Starting phenix.real_space_refine on Sun Feb 25 13:03:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwg_23052/02_2024/7kwg_23052.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwg_23052/02_2024/7kwg_23052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwg_23052/02_2024/7kwg_23052.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwg_23052/02_2024/7kwg_23052.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwg_23052/02_2024/7kwg_23052.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwg_23052/02_2024/7kwg_23052.pdb" } resolution = 3.75 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= 0.012 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 1584 5.49 5 S 48 5.16 5 C 26410 2.51 5 N 9559 2.21 5 O 14269 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b GLU 11": "OE1" <-> "OE2" Residue "b ARG 113": "NH1" <-> "NH2" Residue "b GLU 133": "OE1" <-> "OE2" Residue "b GLU 136": "OE1" <-> "OE2" Residue "b GLU 140": "OE1" <-> "OE2" Residue "b GLU 195": "OE1" <-> "OE2" Residue "c GLU 55": "OE1" <-> "OE2" Residue "c GLU 57": "OE1" <-> "OE2" Residue "c GLU 124": "OE1" <-> "OE2" Residue "c PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 187": "OE1" <-> "OE2" Residue "d ARG 29": "NH1" <-> "NH2" Residue "d ARG 66": "NH1" <-> "NH2" Residue "d GLU 153": "OE1" <-> "OE2" Residue "d GLU 156": "OE1" <-> "OE2" Residue "d GLU 196": "OE1" <-> "OE2" Residue "d ARG 200": "NH1" <-> "NH2" Residue "e ARG 4": "NH1" <-> "NH2" Residue "e GLU 10": "OE1" <-> "OE2" Residue "e GLU 13": "OE1" <-> "OE2" Residue "e GLU 65": "OE1" <-> "OE2" Residue "e GLU 78": "OE1" <-> "OE2" Residue "e GLU 162": "OE1" <-> "OE2" Residue "f GLU 24": "OE1" <-> "OE2" Residue "f GLU 96": "OE1" <-> "OE2" Residue "g ARG 10": "NH1" <-> "NH2" Residue "g GLU 63": "OE1" <-> "OE2" Residue "g GLU 64": "OE1" <-> "OE2" Residue "g ARG 79": "NH1" <-> "NH2" Residue "g ARG 95": "NH1" <-> "NH2" Residue "g GLU 146": "OE1" <-> "OE2" Residue "h ARG 13": "NH1" <-> "NH2" Residue "h GLU 53": "OE1" <-> "OE2" Residue "h ASP 54": "OD1" <-> "OD2" Residue "i ARG 9": "NH1" <-> "NH2" Residue "i GLU 27": "OE1" <-> "OE2" Residue "i GLU 39": "OE1" <-> "OE2" Residue "i GLU 58": "OE1" <-> "OE2" Residue "i GLU 91": "OE1" <-> "OE2" Residue "i ARG 111": "NH1" <-> "NH2" Residue "j ARG 53": "NH1" <-> "NH2" Residue "j GLU 99": "OE1" <-> "OE2" Residue "k GLU 17": "OE1" <-> "OE2" Residue "l ARG 49": "NH1" <-> "NH2" Residue "l ARG 107": "NH1" <-> "NH2" Residue "l ARG 127": "NH1" <-> "NH2" Residue "m ARG 14": "NH1" <-> "NH2" Residue "m TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 72": "OE1" <-> "OE2" Residue "m ARG 87": "NH1" <-> "NH2" Residue "m ARG 92": "NH1" <-> "NH2" Residue "m ARG 93": "NH1" <-> "NH2" Residue "n ARG 23": "NH1" <-> "NH2" Residue "n PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 19": "OE1" <-> "OE2" Residue "o ARG 53": "NH1" <-> "NH2" Residue "o ARG 88": "NH1" <-> "NH2" Residue "p PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 26": "NH1" <-> "NH2" Residue "q TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 76": "NH1" <-> "NH2" Residue "r ARG 10": "NH1" <-> "NH2" Residue "r ARG 11": "NH1" <-> "NH2" Residue "s GLU 20": "OE1" <-> "OE2" Residue "s GLU 23": "OE1" <-> "OE2" Residue "s PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 55": "NH1" <-> "NH2" Residue "s GLU 64": "OE1" <-> "OE2" Residue "s ARG 78": "NH1" <-> "NH2" Residue "t GLU 15": "OE1" <-> "OE2" Residue "t GLU 48": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 51870 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 693 Classifications: {'RNA': 32} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 4, 'rna3p_pur': 13, 'rna3p_pyr': 5} Link IDs: {'rna2p': 14, 'rna3p': 17} Chain: "a" Number of atoms: 33226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1552, 33226 Classifications: {'RNA': 1552} Modifications used: {'rna2p_pur': 125, 'rna2p_pyr': 95, 'rna3p_pur': 742, 'rna3p_pyr': 590} Link IDs: {'rna2p': 220, 'rna3p': 1331} Chain: "b" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1802 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "c" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1596 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 3, 'TRANS': 198} Chain: "d" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1595 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain breaks: 1 Chain: "e" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1239 Classifications: {'peptide': 165} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain: "f" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 798 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "g" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1177 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain breaks: 1 Chain: "h" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1032 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "i" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 987 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "j" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 773 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 6, 'TRANS': 90} Chain: "k" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 880 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "l" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1058 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "m" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 584 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain breaks: 2 Chain: "n" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 497 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "o" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 738 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "p" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 712 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 84} Chain: "q" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 707 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "r" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 580 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "s" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 590 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "t" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 606 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Time building chain proxies: 26.24, per 1000 atoms: 0.51 Number of scatterers: 51870 At special positions: 0 Unit cell: (145.18, 245.14, 183.26, 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 48 16.00 P 1584 15.00 O 14269 8.00 N 9559 7.00 C 26410 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 26.48 Conformation dependent library (CDL) restraints added in 3.9 seconds 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4182 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 24 sheets defined 35.2% alpha, 15.3% beta 483 base pairs and 891 stacking pairs defined. Time for finding SS restraints: 22.56 Creating SS restraints... Processing helix chain 'b' and resid 42 through 60 removed outlier: 3.607A pdb=" N VAL b 47 " --> pdb=" O LEU b 43 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS b 58 " --> pdb=" O TYR b 54 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL b 60 " --> pdb=" O PHE b 56 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 88 removed outlier: 3.990A pdb=" N VAL b 80 " --> pdb=" O ALA b 76 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLU b 85 " --> pdb=" O LYS b 81 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG b 86 " --> pdb=" O SER b 82 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 108 Processing helix chain 'b' and resid 108 through 117 removed outlier: 4.824A pdb=" N ILE b 114 " --> pdb=" O ARG b 110 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER b 115 " --> pdb=" O ILE b 111 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE b 117 " --> pdb=" O ARG b 113 " (cutoff:3.500A) Processing helix chain 'b' and resid 118 through 120 No H-bonds generated for 'chain 'b' and resid 118 through 120' Processing helix chain 'b' and resid 130 through 147 removed outlier: 3.934A pdb=" N VAL b 134 " --> pdb=" O PRO b 130 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL b 135 " --> pdb=" O LYS b 131 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N GLU b 136 " --> pdb=" O LYS b 132 " (cutoff:3.500A) Processing helix chain 'b' and resid 169 through 178 removed outlier: 3.644A pdb=" N ILE b 173 " --> pdb=" O GLU b 169 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS b 178 " --> pdb=" O ALA b 174 " (cutoff:3.500A) Processing helix chain 'b' and resid 206 through 219 removed outlier: 4.375A pdb=" N LEU b 213 " --> pdb=" O ALA b 209 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS b 216 " --> pdb=" O LEU b 212 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N MET b 217 " --> pdb=" O LEU b 213 " (cutoff:3.500A) Processing helix chain 'b' and resid 221 through 226 Processing helix chain 'c' and resid 6 through 11 removed outlier: 3.520A pdb=" N LEU c 10 " --> pdb=" O ASN c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 50 removed outlier: 3.975A pdb=" N LEU c 32 " --> pdb=" O PHE c 28 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS c 33 " --> pdb=" O ALA c 29 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLU c 34 " --> pdb=" O SER c 30 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN c 44 " --> pdb=" O LYS c 40 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU c 45 " --> pdb=" O PHE c 41 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS c 47 " --> pdb=" O ASP c 43 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLU c 48 " --> pdb=" O ASN c 44 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER c 50 " --> pdb=" O LEU c 46 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 75 removed outlier: 3.820A pdb=" N MET c 74 " --> pdb=" O LYS c 71 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL c 75 " --> pdb=" O PRO c 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 71 through 75' Processing helix chain 'c' and resid 81 through 95 removed outlier: 3.518A pdb=" N ASP c 95 " --> pdb=" O ASN c 91 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 110 Processing helix chain 'c' and resid 111 through 125 removed outlier: 3.668A pdb=" N VAL c 115 " --> pdb=" O ASP c 111 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 