Starting phenix.real_space_refine (version: dev) on Thu Dec 22 21:36:20 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwg_23052/12_2022/7kwg_23052.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwg_23052/12_2022/7kwg_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_23052/12_2022/7kwg_23052.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwg_23052/12_2022/7kwg_23052.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwg_23052/12_2022/7kwg_23052.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwg_23052/12_2022/7kwg_23052.pdb" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Convert atoms to be neutral 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 29.42, per 1000 atoms: 0.57 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: 28.26 Conformation dependent library (CDL) restraints added in 3.2 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: 21.13 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: 44.82 Time building geometry restraints manager: 30.05 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: 28774 35.91 - 71.82: 1414 71.82 - 107.73: 117 107.73 - 143.64: 10 143.64 - 179.55: 12 Dihedral angle restraints: 30327 sinusoidal: 23846 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 30324 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 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. 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: 0.930 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: 9.580 Check model and map are aligned: 0.800 Convert atoms to be neutral: 0.440 Process input model: 171.840 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 187.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 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 : 17.123 179.553 26145 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.75 % Favored : 88.84 % Rotamer Outliers : 2.86 % 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 *********************** 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 : 3.321 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 outliers start: 55 outliers final: 18 residues processed: 463 average time/residue: 0.6809 time to fit residues: 503.2672 Evaluate side-chains 323 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 305 time to evaluate : 3.199 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4883 time to fit residues: 19.4824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 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: 6.9990 chunk 218 optimal weight: 2.9990 chunk 340 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 88 ASN ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 99 HIS c 133 GLN d 8 ASN 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 153 HIS h 18 ASN i 77 GLN ** i 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 15 HIS k 18 ASN k 101 GLN ** 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: 0.8318 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.103 56187 Z= 0.448 Angle : 0.817 10.725 83658 Z= 0.410 Chirality : 0.042 0.328 10641 Planarity : 0.006 0.085 4733 Dihedral : 16.083 178.305 21516 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.34 % Favored : 89.52 % Rotamer Outliers : 4.57 % 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: -4.42 (0.14), residues: 2205 helix: -2.42 (0.15), residues: 756 sheet: -3.10 (0.25), residues: 337 loop : -3.28 (0.15), residues: 1112 *********************** 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 418 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 330 time to evaluate : 3.387 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 outliers start: 88 outliers final: 53 residues processed: 388 average time/residue: 0.6737 time to fit residues: 431.2264 Evaluate side-chains 359 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 306 time to evaluate : 3.489 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.4684 time to fit residues: 50.1895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 30.0000 chunk 231 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 341 optimal weight: 0.0670 chunk 368 optimal weight: 2.9990 chunk 303 optimal weight: 0.4980 chunk 338 optimal weight: 2.9990 chunk 116 optimal weight: 50.0000 chunk 273 optimal weight: 8.9990 overall best weight: 1.5122 ------------------------------------------------------------------------------- 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 115 ASN e 145 GLN e 166 ASN i 128 GLN j 64 GLN k 101 GLN l 29 ASN l 90 HIS ** l 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 ASN p 46 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 56187 Z= 0.170 Angle : 0.588 9.121 83658 Z= 0.304 Chirality : 0.034 0.276 10641 Planarity : 0.005 0.071 4733 Dihedral : 15.599 178.574 21516 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.48 % Favored : 91.47 % Rotamer Outliers : 2.29 % 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: -3.52 (0.16), residues: 2205 helix: -1.20 (0.17), residues: 771 sheet: -2.92 (0.26), residues: 339 loop : -3.03 (0.16), residues: 1095 *********************** 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 384 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 340 time to evaluate : 3.262 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 outliers start: 44 outliers final: 24 residues processed: 373 average time/residue: 0.6756 time to fit residues: 414.1779 Evaluate side-chains 320 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 296 time to evaluate : 3.554 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.4972 time to fit residues: 26.1737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 0.5980 chunk 256 optimal weight: 8.9990 chunk 177 optimal weight: 0.1980 chunk 37 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 229 optimal weight: 0.8980 chunk 342 optimal weight: 3.9990 chunk 362 optimal weight: 40.0000 chunk 178 optimal weight: 8.9990 chunk 324 optimal weight: 