowed : 24.74 % Favored : 68.58 % 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: -1.29 (0.17), residues: 2311 helix: -0.40 (0.17), residues: 862 sheet: -0.54 (0.26), residues: 375 loop : -1.27 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 22 HIS 0.035 0.002 HIS O 38 PHE 0.044 0.003 PHE F 78 TYR 0.031 0.003 TYR H 128 ARG 0.010 0.001 ARG R 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 365 time to evaluate : 3.078 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: B 103 TRP cc_start: 0.7438 (t60) cc_final: 0.7175 (t60) REVERT: B 121 GLN cc_start: 0.8123 (mp10) cc_final: 0.7524 (mp10) REVERT: B 153 MET cc_start: 0.6253 (OUTLIER) cc_final: 0.5674 (mtm) REVERT: B 174 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7393 (tp30) REVERT: C 128 MET cc_start: 0.3765 (ttm) cc_final: 0.3278 (ttm) REVERT: D 78 GLU cc_start: 0.7867 (tt0) cc_final: 0.7361 (tm-30) REVERT: D 88 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8451 (tm-30) REVERT: D 124 MET cc_start: 0.8031 (mtp) cc_final: 0.7688 (ttm) REVERT: D 178 MET cc_start: 0.6849 (OUTLIER) cc_final: 0.6250 (ptt) REVERT: E 31 PHE cc_start: 0.7458 (m-10) cc_final: 0.7153 (m-80) REVERT: E 64 MET cc_start: 0.8664 (tmm) cc_final: 0.8177 (tmm) REVERT: F 65 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6086 (pp20) REVERT: F 88 MET cc_start: 0.8886 (tpp) cc_final: 0.8650 (tmm) REVERT: G 32 ASP cc_start: 0.6079 (t0) cc_final: 0.5825 (t0) REVERT: G 66 GLU cc_start: 0.6260 (mt-10) cc_final: 0.6033 (pp20) REVERT: H 3 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8210 (tpt) REVERT: H 15 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7194 (ttm110) REVERT: H 66 PHE cc_start: 0.8532 (t80) cc_final: 0.8311 (t80) REVERT: H 72 VAL cc_start: 0.7442 (p) cc_final: 0.7156 (p) REVERT: H 73 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.6223 (pm20) REVERT: H 111 MET cc_start: 0.8466 (pmm) cc_final: 0.7963 (ptp) REVERT: H 113 ASP cc_start: 0.8564 (p0) cc_final: 0.7964 (p0) REVERT: I 91 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7231 (pm20) REVERT: J 28 THR cc_start: 0.8070 (p) cc_final: 0.7699 (t) REVERT: K 40 ASN cc_start: 0.6710 (m-40) cc_final: 0.6316 (t0) REVERT: M 82 LEU cc_start: 0.1689 (OUTLIER) cc_final: 0.1324 (pp) REVERT: O 24 SER cc_start: 0.8315 (t) cc_final: 0.7785 (p) REVERT: P 53 ASP cc_start: 0.8736 (p0) cc_final: 0.8115 (p0) REVERT: Q 17 MET cc_start: 0.8329 (pmm) cc_final: 0.7781 (pmm) REVERT: Q 49 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6908 (pm20) REVERT: Q 57 ASP cc_start: 0.8889 (t0) cc_final: 0.8548 (t0) REVERT: Q 65 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8447 (mtp-110) REVERT: S 31 ARG cc_start: 0.3390 (mtp180) cc_final: 0.2619 (ppt170) REVERT: S 65 MET cc_start: 0.0501 (mtt) cc_final: 0.0254 (mtt) REVERT: N 6 LYS cc_start: 0.7069 (mtpt) cc_final: 0.6763 (ttmm) REVERT: N 88 MET cc_start: 0.7633 (mmp) cc_final: 0.7264 (mmp) outliers start: 130 outliers final: 83 residues processed: 460 average time/residue: 0.7288 time to fit residues: 554.4189 Evaluate side-chains 411 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 318 time to evaluate : 3.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain H residue 3 MET Chi-restraints excluded: chain H residue 15 ARG Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 77 TYR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 49 GLU Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 53 CYS Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 65 ARG Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain S residue 79 TYR Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain X residue 18 PHE Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 81 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 328 optimal weight: 40.0000 chunk 250 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 223 optimal weight: 40.0000 chunk 334 optimal weight: 10.0000 chunk 353 optimal weight: 30.0000 chunk 174 optimal weight: 1.9990 chunk 316 optimal weight: 30.0000 chunk 95 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 ASN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 53204 Z= 0.198 Angle : 0.635 13.335 78899 Z= 0.325 Chirality : 0.036 0.228 9984 Planarity : 0.004 0.053 4693 Dihedral : 23.584 178.061 25005 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.93 % Favored : 93.90 % Rotamer: Outliers : 4.83 % Allowed : 27.10 % Favored : 68.07 % 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: -0.98 (0.17), residues: 2311 helix: -0.05 (0.17), residues: 868 sheet: -0.35 (0.27), residues: 358 loop : -1.19 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 95 HIS 0.011 0.001 HIS O 38 PHE 0.058 0.002 PHE F 78 TYR 0.015 0.002 TYR H 128 ARG 0.005 0.000 ARG P 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 352 time to evaluate : 3.291 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: B 103 TRP cc_start: 0.7577 (t60) cc_final: 0.7279 (t60) REVERT: B 121 GLN cc_start: 0.8030 (mp10) cc_final: 0.7429 (mp10) REVERT: B 174 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7326 (tp30) REVERT: B 197 PHE cc_start: 0.8078 (m-80) cc_final: 0.7874 (m-80) REVERT: B 202 ASN cc_start: 0.7381 (t0) cc_final: 0.6691 (t0) REVERT: C 28 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7517 (m-80) REVERT: D 75 TYR cc_start: 0.8449 (m-80) cc_final: 0.8225 (m-80) REVERT: D 78 GLU cc_start: 0.8150 (tt0) cc_final: 0.7676 (tp30) REVERT: D 88 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8363 (tm-30) REVERT: D 124 MET cc_start: 0.8027 (mtp) cc_final: 0.7564 (ttm) REVERT: E 31 PHE cc_start: 0.7645 (m-10) cc_final: 0.6961 (m-80) REVERT: E 64 MET cc_start: 0.8666 (tmm) cc_final: 0.8135 (tmm) REVERT: F 5 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7951 (tm-30) REVERT: F 6 ILE cc_start: 0.8436 (mp) cc_final: 0.8009 (mp) REVERT: F 21 MET cc_start: 0.7946 (mpp) cc_final: 0.7295 (mpp) REVERT: F 58 HIS cc_start: 0.6181 (OUTLIER) cc_final: 0.5889 (t-170) REVERT: F 62 MET cc_start: 0.7729 (ptp) cc_final: 0.7526 (pmm) REVERT: F 65 GLU cc_start: 0.6706 (OUTLIER) cc_final: 0.6503 (tp30) REVERT: F 88 MET cc_start: 0.8768 (tpp) cc_final: 0.7253 (tmm) REVERT: G 32 ASP cc_start: 0.5814 (t0) cc_final: 0.5509 (t0) REVERT: H 3 MET cc_start: 0.8475 (tpt) cc_final: 0.7847 (tpt) REVERT: H 15 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.6982 (ttm170) REVERT: H 52 GLU cc_start: 0.8071 (pp20) cc_final: 0.7840 (pp20) REVERT: H 58 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.6656 (mp0) REVERT: H 66 PHE cc_start: 0.8545 (t80) cc_final: 0.8275 (t80) REVERT: H 89 LYS cc_start: 0.8226 (ptpt) cc_final: 0.7692 (pttm) REVERT: H 111 MET cc_start: 0.8322 (pmm) cc_final: 0.7631 (ptp) REVERT: H 113 ASP cc_start: 0.8425 (p0) cc_final: 0.8071 (p0) REVERT: J 28 THR cc_start: 0.8172 (p) cc_final: 0.7806 (t) REVERT: K 40 ASN cc_start: 0.6266 (m-40) cc_final: 0.5794 (t0) REVERT: L 75 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8138 (tm-30) REVERT: M 82 LEU cc_start: 0.1024 (OUTLIER) cc_final: 0.0801 (pp) REVERT: O 24 SER cc_start: 0.7980 (t) cc_final: 0.7433 (p) REVERT: P 53 ASP cc_start: 0.8707 (p0) cc_final: 0.8114 (p0) REVERT: Q 17 MET cc_start: 0.8206 (pmm) cc_final: 0.7719 (ptp) REVERT: Q 49 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6851 (pm20) REVERT: Q 65 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8453 (mtm110) REVERT: S 31 ARG cc_start: 0.3211 (mtp180) cc_final: 0.2427 (ppt170) REVERT: T 59 ASP cc_start: 0.8763 (t70) cc_final: 0.8243 (t70) REVERT: N 88 MET cc_start: 0.7433 (mmp) cc_final: 0.6960 (mmt) outliers start: 94 outliers final: 68 residues processed: 413 average time/residue: 0.6458 time to fit residues: 436.2115 Evaluate side-chains 400 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 322 time to evaluate : 3.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain F residue 58 HIS Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain H residue 15 ARG Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 77 TYR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 49 GLU Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 53 CYS Chi-restraints excluded: chain Q residue 65 ARG Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain S residue 79 TYR Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 36 TYR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 81 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 294 optimal weight: 20.0000 chunk 200 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 263 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 301 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 180 optimal weight: 6.9990 chunk 317 optimal weight: 50.0000 chunk 89 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN D 40 GLN E 122 ASN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 ASN ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 125 GLN ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 HIS R 31 ASN R 75 GLN S 51 HIS ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 53204 Z= 0.423 Angle : 0.867 11.673 78899 Z= 0.434 Chirality : 0.045 0.250 9984 Planarity : 0.006 0.083 4693 Dihedral : 23.952 179.795 25005 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.92 % Favored : 91.99 % Rotamer: Outliers : 7.65 % Allowed : 26.39 % Favored : 65.97 % 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: -1.48 (0.17), residues: 2311 helix: -0.38 (0.17), residues: 877 sheet: -0.87 (0.26), residues: 371 loop : -1.47 (0.19), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 95 HIS 0.007 0.002 HIS O 51 PHE 0.046 0.003 PHE F 78 TYR 0.020 0.003 TYR D 135 ARG 0.011 0.001 ARG M 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 322 time to evaluate : 3.334 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: B 8 MET cc_start: 0.7590 (tpt) cc_final: 0.7214 (tpt) REVERT: B 100 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8279 (tt) REVERT: B 117 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6724 (mm-30) REVERT: B 121 GLN cc_start: 0.7984 (mp10) cc_final: 0.7303 (mp10) REVERT: B 125 PHE cc_start: 0.4207 (OUTLIER) cc_final: 0.3225 (p90) REVERT: B 153 MET cc_start: 0.6233 (OUTLIER) cc_final: 0.5935 (mtm) REVERT: B 174 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7420 (tp30) REVERT: D 13 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7801 (ttm170) REVERT: D 78 GLU cc_start: 0.8440 (tt0) cc_final: 0.7908 (tp30) REVERT: D 88 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8515 (tm-30) REVERT: D 124 MET cc_start: 0.7971 (mtp) cc_final: 0.7752 (mtp) REVERT: D 178 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6597 (ptt) REVERT: D 191 LEU cc_start: 0.9103 (tp) cc_final: 0.8822 (tt) REVERT: E 20 ARG cc_start: 0.8956 (tmm-80) cc_final: 0.8631 (ttt-90) REVERT: E 31 PHE cc_start: 0.7681 (m-10) cc_final: 0.7223 (m-10) REVERT: E 78 ASN cc_start: 0.9184 (p0) cc_final: 0.8929 (p0) REVERT: E 96 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8764 (ptp) REVERT: F 21 MET cc_start: 0.8060 (mpp) cc_final: 0.7630 (mpp) REVERT: F 79 ARG cc_start: 0.8501 (tpp80) cc_final: 0.8277 (tpp80) REVERT: G 143 MET cc_start: 0.3053 (ppp) cc_final: 0.2715 (pmm) REVERT: H 15 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.6971 (ttm110) REVERT: H 52 GLU cc_start: 0.8073 (pp20) cc_final: 0.7754 (pp20) REVERT: H 58 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.6616 (mp0) REVERT: H 66 PHE cc_start: 0.8484 (t80) cc_final: 0.8217 (t80) REVERT: H 75 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7923 (mm) REVERT: H 96 MET cc_start: 0.7312 (mtp) cc_final: 0.6707 (mtp) REVERT: H 111 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7856 (ptp) REVERT: H 113 ASP cc_start: 0.8488 (p0) cc_final: 0.8128 (p0) REVERT: I 49 GLN cc_start: 0.6239 (tt0) cc_final: 0.5906 (tp40) REVERT: I 91 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7118 (pm20) REVERT: K 40 ASN cc_start: 0.6669 (m-40) cc_final: 0.6198 (t0) REVERT: L 25 GLU cc_start: 0.8966 (pm20) cc_final: 0.8694 (pm20) REVERT: L 40 THR cc_start: 0.7901 (m) cc_final: 0.7504 (t) REVERT: M 82 LEU cc_start: 0.1279 (OUTLIER) cc_final: 0.1001 (pp) REVERT: P 45 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7148 (pm20) REVERT: P 52 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8150 (mp) REVERT: P 53 ASP cc_start: 0.8706 (p0) cc_final: 0.8029 (p0) REVERT: Q 17 MET cc_start: 0.8294 (pmm) cc_final: 0.8041 (ptp) REVERT: Q 30 LYS cc_start: 0.8415 (tttt) cc_final: 0.8181 (ttmm) REVERT: Q 49 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6777 (pm20) REVERT: Q 57 ASP cc_start: 0.8844 (t0) cc_final: 0.8568 (t0) REVERT: Q 65 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.8688 (mtp-110) REVERT: S 31 ARG cc_start: 0.2553 (mtp180) cc_final: 0.1835 (ppt170) REVERT: S 43 MET cc_start: 0.4735 (mpp) cc_final: 0.4479 (mpp) REVERT: T 40 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8592 (tm-30) REVERT: N 88 MET cc_start: 0.7165 (mmp) cc_final: 0.6743 (mmm) outliers start: 149 outliers final: 95 residues processed: 425 average time/residue: 0.6481 time to fit residues: 451.1440 Evaluate side-chains 412 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 300 time to evaluate : 3.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain F residue 58 HIS Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain H residue 15 ARG Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 77 TYR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 105 PHE Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 49 GLU Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 53 CYS Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 65 ARG Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 38 LYS Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 70 TYR Chi-restraints excluded: chain S residue 40 PHE Chi-restraints excluded: chain S residue 79 TYR Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 36 TYR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain X residue 18 PHE Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 81 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 119 optimal weight: 20.0000 chunk 318 optimal weight: 40.0000 chunk 69 optimal weight: 0.0030 chunk 207 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 chunk 354 optimal weight: 10.0000 chunk 293 optimal weight: 20.0000 chunk 163 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 chunk 185 optimal weight: 0.2980 overall best weight: 2.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN D 196 ASN E 122 ASN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 ASN I 30 ASN ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 ASN ** K 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 HIS ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.5348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 53204 Z= 0.191 Angle : 0.644 13.631 78899 Z= 0.329 Chirality : 0.037 0.266 9984 Planarity : 0.004 0.055 4693 Dihedral : 23.741 178.812 25005 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.62 % Favored : 93.34 % Rotamer: Outliers : 5.75 % Allowed : 27.67 % Favored : 66.58 % 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: -1.03 (0.17), residues: 2311 helix: 0.05 (0.17), residues: 862 sheet: -0.50 (0.27), residues: 348 loop : -1.30 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 95 HIS 0.006 0.001 HIS F 3 PHE 0.027 0.002 PHE F 78 TYR 0.017 0.002 TYR R 70 ARG 0.014 0.001 ARG I 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 342 time to evaluate : 3.267 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: B 8 MET cc_start: 0.7344 (tpt) cc_final: 0.6941 (tpt) REVERT: B 100 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8288 (tt) REVERT: B 121 GLN cc_start: 0.7946 (mp10) cc_final: 0.7316 (mp10) REVERT: B 153 MET cc_start: 0.6353 (OUTLIER) cc_final: 0.5975 (mtm) REVERT: B 197 PHE cc_start: 0.7993 (m-80) cc_final: 0.7703 (m-80) REVERT: C 28 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7547 (m-80) REVERT: D 78 GLU cc_start: 0.8197 (tt0) cc_final: 0.7772 (tp30) REVERT: D 88 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8483 (tm-30) REVERT: D 124 MET cc_start: 0.7983 (mtp) cc_final: 0.7756 (mtp) REVERT: D 164 GLN cc_start: 0.9051 (tt0) cc_final: 0.8732 (mm-40) REVERT: D 191 LEU cc_start: 0.9116 (tp) cc_final: 0.8838 (tt) REVERT: E 20 ARG cc_start: 0.8888 (tmm-80) cc_final: 0.8157 (ttt-90) REVERT: E 31 PHE cc_start: 0.7652 (m-10) cc_final: 0.6758 (m-80) REVERT: E 78 ASN cc_start: 0.8963 (p0) cc_final: 0.8652 (p0) REVERT: F 5 GLU cc_start: 0.8315 (tm-30) cc_final: 0.8010 (tm-30) REVERT: F 21 MET cc_start: 0.7935 (mpp) cc_final: 0.7522 (mpp) REVERT: F 88 MET cc_start: 0.8777 (tpp) cc_final: 0.7672 (tmm) REVERT: H 52 GLU cc_start: 0.8099 (pp20) cc_final: 0.7738 (pp20) REVERT: H 58 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.6566 (mp0) REVERT: H 66 PHE cc_start: 0.8396 (t80) cc_final: 0.8097 (t80) REVERT: H 96 MET cc_start: 0.7375 (mtp) cc_final: 0.6738 (mtp) REVERT: H 111 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7772 (ptp) REVERT: H 113 ASP cc_start: 0.8453 (p0) cc_final: 0.8025 (p0) REVERT: I 45 MET cc_start: 0.1694 (pmm) cc_final: 0.1404 (pmm) REVERT: I 49 GLN cc_start: 0.6116 (tt0) cc_final: 0.5859 (tp40) REVERT: J 47 GLU cc_start: 0.7398 (tp30) cc_final: 0.7172 (tp30) REVERT: K 40 ASN cc_start: 0.6352 (m-40) cc_final: 0.5774 (t0) REVERT: L 40 THR cc_start: 0.7884 (m) cc_final: 0.7548 (t) REVERT: M 82 LEU cc_start: 0.1188 (OUTLIER) cc_final: 0.0767 (pp) REVERT: O 37 ASN cc_start: 0.8766 (m110) cc_final: 0.8374 (p0) REVERT: O 47 LYS cc_start: 0.8600 (tppp) cc_final: 0.8319 (tppp) REVERT: P 53 ASP cc_start: 0.8841 (p0) cc_final: 0.8255 (p0) REVERT: P 76 LYS cc_start: 0.8585 (tptm) cc_final: 0.8382 (mmtm) REVERT: Q 17 MET cc_start: 0.8166 (pmm) cc_final: 0.7920 (ptp) REVERT: Q 49 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6993 (pm20) REVERT: Q 65 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8443 (mtp-110) REVERT: S 43 MET cc_start: 0.4083 (mpp) cc_final: 0.3846 (mpp) REVERT: T 43 ASP cc_start: 0.8442 (t0) cc_final: 0.8224 (t0) REVERT: N 85 GLU cc_start: 0.9053 (pt0) cc_final: 0.8365 (pp20) REVERT: N 88 MET cc_start: 0.7318 (mmp) cc_final: 0.6899 (mmm) outliers start: 112 outliers final: 82 residues processed: 413 average time/residue: 0.6277 time to fit residues: 427.9510 Evaluate side-chains 405 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 315 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 77 TYR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 49 GLU Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 53 CYS Chi-restraints excluded: chain Q residue 65 ARG Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 70 TYR Chi-restraints excluded: chain S residue 40 PHE Chi-restraints excluded: chain S residue 79 TYR Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 36 TYR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain X residue 18 PHE Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 81 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 341 optimal weight: 40.0000 chunk 39 optimal weight: 9.9990 chunk 201 optimal weight: 30.0000 chunk 258 optimal weight: 10.0000 chunk 200 optimal weight: 8.9990 chunk 298 optimal weight: 10.0000 chunk 197 optimal weight: 20.0000 chunk 352 optimal weight: 30.0000 chunk 220 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 162 optimal weight: 30.0000 overall best weight: 9.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 ASN ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 HIS K 28 ASN ** K 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 50 HIS R 31 ASN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.6296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 53204 Z= 0.494 Angle : 0.956 14.536 78899 Z= 0.474 Chirality : 0.048 0.274 9984 Planarity : 0.007 0.077 4693 Dihedral : 24.239 179.649 25005 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 22.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.87 % Favored : 91.00 % Rotamer: Outliers : 7.34 % Allowed : 26.49 % Favored : 66.17 % 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: -1.69 (0.17), residues: 2311 helix: -0.52 (0.17), residues: 863 sheet: -1.10 (0.26), residues: 367 loop : -1.56 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.004 TRP B 95 HIS 0.011 0.002 HIS O 51 PHE 0.021 0.003 PHE X 18 TYR 0.025 0.003 TYR F 4 ARG 0.021 0.001 ARG I 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 309 time to evaluate : 3.114 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: B 100 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8281 (tt) REVERT: B 121 GLN cc_start: 0.8030 (mp10) cc_final: 0.7392 (mp10) REVERT: B 153 MET cc_start: 0.5930 (OUTLIER) cc_final: 0.5410 (mtm) REVERT: B 161 PHE cc_start: 0.7352 (t80) cc_final: 0.7015 (t80) REVERT: C 74 ILE cc_start: 0.4775 (OUTLIER) cc_final: 0.4385 (pt) REVERT: D 78 GLU cc_start: 0.8580 (tt0) cc_final: 0.8066 (tp30) REVERT: D 88 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8610 (tm-30) REVERT: D 124 MET cc_start: 0.7967 (mtp) cc_final: 0.7746 (mtp) REVERT: D 178 MET cc_start: 0.6648 (OUTLIER) cc_final: 0.6290 (ptm) REVERT: D 191 LEU cc_start: 0.8926 (tp) cc_final: 0.8623 (tp) REVERT: E 31 PHE cc_start: 0.7671 (m-10) cc_final: 0.7393 (m-80) REVERT: E 78 ASN cc_start: 0.9068 (p0) cc_final: 0.8820 (p0) REVERT: F 1 MET cc_start: 0.6236 (mmm) cc_final: 0.6019 (mmm) REVERT: F 21 MET cc_start: 0.8165 (mpp) cc_final: 0.7650 (mpp) REVERT: F 23 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8649 (mm-30) REVERT: H 15 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6727 (ttm110) REVERT: H 58 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.6963 (mp0) REVERT: H 73 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6664 (pm20) REVERT: H 96 MET cc_start: 0.7401 (mtp) cc_final: 0.6806 (mtp) REVERT: H 111 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.7866 (ptp) REVERT: H 113 ASP cc_start: 0.8591 (p0) cc_final: 0.8169 (p0) REVERT: I 49 GLN cc_start: 0.6860 (tt0) cc_final: 0.6489 (tp40) REVERT: K 28 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.6705 (t0) REVERT: K 40 ASN cc_start: 0.6780 (m-40) cc_final: 0.6300 (t0) REVERT: L 40 THR cc_start: 0.7968 (m) cc_final: 0.7703 (t) REVERT: M 71 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7361 (mt-10) REVERT: M 82 LEU cc_start: 0.1293 (OUTLIER) cc_final: 0.1070 (pp) REVERT: P 52 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8198 (mp) REVERT: P 53 ASP cc_start: 0.8711 (p0) cc_final: 0.7981 (p0) REVERT: Q 49 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7012 (pm20) REVERT: Q 57 ASP cc_start: 0.8881 (t0) cc_final: 0.8672 (t0) REVERT: S 43 MET cc_start: 0.4038 (mpp) cc_final: 0.3756 (mpp) REVERT: T 78 ASN cc_start: 0.7821 (OUTLIER) cc_final: 0.7563 (t0) outliers start: 143 outliers final: 106 residues processed: 415 average time/residue: 0.6281 time to fit residues: 428.2604 Evaluate side-chains 403 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 284 time to evaluate : 3.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 58 HIS Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 52 ARG Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 125 ASP Chi-restraints excluded: chain H residue 3 MET Chi-restraints excluded: chain H residue 15 ARG Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 91 GLU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 28 ASN Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 77 TYR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 105 PHE Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 44 SER Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 49 GLU Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 53 CYS Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 65 ARG Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain S residue 40 PHE Chi-restraints excluded: chain S residue 79 TYR Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 36 TYR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 78 ASN Chi-restraints excluded: chain X residue 18 PHE Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 43 GLU Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 81 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 218 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 210 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 224 optimal weight: 20.0000 chunk 240 optimal weight: 9.9990 chunk 174 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 277 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 ASN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 ASN ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.6152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 53204 Z= 0.210 Angle : 0.679 15.914 78899 Z= 0.348 Chirality : 0.038 0.271 9984 Planarity : 0.005 0.057 4693 Dihedral : 23.939 178.580 25005 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.32 % Favored : 93.60 % Rotamer: Outliers : 6.06 % Allowed : 27.93 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.17), residues: 2311 helix: -0.17 (0.17), residues: 880 sheet: -0.82 (0.27), residues: 349 loop : -1.41 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP B 95 HIS 0.005 0.001 HIS F 3 PHE 0.050 0.002 PHE K 27 TYR 0.028 0.002 TYR C 183 ARG 0.013 0.001 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 329 time to evaluate : 3.229 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: B 121 GLN cc_start: 0.7971 (mp10) cc_final: 0.7351 (mp10) REVERT: B 153 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.5870 (mtm) REVERT: B 197 PHE cc_start: 0.8047 (m-80) cc_final: 0.7812 (m-80) REVERT: C 5 HIS cc_start: 0.6792 (t70) cc_final: 0.6288 (t70) REVERT: C 28 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7575 (m-80) REVERT: C 74 ILE cc_start: 0.4613 (OUTLIER) cc_final: 0.4219 (pt) REVERT: C 92 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7835 (p0) REVERT: D 78 GLU cc_start: 0.8140 (tt0) cc_final: 0.7688 (tp30) REVERT: D 88 