142 removed outlier: 3.586A pdb=" N VAL c 132 " --> pdb=" O SER c 128 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 14 removed outlier: 3.750A pdb=" N ARG d 14 " --> pdb=" O LYS d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 45 through 62 removed outlier: 4.064A pdb=" N LEU d 60 " --> pdb=" O LYS d 56 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR d 61 " --> pdb=" O LEU d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 74 removed outlier: 3.852A pdb=" N ILE d 74 " --> pdb=" O ASN d 70 " (cutoff:3.500A) Processing helix chain 'd' and resid 81 through 91 removed outlier: 3.524A pdb=" N MET d 87 " --> pdb=" O GLY d 83 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 101 Processing helix chain 'd' and resid 106 through 116 Processing helix chain 'd' and resid 142 through 146 removed outlier: 3.917A pdb=" N GLN d 146 " --> pdb=" O GLU d 143 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 155 Processing helix chain 'd' and resid 191 through 196 removed outlier: 3.802A pdb=" N VAL d 195 " --> pdb=" O GLU d 191 " (cutoff:3.500A) Processing helix chain 'd' and resid 197 through 200 Processing helix chain 'e' and resid 55 through 66 Processing helix chain 'e' and resid 109 through 116 removed outlier: 3.615A pdb=" N ALA e 113 " --> pdb=" O GLY e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 145 Processing helix chain 'e' and resid 149 through 157 removed outlier: 3.549A pdb=" N VAL e 153 " --> pdb=" O ASN e 149 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 30 removed outlier: 3.609A pdb=" N LYS f 20 " --> pdb=" O GLU f 16 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA f 21 " --> pdb=" O ASP f 17 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU f 22 " --> pdb=" O ALA f 18 " (cutoff:3.500A) Processing helix chain 'f' and resid 72 through 80 removed outlier: 3.562A pdb=" N PHE f 76 " --> pdb=" O ALA f 72 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 30 removed outlier: 4.201A pdb=" N THR g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS g 25 " --> pdb=" O LYS g 21 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 54 removed outlier: 3.682A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER g 45 " --> pdb=" O ARG g 41 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA g 46 " --> pdb=" O ILE g 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 67 removed outlier: 3.707A pdb=" N VAL g 61 " --> pdb=" O ASP g 57 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN g 67 " --> pdb=" O GLU g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 107 Processing helix chain 'g' and resid 119 through 129 removed outlier: 3.656A pdb=" N GLU g 123 " --> pdb=" O ARG g 119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN g 129 " --> pdb=" O LEU g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 133 through 148 Processing helix chain 'h' and resid 5 through 17 Processing helix chain 'h' and resid 31 through 43 Processing helix chain 'h' and resid 97 through 101 Processing helix chain 'h' and resid 114 through 120 Processing helix chain 'i' and resid 31 through 35 Processing helix chain 'i' and resid 52 through 57 Processing helix chain 'i' and resid 74 through 93 Processing helix chain 'i' and resid 96 through 102 Processing helix chain 'j' and resid 14 through 32 removed outlier: 3.974A pdb=" N ILE j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP j 19 " --> pdb=" O HIS j 15 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL j 26 " --> pdb=" O ALA j 22 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU j 27 " --> pdb=" O GLU j 23 " (cutoff:3.500A) Processing helix chain 'j' and resid 82 through 87 Processing helix chain 'k' and resid 53 through 57 removed outlier: 3.562A pdb=" N LYS k 57 " --> pdb=" O GLY k 54 " (cutoff:3.500A) Processing helix chain 'k' and resid 59 through 78 removed outlier: 3.919A pdb=" N SER k 73 " --> pdb=" O THR k 69 " (cutoff:3.500A) Processing helix chain 'k' and resid 93 through 103 removed outlier: 3.515A pdb=" N ILE k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 8 Processing helix chain 'm' and resid 67 through 81 Processing helix chain 'm' and resid 87 through 91 removed outlier: 3.515A pdb=" N HIS m 91 " --> pdb=" O GLY m 88 " (cutoff:3.500A) Processing helix chain 'n' and resid 4 through 11 Processing helix chain 'n' and resid 42 through 51 Processing helix chain 'o' and resid 4 through 12 Processing helix chain 'o' and resid 24 through 43 Processing helix chain 'o' and resid 50 through 74 removed outlier: 4.106A pdb=" N ARG o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 86 removed outlier: 3.518A pdb=" N TYR o 78 " --> pdb=" O ASP o 74 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY o 86 " --> pdb=" O ILE o 82 " (cutoff:3.500A) Processing helix chain 'p' and resid 55 through 63 Processing helix chain 'p' and resid 68 through 79 Processing helix chain 'p' and resid 79 through 89 removed outlier: 4.180A pdb=" N LYS p 83 " --> pdb=" O GLY p 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 30 through 35 Processing helix chain 'r' and resid 46 through 51 Processing helix chain 'r' and resid 53 through 70 Processing helix chain 's' and resid 15 through 20 removed outlier: 3.836A pdb=" N VAL s 19 " --> pdb=" O LEU s 15 " (cutoff:3.500A) Processing helix chain 't' and resid 8 through 38 removed outlier: 4.163A pdb=" N LYS t 12 " --> pdb=" O ILE t 8 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN t 24 " --> pdb=" O ARG t 20 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA t 27 " --> pdb=" O SER t 23 " (cutoff:3.500A) Processing helix chain 't' and resid 45 through 60 removed outlier: 3.903A pdb=" N SER t 51 " --> pdb=" O ASN t 47 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS t 55 " --> pdb=" O SER t 51 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL t 57 " --> pdb=" O ALA t 53 " (cutoff:3.500A) Processing helix chain 't' and resid 74 through 79 removed outlier: 3.706A pdb=" N MET t 79 " --> pdb=" O LYS t 75 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'b' and resid 31 through 35 removed outlier: 7.130A pdb=" N ILE b 40 " --> pdb=" O PHE b 32 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLU b 34 " --> pdb=" O ILE b 38 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE b 38 " --> pdb=" O GLU b 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'b' and resid 90 through 92 removed outlier: 6.833A pdb=" N PHE b 69 " --> pdb=" O ILE b 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 20 through 21 removed outlier: 7.230A pdb=" N HIS c 68 " --> pdb=" O SER c 52 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL c 54 " --> pdb=" O ALA c 66 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA c 66 " --> pdb=" O VAL c 54 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE c 56 " --> pdb=" O ASN c 64 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASN c 64 " --> pdb=" O ILE c 56 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ILE c 63 " --> pdb=" O HIS c 99 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASN c 101 " --> pdb=" O ILE c 63 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE c 65 " --> pdb=" O ASN c 101 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE c 103 " --> pdb=" O ILE c 65 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE c 67 " --> pdb=" O ILE c 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'c' and resid 162 through 166 Processing sheet with id=AA5, first strand: chain 'c' and resid 162 through 166 Processing sheet with id=AA6, first strand: chain 'c' and resid 187 through 190 Processing sheet with id=AA7, first strand: chain 'd' and resid 120 through 121 Processing sheet with id=AA8, first strand: chain 'e' and resid 14 through 21 removed outlier: 5.340A pdb=" N VAL e 15 " --> pdb=" O VAL e 38 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL e 38 " --> pdb=" O VAL e 15 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY e 51 " --> pdb=" O ALA e 35 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'e' and resid 85 through 87 removed outlier: 6.589A pdb=" N ILE e 106 " --> pdb=" O SER e 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'f' and resid 36 through 40 removed outlier: 5.532A pdb=" N VAL f 37 " --> pdb=" O LYS f 66 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS f 66 " --> pdb=" O VAL f 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'f' and resid 36 through 40 removed outlier: 5.532A pdb=" N VAL f 37 " --> pdb=" O LYS f 66 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS f 66 " --> pdb=" O VAL f 37 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG f 88 " --> pdb=" O ILE f 9 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'g' and resid 73 through 74 Processing sheet with id=AB4, first strand: chain 'h' and resid 25 through 26 removed outlier: 3.657A pdb=" N ASN h 48 " --> pdb=" O PHE h 63 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'h' and resid 76 through 79 Processing sheet with id=AB6, first strand: chain 'h' and resid 76 through 79 removed outlier: 5.359A pdb=" N ILE h 127 " --> pdb=" O SER h 107 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER h 107 " --> pdb=" O ILE h 127 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA h 129 " --> pdb=" O LEU h 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'i' and resid 8 through 9 Processing sheet with id=AB8, first strand: chain 'i' and resid 12 through 13 Processing sheet with id=AB9, first strand: chain 'j' and resid 36 through 41 removed outlier: 5.032A pdb=" N GLY j 38 " --> pdb=" O ASP j 75 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP j 75 " --> pdb=" O GLY j 38 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU j 99 " --> pdb=" O ARG j 9 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'j' and resid 47 through 52 Processing sheet with id=AC2, first strand: chain 'k' and resid 41 through 45 removed outlier: 3.663A pdb=" N SER k 43 " --> pdb=" O ILE k 34 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLY k 19 " --> pdb=" O GLU k 83 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N THR k 85 " --> pdb=" O GLY k 19 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ALA k 21 " --> pdb=" O THR k 85 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LYS k 87 " --> pdb=" O ALA k 21 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE k 23 " --> pdb=" O LYS k 87 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N VAL k 82 " --> pdb=" O THR k 108 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ILE k 110 " --> pdb=" O VAL k 82 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL k 84 " --> pdb=" O ILE k 110 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'l' and resid 75 through 79 removed outlier: 7.511A pdb=" N TYR l 65 " --> pdb=" O VAL l 50 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL l 50 " --> pdb=" O TYR l 65 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ARG l 67 " --> pdb=" O THR l 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'p' and resid 5 through 11 removed outlier: 4.137A pdb=" N GLY p 38 " --> pdb=" O ILE p 20 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL p 22 " --> pdb=" O GLN p 36 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLN p 36 " --> pdb=" O VAL p 22 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'q' and resid 9 through 19 removed outlier: 16.231A pdb=" N VAL q 9 " --> pdb=" O TYR q 30 " (cutoff:3.500A) removed outlier: 12.802A pdb=" N TYR q 30 " --> pdb=" O VAL q 9 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N VAL q 11 " --> pdb=" O GLU q 28 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N GLU q 28 " --> pdb=" O VAL q 11 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR q 24 " --> pdb=" O VAL q 15 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ASP q 17 " --> pdb=" O THR q 22 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N THR q 22 " --> pdb=" O ASP q 17 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR q 29 " --> pdb=" O TYR q 42 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR q 42 " --> pdb=" O THR q 29 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE q 75 " --> pdb=" O LYS q 47 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU q 77 " --> pdb=" O HIS q 49 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LYS q 62 " --> pdb=" O VAL q 78 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE q 80 " --> pdb=" O ILE q 60 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE q 60 " --> pdb=" O ILE q 80 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 's' and resid 31 through 33 removed outlier: 3.625A pdb=" N TYR s 52 " --> pdb=" O THR s 33 " (cutoff:3.500A) 625 hydrogen bonds defined for protein. 1764 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1201 hydrogen bonds 1946 hydrogen bond angles 0 basepair planarities 483 basepair parallelities 891 stacking parallelities Total time for adding SS restraints: 52.27 Time building geometry restraints manager: 28.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5770 1.32 - 1.44: 24258 1.44 - 1.57: 22909 1.57 - 1.70: 3162 1.70 - 1.82: 88 Bond restraints: 56187 Sorted by residual: bond pdb=" CG1 ILE d 128 " pdb=" CD1 ILE d 128 " ideal model delta sigma weight residual 1.513 1.334 0.179 3.90e-02 6.57e+02 2.10e+01 bond pdb=" CB VAL l 106 " pdb=" CG1 VAL l 106 " ideal model delta sigma weight residual 1.521 1.407 0.114 3.30e-02 9.18e+02 1.18e+01 bond pdb=" C LEU q 26 " pdb=" N VAL q 27 " ideal model delta sigma weight residual 1.331 1.290 0.041 1.27e-02 6.20e+03 1.03e+01 bond pdb=" C ASP b 192 " pdb=" N PRO b 193 " ideal model delta sigma weight residual 1.334 1.404 -0.070 2.34e-02 1.83e+03 9.03e+00 bond pdb=" CG1 ILE p 74 " pdb=" CD1 ILE p 74 " ideal model delta sigma weight residual 1.513 1.397 0.116 3.90e-02 6.57e+02 8.88e+00 ... (remaining 56182 not shown) Histogram of bond angle deviations from ideal: 95.67 - 104.28: 6654 104.28 - 112.88: 32631 112.88 - 121.48: 30087 121.48 - 130.08: 13279 130.08 - 138.68: 1007 Bond angle restraints: 83658 Sorted by residual: angle pdb=" N ASP b 194 " pdb=" CA ASP b 194 " pdb=" C ASP b 194 " ideal model delta sigma weight residual 114.62 104.80 9.82 1.14e+00 7.69e-01 7.42e+01 angle pdb=" N VAL t 39 " pdb=" CA VAL t 39 " pdb=" C VAL t 39 " ideal model delta sigma weight residual 113.71 106.61 7.10 9.50e-01 1.11e+00 5.58e+01 angle pdb=" C ASN i 51 " pdb=" N GLN i 52 " pdb=" CA GLN i 52 " ideal model delta sigma weight residual 120.09 129.04 -8.95 1.25e+00 6.40e-01 5.13e+01 angle pdb=" C3' A a 540 " pdb=" O3' A a 540 " pdb=" P A a 541 " ideal model delta sigma weight residual 120.20 130.92 -10.72 1.50e+00 4.44e-01 5.11e+01 angle pdb=" C ASP t 44 " pdb=" N ASN t 45 " pdb=" CA ASN t 45 " ideal model delta sigma weight residual 122.07 130.78 -8.71 1.43e+00 4.89e-01 3.71e+01 ... (remaining 83653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 31578 35.91 - 71.82: 3841 71.82 - 107.73: 416 107.73 - 143.64: 10 143.64 - 179.55: 12 Dihedral angle restraints: 35857 sinusoidal: 29376 harmonic: 6481 Sorted by residual: dihedral pdb=" O4' U a 477 " pdb=" C1' U a 477 " pdb=" N1 U a 477 " pdb=" C2 U a 477 " ideal model delta sinusoidal sigma weight residual 200.00 20.45 179.55 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U a 315 " pdb=" C1' U a 315 " pdb=" N1 U a 315 " pdb=" C2 U a 315 " ideal model delta sinusoidal sigma weight residual -160.00 13.66 -173.66 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U a 851 " pdb=" C1' U a 851 " pdb=" N1 U a 851 " pdb=" C2 U a 851 " ideal model delta sinusoidal sigma weight residual -160.00 3.37 -163.37 1 1.50e+01 4.44e-03 8.35e+01 ... (remaining 35854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 9690 0.111 - 0.221: 843 0.221 - 0.332: 94 0.332 - 0.442: 9 0.442 - 0.553: 5 Chirality restraints: 10641 Sorted by residual: chirality pdb=" C1' G a 493 " pdb=" O4' G a 493 " pdb=" C2' G a 493 " pdb=" N9 G a 493 " both_signs ideal model delta sigma weight residual False 2.46 1.91 0.55 2.00e-01 2.50e+01 7.64e+00 chirality pdb=" CB VAL p 21 " pdb=" CA VAL p 21 " pdb=" CG1 VAL p 21 " pdb=" CG2 VAL p 21 " both_signs ideal model delta sigma weight residual False -2.63 -2.10 -0.53 2.00e-01 2.50e+01 7.01e+00 chirality pdb=" CB ILE h 127 " pdb=" CA ILE h 127 " pdb=" CG1 ILE h 127 " pdb=" CG2 ILE h 127 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.51 2.00e-01 2.50e+01 6.53e+00 ... (remaining 10638 not shown) Planarity restraints: 4733 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A a1436 " -0.073 2.00e-02 2.50e+03 3.69e-02 3.74e+01 pdb=" N9 A a1436 " 0.091 2.00e-02 2.50e+03 pdb=" C8 A a1436 " -0.013 2.00e-02 2.50e+03 pdb=" N7 A a1436 " -0.008 2.00e-02 2.50e+03 pdb=" C5 A a1436 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A a1436 " -0.010 2.00e-02 2.50e+03 pdb=" N6 A a1436 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A a1436 " -0.014 2.00e-02 2.50e+03 pdb=" C2 A a1436 " 0.000 2.00e-02 2.50e+03 pdb=" N3 A a1436 " 0.008 2.00e-02 2.50e+03 pdb=" C4 A a1436 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS k 118 " -0.034 2.00e-02 2.50e+03 4.24e-02 2.69e+01 pdb=" CG HIS k 118 " 0.090 2.00e-02 2.50e+03 pdb=" ND1 HIS k 118 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 HIS k 118 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 HIS k 118 " -0.010 2.00e-02 2.50e+03 pdb=" NE2 HIS k 118 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A a 945 " -0.069 2.00e-02 2.50e+03 3.05e-02 2.55e+01 pdb=" N9 A a 945 " 0.061 2.00e-02 2.50e+03 pdb=" C8 A a 945 " 0.014 2.00e-02 2.50e+03 pdb=" N7 A a 945 " 0.005 2.00e-02 2.50e+03 pdb=" C5 A a 945 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A a 945 " -0.012 2.00e-02 2.50e+03 pdb=" N6 A a 945 " -0.021 2.00e-02 2.50e+03 pdb=" N1 A a 945 " -0.012 2.00e-02 2.50e+03 pdb=" C2 A a 945 " 0.027 2.00e-02 2.50e+03 pdb=" N3 A a 945 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A a 945 " 0.005 2.00e-02 2.50e+03 ... (remaining 4730 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 13214 2.80 - 3.33: 39653 3.33 - 3.85: 112456 3.85 - 4.38: 125101 4.38 - 4.90: 173347 Nonbonded interactions: 463771 Sorted by model distance: nonbonded pdb=" OE2 GLU h 43 " pdb=" NZ LYS h 116 " model vdw 2.280 2.520 nonbonded pdb=" OP2 C a 530 " pdb=" OH TYR l 79 " model vdw 2.314 2.440 nonbonded pdb=" O2' G a 262 " pdb=" O ASP q 20 " model vdw 2.317 2.440 nonbonded pdb=" O2' A a 401 " pdb=" OP1 G a 493 " model vdw 2.318 2.440 nonbonded pdb=" NE2 GLN b 19 " pdb=" OD2 ASP b 188 " model vdw 2.326 2.520 ... (remaining 463766 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.00 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: 7.370 Check model and map are aligned: 0.760 Set scattering table: 0.450 Process input model: 176.090 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.170 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 189.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.179 56187 Z= 0.568 Angle : 1.433 17.906 83658 Z= 0.687 Chirality : 0.066 0.553 10641 Planarity : 0.010 0.107 4733 Dihedral : 23.588 179.553 31675 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.75 % Favored : 88.84 % Rotamer: Outliers : 2.86 % Allowed : 11.64 % Favored : 85.51 % 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: -5.79 (0.12), residues: 2205 helix: -4.52 (0.08), residues: 749 sheet: -3.32 (0.22), residues: 352 loop : -3.50 (0.14), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP c 200 HIS 0.051 0.003 HIS k 118 PHE 0.036 0.004 PHE b 126 TYR 0.032 0.004 TYR l 108 ARG 0.017 0.001 ARG l 123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 429 time to evaluate : 3.475 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: b 21 ARG cc_start: 0.3231 (OUTLIER) cc_final: 0.2900 (tpt90) REVERT: b 22 ARG cc_start: 0.6929 (ptp-170) cc_final: 0.6573 (mtp180) REVERT: b 79 SER cc_start: 0.7726 (m) cc_final: 0.7277 (t) REVERT: b 104 TYR cc_start: 0.8086 (t80) cc_final: 0.7793 (t80) REVERT: b 116 GLU cc_start: 0.5186 (OUTLIER) cc_final: 0.4681 (tp30) REVERT: b 159 GLN cc_start: 0.7223 (mm-40) cc_final: 0.6929 (mp10) REVERT: b 167 ARG cc_start: 0.6381 (ptm160) cc_final: 0.6062 (ptm160) REVERT: c 17 ASP cc_start: 0.7173 (t70) cc_final: 0.6304 (p0) REVERT: c 35 ASP cc_start: 0.4467 (m-30) cc_final: 0.4243 (m-30) REVERT: c 129 PHE cc_start: 0.7513 (p90) cc_final: 0.7312 (p90) REVERT: c 166 GLN cc_start: 0.7027 (pt0) cc_final: 0.6612 (pm20) REVERT: c 167 TYR cc_start: 0.8146 (m-10) cc_final: 0.7052 (m-10) REVERT: c 189 ASP cc_start: 0.8845 (m-30) cc_final: 0.8637 (m-30) REVERT: d 8 ASN cc_start: 0.8653 (t0) cc_final: 0.8425 (t0) REVERT: d 92 SER cc_start: 0.9220 (m) cc_final: 0.8990 (t) REVERT: d 114 VAL cc_start: 0.8853 (p) cc_final: 0.8623 (t) REVERT: e 12 GLU cc_start: 0.8490 (tt0) cc_final: 0.8234 (tt0) REVERT: e 26 LYS cc_start: 0.6748 (pttt) cc_final: 0.6036 (tptp) REVERT: f 1 MET cc_start: 0.8433 (tpp) cc_final: 0.8189 (mmt) REVERT: f 30 LEU cc_start: 0.8965 (mt) cc_final: 0.8708 (mt) REVERT: f 47 ARG cc_start: 0.8419 (ttt-90) cc_final: 0.8187 (tpt-90) REVERT: f 70 ASN cc_start: 0.7763 (p0) cc_final: 0.7538 (t0) REVERT: f 75 GLU cc_start: 0.7962 (tp30) cc_final: 0.7454 (tp30) REVERT: g 92 ARG cc_start: 0.3430 (ptt90) cc_final: 0.2999 (ttp-170) REVERT: k 16 ILE cc_start: 0.8309 (tt) cc_final: 0.8044 (mp) REVERT: k 101 GLN cc_start: 0.8244 (tt0) cc_final: 0.8019 (tp-100) REVERT: l 60 SER cc_start: 0.8532 (t) cc_final: 0.8256 (t) REVERT: l 116 ASP cc_start: 0.7636 (t70) cc_final: 0.7338 (t70) REVERT: m 57 ARG cc_start: 0.6183 (ptp90) cc_final: 0.5189 (mmm160) REVERT: o 15 TYR cc_start: 0.8093 (m-80) cc_final: 0.7809 (m-80) REVERT: o 22 THR cc_start: 0.7821 (p) cc_final: 0.7347 (m) REVERT: p 36 GLN cc_start: 0.8611 (tt0) cc_final: 0.8389 (tt0) REVERT: p 78 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7020 (tm-30) REVERT: q 56 LYS cc_start: 0.8516 (mtmm) cc_final: 0.8167 (mtmm) REVERT: q 66 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8541 (t) REVERT: s 16 MET cc_start: 0.4572 (mmm) cc_final: 0.4163 (mmm) outliers start: 55 outliers final: 18 residues processed: 463 average time/residue: 0.7265 time to fit residues: 535.2186 Evaluate side-chains 341 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 320 time to evaluate : 2.