7.9990 chunk 97 optimal weight: 30.0000 overall best weight: 2.5384 ------------------------------------------------------------------------------- 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 145 GLN f 61 ASN j 15 HIS j 56 HIS j 67 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** p 62 ASN p 87 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 56187 Z= 0.210 Angle : 0.584 9.418 83658 Z= 0.300 Chirality : 0.034 0.315 10641 Planarity : 0.005 0.067 4733 Dihedral : 15.460 179.040 21516 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.44 % Favored : 91.52 % Rotamer Outliers : 2.75 % 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: -3.08 (0.17), residues: 2205 helix: -0.64 (0.18), residues: 779 sheet: -2.67 (0.27), residues: 340 loop : -2.94 (0.16), residues: 1086 *********************** 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 375 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 322 time to evaluate : 3.219 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 outliers start: 53 outliers final: 30 residues processed: 350 average time/residue: 0.6683 time to fit residues: 383.3880 Evaluate side-chains 329 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 299 time to evaluate : 3.156 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.4517 time to fit residues: 29.2675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 4.9990 chunk 205 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 269 optimal weight: 0.5980 chunk 149 optimal weight: 10.0000 chunk 309 optimal weight: 1.9990 chunk 250 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 185 optimal weight: 9.9990 chunk 325 optimal weight: 30.0000 chunk 91 optimal weight: 6.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- 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 145 GLN ** l 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 56187 Z= 0.235 Angle : 0.592 9.773 83658 Z= 0.303 Chirality : 0.034 0.288 10641 Planarity : 0.005 0.065 4733 Dihedral : 15.411 179.074 21516 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.07 % Favored : 90.88 % Rotamer Outliers : 2.23 % 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: -2.77 (0.17), residues: 2205 helix: -0.27 (0.19), residues: 773 sheet: -2.50 (0.27), residues: 347 loop : -2.85 (0.17), residues: 1085 *********************** 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 356 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 313 time to evaluate : 3.294 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 outliers start: 43 outliers final: 26 residues processed: 340 average time/residue: 0.7029 time to fit residues: 388.2766 Evaluate side-chains 326 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 300 time to evaluate : 3.368 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.5363 time to fit residues: 28.0984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 71 optimal weight: 10.0000 chunk 212 optimal weight: 0.6980 chunk 89 optimal weight: 7.9990 chunk 362 optimal weight: 40.0000 chunk 301 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 190 optimal weight: 10.0000 overall best weight: 6.3390 ------------------------------------------------------------------------------- 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 145 GLN f 61 ASN j 15 HIS ** l 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.112 56187 Z= 0.436 Angle : 0.754 9.137 83658 Z= 0.376 Chirality : 0.041 0.292 10641 Planarity : 0.006 0.067 4733 Dihedral : 15.730 179.939 21516 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.93 % Favored : 88.98 % Rotamer Outliers : 3.01 % 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: -2.92 (0.17), residues: 2205 helix: -0.49 (0.18), residues: 773 sheet: -2.53 (0.27), residues: 360 loop : -2.87 (0.17), residues: 1072 *********************** 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 375 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 317 time to evaluate : 3.188 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 outliers start: 58 outliers final: 39 residues processed: 357 average time/residue: 0.6564 time to fit residues: 383.1474 Evaluate side-chains 343 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 304 time to evaluate : 3.512 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.4754 time to fit residues: 38.7817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 206 optimal weight: 0.9990 chunk 264 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 305 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 361 optimal weight: 8.9990 chunk 226 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 chunk 166 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 f 61 ASN l 90 HIS ** l 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 56187 Z= 0.173 Angle : 0.565 11.238 83658 Z= 0.290 Chirality : 0.033 0.278 10641 Planarity : 0.004 0.061 4733 Dihedral : 15.384 178.963 21516 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.53 % Favored : 91.43 % Rotamer Outliers : 1.35 % 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: -2.53 (0.17), residues: 2205 helix: -0.03 (0.19), residues: 771 sheet: -2.35 (0.27), residues: 354 loop : -2.74 (0.17), residues: 1080 *********************** 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 348 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 322 time to evaluate : 3.276 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 outliers start: 26 outliers final: 14 residues processed: 333 average time/residue: 0.6562 time to fit residues: 357.8062 Evaluate side-chains 305 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 291 time to evaluate : 3.117 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.4901 time to fit residues: 16.4934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 223 optimal weight: 8.9990 chunk 144 optimal weight: 20.0000 chunk 215 optimal weight: 5.9990 chunk 108 optimal weight: 50.0000 chunk 71 