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8502 (tm-30) REVERT: D 124 MET cc_start: 0.8046 (mtp) cc_final: 0.7833 (mtp) REVERT: D 164 GLN cc_start: 0.9060 (tt0) cc_final: 0.8731 (mm-40) REVERT: D 191 LEU cc_start: 0.8832 (tp) cc_final: 0.8524 (tt) REVERT: E 20 ARG cc_start: 0.8939 (tmm-80) cc_final: 0.8400 (ttt-90) REVERT: E 31 PHE cc_start: 0.7660 (m-10) cc_final: 0.6944 (m-80) REVERT: E 78 ASN cc_start: 0.9001 (p0) cc_final: 0.8716 (p0) REVERT: F 21 MET cc_start: 0.8062 (mpp) cc_final: 0.7616 (mpp) REVERT: G 109 LYS cc_start: 0.7201 (ptmm) cc_final: 0.6355 (tppt) REVERT: H 15 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6985 (ttm170) REVERT: H 52 GLU cc_start: 0.7727 (pp20) cc_final: 0.7439 (pp20) REVERT: H 58 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.6461 (mp0) REVERT: H 66 PHE cc_start: 0.8423 (t80) cc_final: 0.8180 (t80) REVERT: H 85 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8716 (tp) REVERT: H 96 MET cc_start: 0.7462 (mtp) cc_final: 0.6807 (mtp) REVERT: H 111 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.7794 (ptp) REVERT: H 113 ASP cc_start: 0.8491 (p0) cc_final: 0.8037 (p0) REVERT: I 49 GLN cc_start: 0.7163 (tt0) cc_final: 0.6857 (tp40) REVERT: I 91 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7102 (pm20) REVERT: J 47 GLU cc_start: 0.7242 (tp30) cc_final: 0.6996 (tp30) REVERT: K 28 ASN cc_start: 0.8059 (m-40) cc_final: 0.6393 (t0) REVERT: K 40 ASN cc_start: 0.6578 (m-40) cc_final: 0.5802 (t0) REVERT: M 82 LEU cc_start: 0.1143 (OUTLIER) cc_final: 0.0907 (pp) REVERT: O 37 ASN cc_start: 0.8837 (m-40) cc_final: 0.8523 (p0) REVERT: P 52 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8131 (mp) REVERT: P 53 ASP cc_start: 0.8828 (p0) cc_final: 0.8276 (p0) REVERT: Q 49 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6835 (pm20) REVERT: Q 65 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8516 (mtp-110) REVERT: S 43 MET cc_start: 0.3927 (mpp) cc_final: 0.3708 (mpp) REVERT: N 85 GLU cc_start: 0.9017 (pt0) cc_final: 0.8334 (pp20) REVERT: N 88 MET cc_start: 0.7428 (mmp) cc_final: 0.6839 (mmt) outliers start: 118 outliers final: 91 residues processed: 406 average time/residue: 0.6290 time to fit residues: 421.2050 Evaluate side-chains 409 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 306 time to evaluate : 3.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 58 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 52 ARG Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain H residue 3 MET Chi-restraints excluded: chain H residue 15 ARG Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 94 ARG Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 77 TYR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 44 SER Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 49 GLU Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 65 ARG Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 38 LYS Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 70 TYR Chi-restraints excluded: chain S residue 40 PHE Chi-restraints excluded: chain S residue 79 TYR Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 36 TYR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain X residue 18 PHE Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 81 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 320 optimal weight: 30.0000 chunk 337 optimal weight: 40.0000 chunk 308 optimal weight: 30.0000 chunk 328 optimal weight: 40.0000 chunk 197 optimal weight: 30.0000 chunk 143 optimal weight: 20.0000 chunk 258 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 297 optimal weight: 9.9990 chunk 310 optimal weight: 30.0000 chunk 327 optimal weight: 30.0000 overall best weight: 14.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 ASN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN R 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.7024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.107 53204 Z= 0.712 Angle : 1.169 17.318 78899 Z= 0.571 Chirality : 0.057 0.318 9984 Planarity : 0.008 0.090 4693 Dihedral : 24.523 179.378 25005 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 28.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.04 % Favored : 89.79 % Rotamer: Outliers : 7.65 % Allowed : 27.36 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.16), residues: 2311 helix: -1.00 (0.16), residues: 884 sheet: -1.57 (0.26), residues: 355 loop : -1.89 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.005 TRP B 95 HIS 0.013 0.003 HIS O 51 PHE 0.025 0.004 PHE H 66 TYR 0.039 0.004 TYR F 4 ARG 0.019 0.001 ARG M 70 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 291 time to evaluate : 3.243 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: B 121 GLN cc_start: 0.7535 (mp10) cc_final: 0.7046 (mp10) REVERT: B 153 MET cc_start: 0.5965 (OUTLIER) cc_final: 0.5417 (mtm) REVERT: B 161 PHE cc_start: 0.7320 (t80) cc_final: 0.6989 (t80) REVERT: B 197 PHE cc_start: 0.7975 (m-80) cc_final: 0.7681 (m-80) REVERT: C 5 HIS cc_start: 0.7055 (t70) cc_final: 0.6415 (t70) REVERT: C 74 ILE cc_start: 0.5169 (OUTLIER) cc_final: 0.4771 (pt) REVERT: D 78 GLU cc_start: 0.8551 (tt0) cc_final: 0.7995 (tp30) REVERT: D 105 MET cc_start: 0.8464 (mmm) cc_final: 