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 21 ARG Chi-restraints excluded: chain b residue 90 PHE Chi-restraints excluded: chain b residue 116 GLU Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain d residue 9 TRP Chi-restraints excluded: chain e residue 163 GLU Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 56 LYS Chi-restraints excluded: chain h residue 57 GLN Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 129 LEU Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain r residue 76 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 30.0000 chunk 284 optimal weight: 40.0000 chunk 157 optimal weight: 20.0000 chunk 97 optimal weight: 30.0000 chunk 191 optimal weight: 10.0000 chunk 151 optimal weight: 20.0000 chunk 293 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 178 optimal weight: 8.9990 chunk 218 optimal weight: 2.9990 chunk 340 optimal weight: 6.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 159 GLN c 88 ASN ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 99 HIS c 133 GLN d 35 GLN d 36 HIS d 67 GLN d 82 HIS ** d 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 118 HIS d 146 GLN d 166 ASN f 53 ASN g 28 ASN g 130 ASN g 148 ASN g 153 HIS h 18 ASN i 77 GLN ** i 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 15 HIS k 18 ASN ** l 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 74 ASN m 76 ASN n 14 GLN n 52 GLN ** o 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS p 72 HIS r 57 GLN s 57 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.106 56187 Z= 0.503 Angle : 0.863 10.461 83658 Z= 0.430 Chirality : 0.044 0.339 10641 Planarity : 0.007 0.088 4733 Dihedral : 24.012 178.260 27086 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.57 % Favored : 89.30 % Rotamer: Outliers : 5.19 % Allowed : 18.44 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.50 (0.14), residues: 2205 helix: -2.48 (0.15), residues: 764 sheet: -3.16 (0.24), residues: 333 loop : -3.32 (0.15), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP h 132 HIS 0.013 0.002 HIS k 118 PHE 0.022 0.003 PHE i 54 TYR 0.025 0.002 TYR l 108 ARG 0.008 0.001 ARG h 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 339 time to evaluate : 3.202 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 22 ARG cc_start: 0.7242 (ptp-170) cc_final: 0.6653 (mtp180) REVERT: b 90 PHE cc_start: 0.6302 (OUTLIER) cc_final: 0.5924 (p90) REVERT: b 95 ARG cc_start: 0.7118 (tpt-90) cc_final: 0.6807 (tpt90) REVERT: b 159 GLN cc_start: 0.7221 (mm110) cc_final: 0.6937 (mp10) REVERT: c 17 ASP cc_start: 0.6902 (t70) cc_final: 0.6329 (p0) REVERT: c 117 GLU cc_start: 0.7909 (tp30) cc_final: 0.7678 (tp30) REVERT: c 166 GLN cc_start: 0.6808 (pt0) cc_final: 0.6169 (pm20) REVERT: c 167 TYR cc_start: 0.8281 (m-10) cc_final: 0.7404 (m-10) REVERT: d 191 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7452 (pm20) REVERT: e 26 LYS cc_start: 0.6838 (pttt) cc_final: 0.6101 (tptp) REVERT: f 8 TYR cc_start: 0.8712 (p90) cc_final: 0.8462 (p90) REVERT: f 20 LYS cc_start: 0.8747 (tmtt) cc_final: 0.8226 (tppt) REVERT: f 38 LEU cc_start: 0.9004 (tp) cc_final: 0.8779 (tp) REVERT: f 41 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7745 (ttmm) REVERT: f 61 ASN cc_start: 0.8324 (OUTLIER) cc_final: 0.7628 (p0) REVERT: f 70 ASN cc_start: 0.7930 (p0) cc_final: 0.7648 (t0) REVERT: g 92 ARG cc_start: 0.2954 (ptt90) cc_final: 0.2563 (ttp-170) REVERT: k 77 HIS cc_start: 0.7123 (m-70) cc_final: 0.6823 (m-70) REVERT: k 93 ARG cc_start: 0.8665 (mtp-110) cc_final: 0.7785 (ttm110) REVERT: l 60 SER cc_start: 0.8578 (t) cc_final: 0.8347 (t) REVERT: l 110 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8266 (pt) REVERT: l 116 ASP cc_start: 0.7920 (t70) cc_final: 0.7675 (t70) REVERT: m 57 ARG cc_start: 0.5614 (ptp90) cc_final: 0.4852 (mmm160) REVERT: o 15 TYR cc_start: 0.8146 (m-80) cc_final: 0.7946 (m-80) REVERT: o 36 ILE cc_start: 0.8667 (pt) cc_final: 0.8420 (mt) REVERT: p 24 ASP cc_start: 0.8735 (t70) cc_final: 0.8431 (t0) REVERT: p 36 GLN cc_start: 0.8861 (tt0) cc_final: 0.8566 (tt0) REVERT: p 69 ASP cc_start: 0.7906 (m-30) cc_final: 0.7653 (m-30) REVERT: p 78 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7381 (tm-30) REVERT: q 56 LYS cc_start: 0.8559 (mtmm) cc_final: 0.8271 (mtmm) REVERT: q 66 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8608 (t) outliers start: 100 outliers final: 66 residues processed: 407 average time/residue: 0.6801 time to fit residues: 454.0613 Evaluate side-chains 379 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 308 time to evaluate : 3.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 90 PHE Chi-restraints excluded: chain b residue 116 GLU Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 143 LEU Chi-restraints excluded: chain c residue 180 ASP Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 81 VAL Chi-restraints excluded: chain d residue 122 ASP Chi-restraints excluded: chain d residue 149 ASN Chi-restraints excluded: chain d residue 191 GLU Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 94 VAL Chi-restraints excluded: chain e residue 124 LEU Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 76 PHE Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain g residue 73 LEU Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 56 LYS Chi-restraints excluded: chain h residue 57 GLN Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain i residue 24 VAL Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain l residue 129 LEU Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain o residue 72 SER Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain o residue 85 LEU Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 49 GLU Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 87 GLN Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 42 TYR Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 26 ILE Chi-restraints excluded: chain r residue 52 THR Chi-restraints excluded: chain r residue 73 LEU Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 22 ILE Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 54 VAL Chi-restraints excluded: chain t residue 74 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 50.0000 chunk 105 optimal weight: 50.0000 chunk 283 optimal weight: 40.0000 chunk 231 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 341 optimal weight: 3.9990 chunk 368 optimal weight: 4.9990 chunk 303 optimal weight: 1.9990 chunk 338 optimal weight: 0.8980 chunk 116 optimal weight: 50.0000 chunk 273 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 8 GLN ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 8 ASN d 115 ASN e 145 GLN e 166 ASN h 57 GLN i 128 GLN j 15 HIS j 64 GLN k 101 GLN l 29 ASN ** l 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 56187 Z= 0.219 Angle : 0.618 8.887 83658 Z= 0.318 Chirality : 0.036 0.282 10641 Planarity : 0.005 0.072 4733 Dihedral : 23.808 179.002 27072 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.66 % Favored : 91.29 % Rotamer: Outliers : 4.68 % Allowed : 21.51 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.16), residues: 2205 helix: -1.28 (0.17), residues: 777 sheet: -2.92 (0.25), residues: 350 loop : -3.07 (0.16), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP k 44 HIS 0.019 0.002 HIS j 15 PHE 0.015 0.002 PHE c 129 TYR 0.023 0.002 TYR l 108 ARG 0.006 0.000 ARG n 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 336 time to evaluate : 3.296 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 22 ARG cc_start: 0.7378 (ptp-170) cc_final: 0.6648 (mtp180) REVERT: b 95 ARG cc_start: 0.7114 (tpt-90) cc_final: 0.6671 (tpt90) REVERT: b 152 ARG cc_start: 0.5484 (mtp85) cc_final: 0.5245 (mmm-85) REVERT: b 159 GLN cc_start: 0.7461 (mm110) cc_final: 0.7096 (mp10) REVERT: c 129 PHE cc_start: 0.8168 (p90) cc_final: 0.7755 (p90) REVERT: c 166 GLN cc_start: 0.6726 (pt0) cc_final: 0.6196 (pm20) REVERT: c 167 TYR cc_start: 0.8301 (m-10) cc_final: 0.7535 (m-10) REVERT: d 8 ASN cc_start: 0.8777 (t160) cc_final: 0.8162 (t0) REVERT: e 12 GLU cc_start: 0.8575 (tt0) cc_final: 0.8252 (tt0) REVERT: e 26 LYS cc_start: 0.6587 (pttt) cc_final: 0.6062 (tptp) REVERT: e 160 THR cc_start: 0.8864 (p) cc_final: 0.8566 (p) REVERT: f 38 LEU cc_start: 0.8915 (tp) cc_final: 0.8703 (tp) REVERT: f 70 ASN cc_start: 0.7908 (p0) cc_final: 0.7600 (t0) REVERT: f 78 ARG cc_start: 0.8476 (tmm-80) cc_final: 0.8246 (ttp80) REVERT: g 92 ARG cc_start: 0.2901 (ptt90) cc_final: 0.2455 (ttp-170) REVERT: h 35 GLU cc_start: 0.7495 (tp30) cc_final: 0.7261 (mt-10) REVERT: k 77 HIS cc_start: 0.7136 (m-70) cc_final: 0.6602 (m-70) REVERT: k 93 ARG cc_start: 0.8615 (mtp-110) cc_final: 0.7769 (ttm110) REVERT: l 60 SER cc_start: 0.8155 (t) cc_final: 0.7839 (t) REVERT: l 108 TYR cc_start: 0.8592 (m-80) cc_final: 0.8278 (m-80) REVERT: l 116 ASP cc_start: 0.7824 (t70) cc_final: 0.7556 (t70) REVERT: m 57 ARG cc_start: 0.5507 (ptp90) cc_final: 0.4709 (mmm160) REVERT: o 15 TYR cc_start: 0.7971 (m-80) cc_final: 0.7721 (m-80) REVERT: p 50 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9096 (pt) REVERT: p 78 GLU cc_start: 0.7454 (tm-30) cc_final: 0.7107 (tm-30) REVERT: q 19 MET cc_start: 0.8588 (mtm) cc_final: 0.8261 (mtm) REVERT: q 66 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8507 (t) outliers start: 90 outliers final: 55 residues processed: 395 average time/residue: 0.7000 time to fit residues: 451.4922 Evaluate side-chains 365 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 308 time to evaluate : 3.