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 229 optimal weight: 0.9980 chunk 246 optimal weight: 30.0000 chunk 178 optimal weight: 20.0000 chunk 33 optimal weight: 7.9990 chunk 284 optimal weight: 20.0000 overall best weight: 6.5988 ------------------------------------------------------------------------------- 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 f 61 ASN j 15 HIS l 39 ASN ** l 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 41 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.105 56187 Z= 0.448 Angle : 0.761 10.100 83658 Z= 0.378 Chirality : 0.041 0.290 10641 Planarity : 0.005 0.066 4733 Dihedral : 15.721 179.958 21516 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.29 % Favored : 88.62 % Rotamer Outliers : 2.13 % 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: -2.73 (0.17), residues: 2205 helix: -0.36 (0.19), residues: 755 sheet: -2.27 (0.29), residues: 325 loop : -2.77 (0.17), residues: 1125 *********************** 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 348 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 307 time to evaluate : 3.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 33 residues processed: 329 average time/residue: 0.6600 time to fit residues: 355.1502 Evaluate side-chains 333 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 300 time to evaluate : 3.210 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.4607 time to fit residues: 31.9676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 315 optimal weight: 0.9980 chunk 336 optimal weight: 0.9980 chunk 202 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 264 optimal weight: 0.9980 chunk 103 optimal weight: 40.0000 chunk 304 optimal weight: 1.9990 chunk 318 optimal weight: 6.9990 chunk 335 optimal weight: 0.6980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 HIS ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 ASN e 145 GLN l 90 HIS ** o 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 56187 Z= 0.146 Angle : 0.562 12.335 83658 Z= 0.287 Chirality : 0.033 0.285 10641 Planarity : 0.004 0.061 4733 Dihedral : 15.348 178.739 21516 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer Outliers : 0.73 % 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: -2.33 (0.18), residues: 2205 helix: 0.12 (0.19), residues: 765 sheet: -2.25 (0.28), residues: 347 loop : -2.60 (0.17), residues: 1093 *********************** 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 313 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 299 time to evaluate : 3.338 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 outliers start: 14 outliers final: 9 residues processed: 308 average time/residue: 0.6436 time to fit residues: 325.8685 Evaluate side-chains 295 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 286 time to evaluate : 3.138 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4603 time to fit residues: 11.3292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 221 optimal weight: 5.9990 chunk 356 optimal weight: 0.9990 chunk 217 optimal weight: 0.2980 chunk 168 optimal weight: 7.9990 chunk 247 optimal weight: 30.0000 chunk 373 optimal weight: 0.0030 chunk 343 optimal weight: 1.9990 chunk 297 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 229 optimal weight: 0.0970 chunk 182 optimal weight: 20.0000 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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 8 ASN d 39 ASN j 15 HIS ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 53 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 56187 Z= 0.127 Angle : 0.525 12.723 83658 Z= 0.268 Chirality : 0.031 0.305 10641 Planarity : 0.004 0.061 4733 Dihedral : 15.065 177.859 21516 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.07 % Favored : 91.88 % Rotamer Outliers : 0.52 % 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: -1.99 (0.18), residues: 2205 helix: 0.49 (0.20), residues: 767 sheet: -2.10 (0.28), residues: 347 loop : -2.45 (0.17), residues: 1091 ********************** 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 331 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 321 time to evaluate : 3.141 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 outliers start: 10 outliers final: 5 residues processed: 325 average time/residue: 0.6626 time to fit residues: 351.7287 Evaluate side-chains 281 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 276 time to evaluate : 3.006 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4652 time to fit residues: 7.4567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 236 optimal weight: 3.9990 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: 0.9990 chunk 124 optimal weight: 40.0000 chunk 305 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 ASN d 146 GLN d 159 ASN e 145 GLN ** j 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 13 GLN l 90 HIS ** l 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 41 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.146847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3415 r_free = 0.3415 target = 0.106463 restraints weight = 99777.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.102593 restraints weight = 117455.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.103206 restraints weight = 103630.424| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.096 56187 Z= 0.401 Angle : 0.727 10.669 83658 Z= 0.358 Chirality : 0.039 0.347 10641 Planarity : 0.005 0.063 4733 Dihedral : 15.364 179.575 21516 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.98 % Favored : 89.98 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.17), residues: 2205 helix: 0.07 (0.19), residues: 768 sheet: -2.18 (0.28), residues: 351 loop : -2.64 (0.17), residues: 1086 =============================================================================== Job complete usr+sys time: 7777.86 seconds wall clock time: 143 minutes 50.40 seconds (8630.40 seconds total)