0.8025 (mmt) REVERT: D 124 MET cc_start: 0.7954 (mtp) cc_final: 0.7727 (mtp) REVERT: D 164 GLN cc_start: 0.9110 (tt0) cc_final: 0.8711 (mm-40) REVERT: D 178 MET cc_start: 0.6298 (OUTLIER) cc_final: 0.6001 (ptm) REVERT: D 191 LEU cc_start: 0.8766 (tp) cc_final: 0.8563 (tp) REVERT: E 31 PHE cc_start: 0.7774 (m-10) cc_final: 0.7501 (m-80) REVERT: F 1 MET cc_start: 0.6436 (mmm) cc_final: 0.6042 (mmm) REVERT: F 21 MET cc_start: 0.8314 (mpp) cc_final: 0.7773 (mpp) REVERT: F 23 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8681 (mm-30) REVERT: F 90 MET cc_start: 0.8971 (mtp) cc_final: 0.8744 (mmm) REVERT: G 109 LYS cc_start: 0.7560 (ptmm) cc_final: 0.6842 (tppt) REVERT: H 15 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6703 (ttm170) REVERT: H 58 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.6834 (mp0) REVERT: H 85 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8741 (tp) REVERT: H 96 MET cc_start: 0.7562 (mtp) cc_final: 0.6964 (mtp) REVERT: H 111 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7660 (ptp) REVERT: H 113 ASP cc_start: 0.8596 (p0) cc_final: 0.7991 (p0) REVERT: I 91 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8262 (mm-30) REVERT: J 19 ASP cc_start: 0.7296 (t70) cc_final: 0.6860 (m-30) REVERT: J 20 GLN cc_start: 0.7080 (pp30) cc_final: 0.6847 (pp30) REVERT: J 72 ARG cc_start: 0.6195 (OUTLIER) cc_final: 0.5928 (mmt180) REVERT: K 28 ASN cc_start: 0.8229 (m-40) cc_final: 0.6954 (t0) REVERT: K 40 ASN cc_start: 0.6630 (m-40) cc_final: 0.5973 (t0) REVERT: O 37 ASN cc_start: 0.9000 (m-40) cc_final: 0.8794 (p0) REVERT: O 47 LYS cc_start: 0.8871 (tppp) cc_final: 0.8658 (ttmm) REVERT: P 52 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8260 (mp) REVERT: P 53 ASP cc_start: 0.8635 (p0) cc_final: 0.8090 (p0) REVERT: Q 8 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8177 (mm) REVERT: Q 11 ARG cc_start: 0.8723 (ttm-80) cc_final: 0.8461 (ttm-80) REVERT: Q 49 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7317 (pm20) REVERT: S 43 MET cc_start: 0.4303 (mpp) cc_final: 0.4025 (mpp) REVERT: X 18 PHE cc_start: 0.5375 (OUTLIER) cc_final: 0.5083 (p90) REVERT: N 88 MET cc_start: 0.7431 (mmp) cc_final: 0.6577 (mmm) outliers start: 149 outliers final: 114 residues processed: 396 average time/residue: 0.6335 time to fit residues: 412.5700 Evaluate side-chains 406 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 279 time to evaluate : 3.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 58 HIS Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 125 ASP Chi-restraints excluded: chain H residue 3 MET Chi-restraints excluded: chain H residue 15 ARG Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 91 GLU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 72 ARG Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 77 TYR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 105 PHE Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 44 SER Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 49 GLU Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 53 CYS Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 65 ARG Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 38 LYS Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain S residue 40 PHE Chi-restraints excluded: chain S residue 79 TYR Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 36 TYR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain X residue 18 PHE Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 81 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 215 optimal weight: 0.9990 chunk 347 optimal weight: 40.0000 chunk 212 optimal weight: 0.8980 chunk 164 optimal weight: 8.9990 chunk 241 optimal weight: 0.7980 chunk 364 optimal weight: 7.9990 chunk 335 optimal weight: 30.0000 chunk 290 optimal weight: 0.9980 chunk 30 optimal weight: 20.0000 chunk 224 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 ASN ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN ** K 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.6700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 53204 Z= 0.186 Angle : 0.699 16.621 78899 Z= 0.358 Chirality : 0.039 0.265 9984 Planarity : 0.005 0.061 4693 Dihedral : 24.083 179.826 25005 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.05 % Favored : 92.86 % Rotamer: Outliers : 5.03 % Allowed : 29.93 % Favored : 65.04 % 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: -1.58 (0.17), residues: 2311 helix: -0.37 (0.17), residues: 886 sheet: -1.09 (0.28), residues: 320 loop : -1.55 (0.18), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 95 HIS 0.005 0.001 HIS K 22 PHE 0.055 0.002 PHE H 66 TYR 0.031 0.002 TYR R 32 ARG 0.013 0.001 ARG D 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 330 time to evaluate : 3.