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 104 TYR Chi-restraints excluded: chain b residue 116 GLU Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 180 ASP Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain c residue 185 HIS Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 122 ASP Chi-restraints excluded: chain d residue 170 ASP Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 124 LEU Chi-restraints excluded: chain e residue 127 SER Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 56 LYS Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain i residue 24 VAL Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 56 VAL Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain m residue 61 ASP Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 49 GLU Chi-restraints excluded: chain p residue 50 ILE Chi-restraints excluded: chain p residue 87 GLN Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 42 TYR Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain q residue 85 VAL Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 16 CYS Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 26 ILE Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 73 LEU Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 22 ILE Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 50 VAL Chi-restraints excluded: chain t residue 54 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 3.9990 chunk 256 optimal weight: 7.9990 chunk 177 optimal weight: 0.5980 chunk 37 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 229 optimal weight: 5.9990 chunk 342 optimal weight: 7.9990 chunk 362 optimal weight: 30.0000 chunk 178 optimal weight: 3.9990 chunk 324 optimal weight: 9.9990 chunk 97 optimal weight: 30.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 64 ASN c 68 HIS ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 135 ASN e 145 GLN k 101 GLN l 90 HIS ** l 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 ASN o 50 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 56187 Z= 0.301 Angle : 0.662 8.801 83658 Z= 0.336 Chirality : 0.037 0.331 10641 Planarity : 0.005 0.069 4733 Dihedral : 23.748 179.159 27064 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.80 % Favored : 90.16 % Rotamer: Outliers : 5.71 % Allowed : 22.39 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.16), residues: 2205 helix: -0.82 (0.18), residues: 782 sheet: -2.73 (0.27), residues: 331 loop : -3.08 (0.16), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP d 9 HIS 0.013 0.002 HIS o 51 PHE 0.015 0.002 PHE c 129 TYR 0.026 0.002 TYR l 108 ARG 0.009 0.000 ARG n 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 319 time to evaluate : 3.187 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: b 22 ARG cc_start: 0.7651 (ptp-170) cc_final: 0.6940 (mtp180) REVERT: b 95 ARG cc_start: 0.7278 (tpt-90) cc_final: 0.6884 (tpt90) REVERT: b 126 PHE cc_start: 0.4883 (OUTLIER) cc_final: 0.3648 (p90) REVERT: b 135 VAL cc_start: 0.7462 (OUTLIER) cc_final: 0.7173 (p) REVERT: b 152 ARG cc_start: 0.5463 (mtp85) cc_final: 0.5239 (mmm-85) REVERT: b 159 GLN cc_start: 0.7421 (mm110) cc_final: 0.7033 (mp10) REVERT: c 129 PHE cc_start: 0.8163 (p90) cc_final: 0.7823 (p90) REVERT: c 166 GLN cc_start: 0.6749 (pt0) cc_final: 0.6244 (pm20) REVERT: c 167 TYR cc_start: 0.8354 (m-10) cc_final: 0.7474 (m-10) REVERT: d 8 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8227 (t0) REVERT: e 26 LYS cc_start: 0.6680 (pttt) cc_final: 0.5966 (tptp) REVERT: f 20 LYS cc_start: 0.8705 (tmtt) cc_final: 0.8214 (tppt) REVERT: f 61 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7837 (p0) REVERT: f 70 ASN cc_start: 0.8075 (p0) cc_final: 0.7737 (t0) REVERT: f 78 ARG cc_start: 0.8449 (tmm-80) cc_final: 0.8237 (ttp80) REVERT: f 93 ARG cc_start: 0.8007 (ttt180) cc_final: 0.7712 (ttm-80) REVERT: g 92 ARG cc_start: 0.2930 (ptt90) cc_final: 0.2456 (ttp-170) REVERT: h 35 GLU cc_start: 0.7594 (tp30) cc_final: 0.7342 (mt-10) REVERT: h 98 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8689 (tp) REVERT: k 93 ARG cc_start: 0.8727 (mtp-110) cc_final: 0.7926 (ttm110) REVERT: l 60 SER cc_start: 0.8241 (t) cc_final: 0.7900 (t) REVERT: l 108 TYR cc_start: 0.8637 (m-80) cc_final: 0.8335 (m-80) REVERT: l 110 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8316 (pt) REVERT: l 116 ASP cc_start: 0.7869 (t70) cc_final: 0.7600 (t70) REVERT: m 57 ARG cc_start: 0.5133 (ptp90) cc_final: 0.4105 (mmm160) REVERT: o 15 TYR cc_start: 0.8061 (m-80) cc_final: 0.7787 (m-80) REVERT: p 78 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7370 (tm-30) REVERT: q 19 MET cc_start: 0.8590 (mtm) cc_final: 0.8278 (mtm) outliers start: 110 outliers final: 79 residues processed: 389 average time/residue: 0.6750 time to fit residues: 432.0844 Evaluate side-chains 386 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 301 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 79 SER Chi-restraints excluded: chain b residue 114 ILE Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 126 PHE Chi-restraints excluded: chain b residue 135 VAL Chi-restraints excluded: chain b residue 137 LEU Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 143 LEU Chi-restraints excluded: chain c residue 180 ASP Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain c residue 185 HIS Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 8 ASN Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 84 GLU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 122 ASP Chi-restraints excluded: chain d residue 170 ASP Chi-restraints excluded: chain e residue 41 ASP Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 94 VAL Chi-restraints excluded: chain e residue 124 LEU Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain g residue 90 GLU Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 56 LYS Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 24 VAL Chi-restraints excluded: chain i residue 56 VAL Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 52 THR Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain m residue 61 ASP Chi-restraints excluded: chain m residue 104 ASN Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain o residue 14 GLU Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 49 GLU Chi-restraints excluded: chain q residue 6 ASP Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 42 TYR Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain q residue 85 VAL Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 16 CYS Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 26 ILE Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 73 LEU Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain s residue 12 ASP Chi-restraints excluded: chain t residue 14 THR Chi-restraints excluded: chain t residue 22 ILE Chi-restraints excluded: chain t residue 32 VAL Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 50 VAL Chi-restraints excluded: chain t residue 54 VAL Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 74 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 0.7980 chunk 205 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 269 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 chunk 309 optimal weight: 0.7980 chunk 250 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 185 optimal weight: 5.9990 chunk 325 optimal weight: 40.0000 chunk 91 optimal weight: 5.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 68 HIS ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 135 ASN e 145 GLN j 56 HIS l 90 HIS ** l 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 56187 Z= 0.185 Angle : 0.569 9.968 83658 Z= 0.292 Chirality : 0.034 0.318 10641 Planarity : 0.004 0.065 4733 Dihedral : 23.640 179.733 27060 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.89 % Favored : 92.06 % Rotamer: Outliers : 4.94 % Allowed : 23.90 % Favored : 71.17 % 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: -2.78 (0.17), residues: 2205 helix: -0.27 (0.19), residues: 765 sheet: -2.60 (0.27), residues: 341 loop : -2.81 (0.17), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 200 HIS 0.013 0.001 HIS k 77 PHE 0.011 0.001 PHE d 68 TYR 0.020 0.001 TYR l 108 ARG 0.008 0.000 ARG n 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 319 time to evaluate : 3.080 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 22 ARG cc_start: 0.7652 (ptp-170) cc_final: 0.6857 (mtp180) REVERT: b 95 ARG cc_start: 0.7241 (tpt-90) cc_final: 0.6886 (tpt90) REVERT: b 126 PHE cc_start: 0.4907 (OUTLIER) cc_final: 0.3636 (p90) REVERT: b 135 VAL cc_start: 0.7522 (OUTLIER) cc_final: 0.7213 (p) REVERT: b 152 ARG cc_start: 0.5584 (mtp85) cc_final: 0.5345 (mmm-85) REVERT: b 159 GLN cc_start: 0.7415 (mm110) cc_final: 0.7045 (mp10) REVERT: c 129 PHE cc_start: 0.8101 (p90) cc_final: 0.7700 (p90) REVERT: c 166 GLN cc_start: 0.6670 (pt0) cc_final: 0.6126 (pm20) REVERT: c 167 TYR cc_start: 0.8337 (m-10) cc_final: 0.7519 (m-10) REVERT: d 8 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8092 (t0) REVERT: e 12 GLU cc_start: 0.8592 (tt0) cc_final: 0.8342 (tt0) REVERT: e 26 LYS cc_start: 0.6560 (pttt) cc_final: 0.5899 (tptp) REVERT: e 31 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7802 (p90) REVERT: f 20 LYS cc_start: 0.8639 (tttt) cc_final: 0.8222 (tppt) REVERT: f 61 ASN cc_start: 0.8187 (OUTLIER) cc_final: 0.7731 (p0) REVERT: f 70 ASN cc_start: 0.8062 (p0) cc_final: 0.7726 (t0) REVERT: f 78 ARG cc_start: 0.8477 (tmm-80) cc_final: 0.8138 (ttp80) REVERT: g 92 ARG cc_start: 0.2966 (ptt90) cc_final: 0.2466 (ttp-170) REVERT: h 35 GLU cc_start: 0.7512 (tp30) cc_final: 0.7298 (mt-10) REVERT: h 98 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8631 (tp) REVERT: i 112 MET cc_start: 0.7829 (mtm) cc_final: 0.7586 (mpp) REVERT: k 27 PHE cc_start: 0.8893 (m-80) cc_final: 0.8679 (m-80) REVERT: k 93 ARG cc_start: 0.8662 (mtp-110) cc_final: 0.7917 (ttm110) REVERT: l 108 TYR cc_start: 0.8502 (m-80) cc_final: 0.8245 (m-80) REVERT: l 116 ASP cc_start: 0.7756 (t70) cc_final: 0.7479 (t70) REVERT: m 57 ARG cc_start: 0.4978 (ptp90) cc_final: 0.4225 (mmm160) REVERT: o 15 TYR cc_start: 0.7927 (m-80) cc_final: 0.7673 (m-80) REVERT: p 78 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7200 (tm-30) REVERT: q 19 MET cc_start: 0.8539 (mtm) cc_final: 0.8245 (mtm) REVERT: q 56 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7872 (pttm) outliers start: 95 outliers final: 71 residues processed: 380 average time/residue: 0.7211 time to fit residues: 447.6520 Evaluate side-chains 384 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 306 time to evaluate : 3.