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.6023 (OUTLIER) cc_final: 0.5493 (mtm) REVERT: C 5 HIS cc_start: 0.6818 (t70) cc_final: 0.6314 (t70) REVERT: C 28 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7513 (m-80) REVERT: C 74 ILE cc_start: 0.4557 (OUTLIER) cc_final: 0.4183 (pt) REVERT: C 92 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7943 (p0) REVERT: D 69 GLU cc_start: 0.8171 (tp30) cc_final: 0.7807 (tp30) REVERT: D 78 GLU cc_start: 0.8233 (tt0) cc_final: 0.7885 (tp30) REVERT: D 117 LEU cc_start: 0.8478 (tt) cc_final: 0.8158 (tp) REVERT: D 164 GLN cc_start: 0.9053 (tt0) cc_final: 0.8694 (mm-40) REVERT: D 178 MET cc_start: 0.6580 (OUTLIER) cc_final: 0.6347 (ptt) REVERT: D 191 LEU cc_start: 0.8762 (tp) cc_final: 0.8433 (tt) REVERT: E 20 ARG cc_start: 0.8906 (tmm-80) cc_final: 0.8353 (ttt-90) REVERT: E 31 PHE cc_start: 0.7661 (m-10) cc_final: 0.6861 (m-80) REVERT: F 1 MET cc_start: 0.6013 (mmm) cc_final: 0.5462 (mmm) REVERT: F 5 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7838 (tm-30) REVERT: F 21 MET cc_start: 0.8054 (mpp) cc_final: 0.7544 (mpp) REVERT: F 88 MET cc_start: 0.8790 (tpp) cc_final: 0.7474 (tmm) REVERT: G 66 GLU cc_start: 0.7243 (tp30) cc_final: 0.6896 (tp30) REVERT: G 109 LYS cc_start: 0.7290 (ptmm) cc_final: 0.6404 (tppt) REVERT: H 15 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.6943 (ttm170) REVERT: H 58 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.6673 (mp0) REVERT: H 96 MET cc_start: 0.7490 (mtp) cc_final: 0.6792 (mtp) REVERT: H 111 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.7722 (ptp) REVERT: H 113 ASP cc_start: 0.8498 (p0) cc_final: 0.8048 (p0) REVERT: I 91 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7218 (pm20) REVERT: K 28 ASN cc_start: 0.7806 (m-40) cc_final: 0.6755 (t0) REVERT: K 38 GLN cc_start: 0.7257 (OUTLIER) cc_final: 0.7019 (pp30) REVERT: K 40 ASN cc_start: 0.6759 (m-40) cc_final: 0.6185 (t0) REVERT: K 85 MET cc_start: 0.6794 (mtp) cc_final: 0.6502 (mtp) REVERT: M 70 ARG cc_start: 0.8604 (ppt170) cc_final: 0.8241 (tmm160) REVERT: O 10 LYS cc_start: 0.9388 (ptmm) cc_final: 0.9036 (ptmm) REVERT: O 47 LYS cc_start: 0.8736 (tppp) cc_final: 0.8457 (ttmm) REVERT: P 52 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8237 (mp) REVERT: P 53 ASP cc_start: 0.8745 (p0) cc_final: 0.8190 (p0) REVERT: P 76 LYS cc_start: 0.9305 (mmtt) cc_final: 0.9101 (mmtm) REVERT: Q 11 ARG cc_start: 0.8610 (ttm-80) cc_final: 0.8356 (ttm-80) REVERT: Q 65 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8611 (mtp-110) REVERT: R 22 ASP cc_start: 0.8599 (t0) cc_final: 0.8361 (t0) REVERT: S 43 MET cc_start: 0.4066 (mpp) cc_final: 0.3826 (mpp) REVERT: T 48 GLN cc_start: 0.8859 (tp40) cc_final: 0.8296 (tm-30) REVERT: T 54 MET cc_start: 0.8376 (tmm) cc_final: 0.7929 (tmm) REVERT: X 18 PHE cc_start: 0.5160 (OUTLIER) cc_final: 0.4927 (p90) REVERT: N 27 LYS cc_start: 0.8243 (mmtm) cc_final: 0.7841 (mtpt) REVERT: N 85 GLU cc_start: 0.9013 (pt0) cc_final: 0.8323 (pp20) REVERT: N 88 MET cc_start: 0.7275 (mmp) cc_final: 0.6590 (mmm) outliers start: 98 outliers final: 74 residues processed: 390 average time/residue: 0.6343 time to fit residues: 408.0133 Evaluate side-chains 401 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 315 time to evaluate : 3.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 58 HIS Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain H residue 3 MET Chi-restraints excluded: chain H residue 15 ARG Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 77 TYR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 53 CYS Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 65 ARG Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain S residue 40 PHE Chi-restraints excluded: chain S residue 79 TYR Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 36 TYR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain X residue 18 PHE Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain N residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 230 optimal weight: 20.0000 chunk 309 optimal weight: 30.0000 chunk 88 optimal weight: 7.9990 chunk 267 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 290 optimal weight: 10.0000 chunk 121 optimal weight: 0.0470 chunk 298 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 53 optimal weight: 0.2980 overall best weight: 3.8284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 ASN I 80 HIS ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.098294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.072737 restraints weight = 197922.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.074012 restraints weight = 85989.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.073776 restraints weight = 63141.582| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.6720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 53204 Z= 0.216 Angle : 0.750 59.198 78899 Z= 0.396 Chirality : 0.039 0.609 9984 Planarity : 0.005 0.059 4693 Dihedral : 24.080 179.882 25005 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.31 % Favored : 92.60 % Rotamer: Outliers : 4.93 % Allowed : 29.67 % Favored : 65.40 % Cbeta Deviations : 0.05 % 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: -1.55 (0.17), residues: 2311 helix: -0.35 (0.17), residues: 881 sheet: -1.08 (0.28), residues: 320 loop : -1.53 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 95 HIS 0.005 0.001 HIS K 22 PHE 0.042 0.002 PHE H 66 TYR 0.022 0.002 TYR R 32 ARG 0.012 0.001 ARG D 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8632.53 seconds wall clock time: 157 minutes 24.17 seconds (9444.17 seconds total)