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 18 HIS Chi-restraints excluded: chain b residue 114 ILE Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 126 PHE Chi-restraints excluded: chain b residue 135 VAL Chi-restraints excluded: chain b residue 142 ASP Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 143 LEU Chi-restraints excluded: chain c residue 180 ASP Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain c residue 185 HIS Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 8 ASN Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 170 ASP Chi-restraints excluded: chain e residue 13 GLU Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 41 ASP Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 94 VAL Chi-restraints excluded: chain e residue 124 LEU Chi-restraints excluded: chain e residue 160 THR Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 36 GLU Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 56 LYS Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain i residue 24 VAL Chi-restraints excluded: chain i residue 56 VAL Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 52 THR Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain m residue 104 ASN Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 42 TYR Chi-restraints excluded: chain q residue 56 LYS Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain q residue 85 VAL Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 16 CYS Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 26 ILE Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 52 THR Chi-restraints excluded: chain r residue 73 LEU Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 22 ILE Chi-restraints excluded: chain t residue 32 VAL Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 50 VAL Chi-restraints excluded: chain t residue 54 VAL Chi-restraints excluded: chain t residue 57 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 121 optimal weight: 40.0000 chunk 326 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 212 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 362 optimal weight: 7.9990 chunk 301 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 190 optimal weight: 30.0000 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 19 GLN ** b 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 HIS ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 145 GLN ** l 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.106 56187 Z= 0.517 Angle : 0.842 9.472 83658 Z= 0.412 Chirality : 0.043 0.335 10641 Planarity : 0.006 0.071 4733 Dihedral : 23.754 179.998 27060 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.66 % Favored : 88.16 % Rotamer: Outliers : 6.96 % Allowed : 23.74 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.17), residues: 2205 helix: -0.60 (0.18), residues: 780 sheet: -2.73 (0.26), residues: 358 loop : -3.05 (0.17), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP d 9 HIS 0.014 0.002 HIS o 51 PHE 0.017 0.002 PHE c 129 TYR 0.029 0.002 TYR l 108 ARG 0.006 0.001 ARG b 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 304 time to evaluate : 3.542 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 22 ARG cc_start: 0.7731 (ptp-170) cc_final: 0.6943 (mtp180) REVERT: b 90 PHE cc_start: 0.6612 (OUTLIER) cc_final: 0.5582 (p90) REVERT: b 126 PHE cc_start: 0.5011 (OUTLIER) cc_final: 0.3570 (p90) REVERT: b 135 VAL cc_start: 0.7520 (OUTLIER) cc_final: 0.7256 (p) REVERT: c 166 GLN cc_start: 0.6710 (pt0) cc_final: 0.6231 (pm20) REVERT: c 167 TYR cc_start: 0.8386 (m-10) cc_final: 0.7520 (m-10) REVERT: d 8 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8241 (t0) REVERT: d 191 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7442 (pm20) REVERT: e 26 LYS cc_start: 0.6868 (pttt) cc_final: 0.6146 (tptp) REVERT: f 70 ASN cc_start: 0.8217 (p0) cc_final: 0.7716 (t0) REVERT: f 78 ARG cc_start: 0.8573 (tmm-80) cc_final: 0.8237 (ttp80) REVERT: g 92 ARG cc_start: 0.3093 (ptt90) cc_final: 0.2494 (ttp-170) REVERT: h 98 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8874 (tp) REVERT: k 93 ARG cc_start: 0.8766 (mtp-110) cc_final: 0.8054 (ttm110) REVERT: l 60 SER cc_start: 0.8604 (t) cc_final: 0.8268 (t) REVERT: l 110 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8473 (pt) REVERT: l 116 ASP cc_start: 0.7975 (t70) cc_final: 0.7653 (t70) REVERT: m 57 ARG cc_start: 0.5139 (ptp90) cc_final: 0.4223 (mmm160) REVERT: o 15 TYR cc_start: 0.8183 (m-80) cc_final: 0.7957 (m-80) REVERT: p 24 ASP cc_start: 0.8720 (t70) cc_final: 0.8364 (t0) REVERT: p 78 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7533 (tm-30) REVERT: q 19 MET cc_start: 0.8613 (mtm) cc_final: 0.8348 (mtm) REVERT: r 27 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8374 (t0) REVERT: s 16 MET cc_start: 0.3980 (mmm) cc_final: 0.3571 (mpp) outliers start: 134 outliers final: 99 residues processed: 396 average time/residue: 0.6709 time to fit residues: 440.2695 Evaluate side-chains 401 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 294 time to evaluate : 3.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 18 HIS Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 79 SER Chi-restraints excluded: chain b residue 90 PHE Chi-restraints excluded: chain b residue 114 ILE Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 126 PHE Chi-restraints excluded: chain b residue 135 VAL Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 143 LEU Chi-restraints excluded: chain c residue 180 ASP Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain c residue 185 HIS Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 8 ASN Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 84 GLU Chi-restraints excluded: chain d residue 88 ILE Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 145 SER Chi-restraints excluded: chain d residue 149 ASN Chi-restraints excluded: chain d residue 170 ASP Chi-restraints excluded: chain d residue 191 GLU Chi-restraints excluded: chain d residue 195 VAL Chi-restraints excluded: chain e residue 13 GLU Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 94 VAL Chi-restraints excluded: chain e residue 127 SER Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 36 GLU Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain g residue 73 LEU Chi-restraints excluded: chain g residue 90 GLU Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 56 LYS Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 117 GLU Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 24 VAL Chi-restraints excluded: chain i residue 56 VAL Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 52 THR Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 74 ILE Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain m residue 61 ASP Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain o residue 14 GLU Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain o residue 85 LEU Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 33 ILE Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain q residue 6 ASP Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 36 TYR Chi-restraints excluded: chain q residue 42 TYR Chi-restraints excluded: chain q residue 56 LYS Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain q residue 85 VAL Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 16 CYS Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 26 ILE Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 33 LEU Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 52 THR Chi-restraints excluded: chain r residue 73 LEU Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain s residue 12 ASP Chi-restraints excluded: chain t residue 14 THR Chi-restraints excluded: chain t residue 22 ILE Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 50 VAL Chi-restraints excluded: chain t residue 54 VAL Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 74 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 206 optimal weight: 0.6980 chunk 264 optimal weight: 0.7980 chunk 205 optimal weight: 0.6980 chunk 305 optimal weight: 0.4980 chunk 202 optimal weight: 0.0770 chunk 361 optimal weight: 9.9990 chunk 226 optimal weight: 1.9990 chunk 220 optimal weight: 6.9990 chunk 166 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 68 HIS ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 ASN e 145 GLN l 90 HIS ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 56187 Z= 0.138 Angle : 0.564 11.656 83658 Z= 0.287 Chirality : 0.033 0.340 10641 Planarity : 0.004 0.061 4733 Dihedral : 23.577 179.616 27059 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.48 % Favored : 91.47 % Rotamer: Outliers : 4.26 % Allowed : 27.22 % Favored : 68.52 % 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: -2.57 (0.17), residues: 2205 helix: -0.01 (0.19), residues: 770 sheet: -2.53 (0.26), residues: 366 loop : -2.74 (0.17), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 22 HIS 0.006 0.001 HIS k 77 PHE 0.019 0.001 PHE c 129 TYR 0.016 0.001 TYR i 96 ARG 0.007 0.000 ARG n 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 321 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 22 ARG cc_start: 0.7594 (ptp-170) cc_final: 0.6605 (mtp180) REVERT: b 83 GLU cc_start: 0.4705 (pt0) cc_final: 0.4136 (pt0) REVERT: b 95 ARG cc_start: 0.7196 (tpt-90) cc_final: 0.6877 (tpt90) REVERT: b 154 MET cc_start: 0.6182 (ttt) cc_final: 0.5690 (ttm) REVERT: b 159 GLN cc_start: 0.7472 (mm110) cc_final: 0.7077 (mp10) REVERT: c 117 GLU cc_start: 0.7670 (tp30) cc_final: 0.6719 (pp20) REVERT: c 129 PHE cc_start: 0.8136 (p90) cc_final: 0.7427 (p90) REVERT: c 166 GLN cc_start: 0.6532 (pt0) cc_final: 0.6078 (pm20) REVERT: c 167 TYR cc_start: 0.8418 (m-10) cc_final: 0.7663 (m-10) REVERT: c 172 VAL cc_start: 0.6773 (OUTLIER) cc_final: 0.6562 (m) REVERT: d 8 ASN cc_start: 0.8653 (OUTLIER) cc_final: 0.8123 (t0) REVERT: e 12 GLU cc_start: 0.8623 (tt0) cc_final: 0.8397 (tt0) REVERT: e 26 LYS cc_start: 0.6525 (pttt) cc_final: 0.5899 (tptp) REVERT: f 60 TYR cc_start: 0.8313 (m-10) cc_final: 0.8100 (m-10) REVERT: f 70 ASN cc_start: 0.8093 (p0) cc_final: 0.7709 (t0) REVERT: f 78 ARG cc_start: 0.8419 (tmm-80) cc_final: 0.8189 (ttp80) REVERT: g 92 ARG cc_start: 0.2892 (ptt90) cc_final: 0.2458 (ttp-170) REVERT: h 10 MET cc_start: 0.8496 (tmm) cc_final: 0.8216 (tmm) REVERT: h 98 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8590 (tp) REVERT: i 96 TYR cc_start: 0.3719 (t80) cc_final: 0.3448 (t80) REVERT: i 125 ARG cc_start: 0.4994 (OUTLIER) cc_final: 0.4696 (tpt170) REVERT: k 27 PHE cc_start: 0.8865 (m-80) cc_final: 0.8665 (m-80) REVERT: k 93 ARG cc_start: 0.8729 (mtp-110) cc_final: 0.8028 (ttm110) REVERT: k 125 LYS cc_start: 0.8145 (ttpt) cc_final: 0.7767 (ttpt) REVERT: l 90 HIS cc_start: 0.8308 (OUTLIER) cc_final: 0.8062 (m-70) REVERT: l 108 TYR cc_start: 0.8321 (m-80) cc_final: 0.8049 (m-80) REVERT: l 110 ILE cc_start: 0.8319 (pt) cc_final: 0.8097 (pt) REVERT: l 116 ASP cc_start: 0.7775 (t70) cc_final: 0.7551 (t70) REVERT: m 57 ARG cc_start: 0.5057 (ptp90) cc_final: 0.4141 (mmm160) REVERT: o 15 TYR cc_start: 0.7861 (m-80) cc_final: 0.7615 (m-80) REVERT: p 78 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7310 (tm-30) REVERT: q 19 MET cc_start: 0.8431 (mtm) cc_final: 0.8169 (mtm) outliers start: 82 outliers final: 56 residues processed: 373 average time/residue: 0.6811 time to fit residues: 418.4451 Evaluate side-chains 361 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 300 time to evaluate : 3.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 18 HIS Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 143 LEU Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 180 ASP Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain c residue 185 HIS Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 8 ASN Chi-restraints excluded: chain d residue 170 ASP Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 151 GLU Chi-restraints excluded: chain e residue 160 THR Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 56 LYS Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 24 VAL Chi-restraints excluded: chain i residue 56 VAL Chi-restraints excluded: chain i residue 125 ARG Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 52 THR Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 90 HIS Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 121 ASP Chi-restraints excluded: chain m residue 104 ASN Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain o residue 72 SER Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 42 TYR Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 56 LYS Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain q residue 85 VAL Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 16 CYS Chi-restraints excluded: chain r residue 26 ILE Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 73 LEU Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 22 ILE Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 57 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 223 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 108 optimal weight: 50.0000 chunk 71 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 229 optimal weight: 3.9990 chunk 246 optimal weight: 40.0000 chunk 178 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 284 optimal weight: 20.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 39 ASN l 90 HIS ** l 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.106 56187 Z= 0.497 Angle : 0.810 9.915 83658 Z= 0.398 Chirality : 0.042 0.373 10641 Planarity : 0.006 0.072 4733 Dihedral : 23.700 179.584 27057 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.25 % Favored : 88.62 % Rotamer: Outliers : 5.82 % Allowed : 26.13 % Favored : 68.05 % 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: -2.91 (0.17), residues: 2205 helix: -0.38 (0.19), residues: 768 sheet: -2.55 (0.27), residues: 348 loop : -2.93 (0.17), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP d 9 HIS 0.013 0.002 HIS l 109 PHE 0.015 0.002 PHE g 47 TYR 0.030 0.002 TYR l 108 ARG 0.008 0.001 ARG t 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 297 time to evaluate : 3.189 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 22 ARG cc_start: 0.7793 (ptp-170) cc_final: 0.6831 (mtp180) REVERT: b 126 PHE cc_start: 0.4434 (OUTLIER) cc_final: 0.3029 (p90) REVERT: c 129 PHE cc_start: 0.8160 (p90) cc_final: 0.7669 (p90) REVERT: c 166 GLN cc_start: 0.6697 (pt0) cc_final: 0.6260 (pm20) REVERT: c 167 TYR cc_start: 0.8407 (m-10) cc_final: 0.7609 (m-10) REVERT: d 8 ASN cc_start: 0.8852 (OUTLIER) cc_final: 0.8229 (t0) REVERT: d 65 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8375 (tp30) REVERT: e 26 LYS cc_start: 0.6845 (pttt) cc_final: 0.6145 (tptp) REVERT: f 24 GLU cc_start: 0.8051 (pp20) cc_final: 0.7588 (pp20) REVERT: f 61 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.7832 (p0) REVERT: f 70 ASN cc_start: 0.8263 (p0) cc_final: 0.7679 (t0) REVERT: f 78 ARG cc_start: 0.8579 (tmm-80) cc_final: 0.8263 (ttp80) REVERT: g 92 ARG cc_start: 0.2920 (ptt90) cc_final: 0.2345 (ttp-170) REVERT: g 120 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7077 (tp) REVERT: h 98 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8821 (tp) REVERT: i 96 TYR cc_start: 0.3609 (t80) cc_final: 0.3298 (t80) REVERT: i 125 ARG cc_start: 0.5121 (OUTLIER) cc_final: 0.4800 (tpt170) REVERT: k 93 ARG cc_start: 0.8773 (mtp-110) cc_final: 0.8097 (ttm110) REVERT: l 60 SER cc_start: 0.8527 (t) cc_final: 0.8175 (t) REVERT: l 110 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8414 (pt) REVERT: l 116 ASP cc_start: 0.8041 (t70) cc_final: 0.7746 (t70) REVERT: m 57 ARG cc_start: 0.5234 (ptp90) cc_final: 0.4189 (mmm160) REVERT: p 24 ASP cc_start: 0.8698 (t70) cc_final: 0.8337 (t0) REVERT: p 78 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7543 (tm-30) REVERT: q 19 MET cc_start: 0.8593 (mtm) cc_final: 0.8339 (mtm) REVERT: q 66 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8427 (t) outliers start: 112 outliers final: 90 residues processed: 373 average time/residue: 0.6809 time to fit residues: 417.0397 Evaluate side-chains 388 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 289 time to evaluate : 3.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 18 HIS Chi-restraints excluded: chain b residue 79 SER Chi-restraints excluded: chain b residue 114 ILE Chi-restraints excluded: chain b residue 126 PHE Chi-restraints excluded: chain b residue 133 GLU Chi-restraints excluded: chain b residue 217 MET Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 143 LEU Chi-restraints excluded: chain c residue 180 ASP Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain c residue 185 HIS Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 8 ASN Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 65 GLU Chi-restraints excluded: chain d residue 84 GLU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 149 ASN Chi-restraints excluded: chain d residue 170 ASP Chi-restraints excluded: chain d residue 195 VAL Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 94 VAL Chi-restraints excluded: chain e residue 160 THR Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 36 GLU Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain g residue 90 GLU Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 56 LYS Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 56 VAL Chi-restraints excluded: chain i residue 125 ARG Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain k residue 119 ASN Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 39 ASN Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 52 THR Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 90 HIS Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain m residue 61 ASP Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain o residue 14 GLU Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 85 LEU Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 42 TYR Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 56 LYS Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain q residue 85 VAL Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 16 CYS Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 26 ILE Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 73 LEU Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain s residue 12 ASP Chi-restraints excluded: chain t residue 14 THR Chi-restraints excluded: chain t residue 22 ILE Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 50 VAL Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 74 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 2.9990 chunk 346 optimal weight: 3.9990 chunk 315 optimal weight: 0.6980 chunk 336 optimal weight: 0.9980 chunk 202 optimal weight: 0.9990 chunk 146 optimal weight: 10.0000 chunk 264 optimal weight: 1.9990 chunk 103 optimal weight: 50.0000 chunk 304 optimal weight: 20.0000 chunk 318 optimal weight: 30.0000 chunk 335 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 68 HIS ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 ASN e 145 GLN ** o 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 56187 Z= 0.156 Angle : 0.568 11.911 83658 Z= 0.291 Chirality : 0.034 0.368 10641 Planarity : 0.004 0.060 4733 Dihedral : 23.597 179.644 27057 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 4.21 % Allowed : 27.22 % Favored : 68.57 % 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: -2.41 (0.17), residues: 2205 helix: 0.13 (0.19), residues: 755 sheet: -2.38 (0.27), residues: 352 loop : -2.64 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 200 HIS 0.014 0.001 HIS o 51 PHE 0.020 0.001 PHE c 129 TYR 0.018 0.001 TYR l 108 ARG 0.010 0.000 ARG f 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 305 time to evaluate : 3.316 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: b 22 ARG cc_start: 0.7611 (ptp-170) cc_final: 0.6637 (mtp180) REVERT: b 83 GLU cc_start: 0.4777 (pt0) cc_final: 0.4254 (pt0) REVERT: b 90 PHE cc_start: 0.6799 (OUTLIER) cc_final: 0.5701 (p90) REVERT: b 95 ARG cc_start: 0.7253 (tpt-90) cc_final: 0.6903 (tpt90) REVERT: b 126 PHE cc_start: 0.4566 (OUTLIER) cc_final: 0.3108 (p90) REVERT: b 159 GLN cc_start: 0.7374 (mm110) cc_final: 0.7113 (mp10) REVERT: c 117 GLU cc_start: 0.7780 (tp30) cc_final: 0.6804 (pp20) REVERT: c 129 PHE cc_start: 0.7966 (p90) cc_final: 0.7311 (p90) REVERT: c 166 GLN cc_start: 0.6651 (pt0) cc_final: 0.6176 (pm20) REVERT: c 167 TYR cc_start: 0.8426 (m-10) cc_final: 0.7580 (m-10) REVERT: d 8 ASN cc_start: 0.8653 (OUTLIER) cc_final: 0.8127 (t0) REVERT: e 12 GLU cc_start: 0.8602 (tt0) cc_final: 0.8384 (tt0) REVERT: e 18 ILE cc_start: 0.8415 (mt) cc_final: 0.8133 (tt) REVERT: e 26 LYS cc_start: 0.6672 (pttt) cc_final: 0.5944 (tptp) REVERT: f 24 GLU cc_start: 0.8015 (pp20) cc_final: 0.7510 (pp20) REVERT: f 61 ASN cc_start: 0.8187 (OUTLIER) cc_final: 0.7714 (p0) REVERT: f 70 ASN cc_start: 0.8122 (p0) cc_final: 0.7719 (t0) REVERT: f 78 ARG cc_start: 0.8444 (tmm-80) cc_final: 0.8096 (ttp80) REVERT: g 92 ARG cc_start: 0.2834 (ptt90) cc_final: 0.2387 (ttp-170) REVERT: h 98 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8625 (tp) REVERT: i 96 TYR cc_start: 0.3631 (t80) cc_final: 0.3412 (t80) REVERT: i 125 ARG cc_start: 0.5124 (OUTLIER) cc_final: 0.4837 (tpt170) REVERT: k 93 ARG cc_start: 0.8680 (mtp-110) cc_final: 0.8010 (ttm110) REVERT: k 125 LYS cc_start: 0.8188 (ttpt) cc_final: 0.7859 (ttpt) REVERT: l 110 ILE cc_start: 0.8409 (pt) cc_final: 0.8108 (pt) REVERT: l 116 ASP cc_start: 0.7760 (t70) cc_final: 0.7503 (t70) REVERT: m 57 ARG cc_start: 0.5176 (ptp90) cc_final: 0.4151 (mmm160) REVERT: o 15 TYR cc_start: 0.7858 (m-80) cc_final: 0.7638 (m-80) REVERT: q 19 MET cc_start: 0.8493 (mtm) cc_final: 0.8227 (mtm) REVERT: q 66 THR cc_start: 0.8261 (OUTLIER) cc_final: 0.7985 (t) outliers start: 81 outliers final: 64 residues processed: 355 average time/residue: 0.6924 time to fit residues: 402.9703 Evaluate side-chains 365 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 294 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 18 HIS Chi-restraints excluded: chain b residue 79 SER Chi-restraints excluded: chain b residue 90 PHE Chi-restraints excluded: chain b residue 114 ILE Chi-restraints excluded: chain b residue 126 PHE Chi-restraints excluded: chain b residue 133 GLU Chi-restraints excluded: chain b residue 217 MET Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain c residue 185 HIS Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 8 ASN Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 138 THR Chi-restraints excluded: chain d residue 170 ASP Chi-restraints excluded: chain d residue 192 GLN Chi-restraints excluded: chain d residue 195 VAL Chi-restraints excluded: chain e residue 41 ASP Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 160 THR Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 56 LYS Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 125 ARG Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain k residue 119 ASN Chi-restraints excluded: chain l residue 52 THR Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain o residue 14 GLU Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 42 TYR Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 56 LYS Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain q residue 85 VAL Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 16 CYS Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 26 ILE Chi-restraints excluded: chain r residue 33 LEU Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 73 LEU Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 14 THR Chi-restraints excluded: chain t residue 22 ILE Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 50 VAL Chi-restraints excluded: chain t residue 54 VAL Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 74 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 221 optimal weight: 8.9990 chunk 356 optimal weight: 2.9990 chunk 217 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 247 optimal weight: 20.0000 chunk 373 optimal weight: 0.9980 chunk 343 optimal weight: 0.8980 chunk 297 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 229 optimal weight: 0.9980 chunk 182 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 ASN e 145 GLN ** o 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS p 46 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 56187 Z= 0.156 Angle : 0.548 12.035 83658 Z= 0.280 Chirality : 0.032 0.380 10641 Planarity : 0.004 0.060 4733 Dihedral : 23.495 179.671 27056 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 3.27 % Allowed : 28.52 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.18), residues: 2205 helix: 0.37 (0.20), residues: 755 sheet: -2.30 (0.27), residues: 356 loop : -2.58 (0.17), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 200 HIS 0.014 0.001 HIS o 50 PHE 0.017 0.001 PHE c 129 TYR 0.015 0.001 TYR l 108 ARG 0.009 0.000 ARG m 109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 310 time to evaluate : 3.213 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: b 22 ARG cc_start: 0.7645 (ptp-170) cc_final: 0.6599 (mtp180) REVERT: b 83 GLU cc_start: 0.4637 (pt0) cc_final: 0.4263 (pt0) REVERT: b 126 PHE cc_start: 0.4598 (OUTLIER) cc_final: 0.3177 (p90) REVERT: b 159 GLN cc_start: 0.7378 (mm110) cc_final: 0.7110 (mp10) REVERT: b 226 GLN cc_start: 0.6224 (mt0) cc_final: 0.5697 (mt0) REVERT: c 117 GLU cc_start: 0.7720 (tp30) cc_final: 0.6791 (pp20) REVERT: c 129 PHE cc_start: 0.7947 (p90) cc_final: 0.7267 (p90) REVERT: c 142 LYS cc_start: 0.7506 (mttt) cc_final: 0.6954 (mttt) REVERT: c 166 GLN cc_start: 0.6698 (pt0) cc_final: 0.6142 (pm20) REVERT: c 167 TYR cc_start: 0.8334 (m-10) cc_final: 0.7553 (m-10) REVERT: d 8 ASN cc_start: 0.8674 (t160) cc_final: 0.8095 (t0) REVERT: e 18 ILE cc_start: 0.8445 (mt) cc_final: 0.8233 (tt) REVERT: e 33 PHE cc_start: 0.8194 (m-80) cc_final: 0.7811 (m-10) REVERT: f 24 GLU cc_start: 0.8069 (pp20) cc_final: 0.7548 (pp20) REVERT: f 61 ASN cc_start: 0.8193 (OUTLIER) cc_final: 0.7720 (p0) REVERT: f 70 ASN cc_start: 0.8095 (p0) cc_final: 0.7700 (t0) REVERT: g 92 ARG cc_start: 0.2807 (ptt90) cc_final: 0.2369 (ttp-170) REVERT: h 10 MET cc_start: 0.8786 (tmm) cc_final: 0.8116 (tmm) REVERT: h 21 ARG cc_start: 0.8394 (mpt180) cc_final: 0.8039 (mpt180) REVERT: h 55 ASP cc_start: 0.7544 (t0) cc_final: 0.7104 (t0) REVERT: h 70 ASP cc_start: 0.7909 (t0) cc_final: 0.7628 (t0) REVERT: h 98 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8644 (tp) REVERT: i 125 ARG cc_start: 0.5050 (OUTLIER) cc_final: 0.4784 (tpt170) REVERT: k 93 ARG cc_start: 0.8669 (mtp-110) cc_final: 0.8012 (ttm110) REVERT: k 125 LYS cc_start: 0.8207 (ttpt) cc_final: 0.7891 (ttpt) REVERT: l 110 ILE cc_start: 0.8459 (pt) cc_final: 0.8173 (pt) REVERT: l 116 ASP cc_start: 0.7760 (t70) cc_final: 0.7493 (t70) REVERT: m 57 ARG cc_start: 0.5229 (ptp90) cc_final: 0.4137 (mmm160) REVERT: q 66 THR cc_start: 0.8115 (OUTLIER) cc_final: 0.7869 (t) REVERT: r 35 LYS cc_start: 0.8715 (mttt) cc_final: 0.8437 (mtpt) outliers start: 63 outliers final: 55 residues processed: 350 average time/residue: 0.6924 time to fit residues: 393.7896 Evaluate side-chains 358 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 298 time to evaluate : 3.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 18 HIS Chi-restraints excluded: chain b residue 79 SER Chi-restraints excluded: chain b residue 114 ILE Chi-restraints excluded: chain b residue 126 PHE Chi-restraints excluded: chain b residue 133 GLU Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain c residue 185 HIS Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 170 ASP Chi-restraints excluded: chain d residue 192 GLN Chi-restraints excluded: chain d residue 195 VAL Chi-restraints excluded: chain e residue 41 ASP Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain i residue 125 ARG Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain o residue 14 GLU Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 36 TYR Chi-restraints excluded: chain q residue 42 TYR Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 56 LYS Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain q residue 85 VAL Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 16 CYS Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 33 LEU Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 73 LEU Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 14 THR Chi-restraints excluded: chain t residue 22 ILE Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 74 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 236 optimal weight: 4.9990 chunk 316 optimal weight: 30.0000 chunk 91 optimal weight: 7.9990 chunk 274 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 297 optimal weight: 3.9990 chunk 124 optimal weight: 40.0000 chunk 305 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 HIS ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 ASN d 146 GLN ** k 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS p 41 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.145094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.113444 restraints weight = 99908.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.108820 restraints weight = 148711.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.105109 restraints weight = 114958.685| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 56187 Z= 0.452 Angle : 0.774 11.100 83658 Z= 0.382 Chirality : 0.041 0.403 10641 Planarity : 0.006 0.069 4733 Dihedral : 23.631 179.667 27052 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.98 % Favored : 88.98 % Rotamer: Outliers : 4.31 % Allowed : 27.32 % Favored : 68.36 % 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: -2.57 (0.17), residues: 2205 helix: -0.05 (0.19), residues: 757 sheet: -2.45 (0.27), residues: 360 loop : -2.72 (0.17), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP d 9 HIS 0.014 0.002 HIS l 109 PHE 0.013 0.002 PHE l 28 TYR 0.033 0.002 TYR l 108 ARG 0.009 0.001 ARG b 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8618.11 seconds wall clock time: 160 minutes 38.00 seconds (9638.00 seconds total)