Starting phenix.real_space_refine on Sun Feb 25 14:51:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boh_12243/02_2024/7boh_12243_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boh_12243/02_2024/7boh_12243.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boh_12243/02_2024/7boh_12243_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boh_12243/02_2024/7boh_12243_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boh_12243/02_2024/7boh_12243_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boh_12243/02_2024/7boh_12243.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boh_12243/02_2024/7boh_12243.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boh_12243/02_2024/7boh_12243_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boh_12243/02_2024/7boh_12243_neut_updated.pdb" } resolution = 2.82 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= 0.003 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1527 5.49 5 Mg 156 5.21 5 S 73 5.16 5 C 26655 2.51 5 N 9685 2.21 5 O 14057 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D ASP 174": "OD1" <-> "OD2" Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "D GLU 202": "OE1" <-> "OE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "F PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 16": "OE1" <-> "OE2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 33": "OE1" <-> "OE2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G GLU 146": "OE1" <-> "OE2" Residue "H ASP 9": "OD1" <-> "OD2" Residue "H PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 73": "OE1" <-> "OE2" Residue "H GLU 91": "OE1" <-> "OE2" Residue "H GLU 124": "OE1" <-> "OE2" Residue "I TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 112": "OE1" <-> "OE2" Residue "J PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 24": "OE1" <-> "OE2" Residue "K ASP 36": "OD1" <-> "OD2" Residue "K TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 41": "OE1" <-> "OE2" Residue "M PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 86": "OE1" <-> "OE2" Residue "O PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 52": "OE1" <-> "OE2" Residue "R TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 73": "OE1" <-> "OE2" Residue "S PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 15": "OE1" <-> "OE2" Residue "T PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 100": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 52154 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 32773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1527, 32773 Classifications: {'RNA': 1527} Modifications used: {'rna2p': 1, 'rna2p_pur': 110, 'rna2p_pyr': 87, 'rna3p': 9, 'rna3p_pur': 753, 'rna3p_pyr': 567} Link IDs: {'rna2p': 198, 'rna3p': 1328} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 6 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1653 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 7, 'TRANS': 203} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "G" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 795 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "S" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "V" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 783 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 154 Unusual residues: {' MG': 154} Classifications: {'undetermined': 154} Link IDs: {None: 153} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 26.37, per 1000 atoms: 0.51 Number of scatterers: 52154 At special positions: 0 Unit cell: (207.9, 208.95, 176.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 73 16.00 P 1527 15.00 Mg 156 11.99 O 14057 8.00 N 9685 7.00 C 26655 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: 28.85 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4528 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 93 helices and 21 sheets defined 39.6% alpha, 16.1% beta 500 base pairs and 894 stacking pairs defined. Time for finding SS restraints: 29.32 Creating SS restraints... Processing helix chain 'B' and resid 6 through 12 removed outlier: 3.706A pdb=" N ALA B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 43 through 63 Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.674A pdb=" N CYS B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 123 Processing helix chain 'B' and resid 131 through 148 Processing helix chain 'B' and resid 170 through 179 Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 207 through 226 Processing helix chain 'C' and resid 9 through 11 No H-bonds generated for 'chain 'C' and resid 9 through 11' Processing helix chain 'C' and resid 29 through 46 Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 79 through 81 No H-bonds generated for 'chain 'C' and resid 79 through 81' Processing helix chain 'C' and resid 83 through 95 removed outlier: 3.661A pdb=" N VAL C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 111 No H-bonds generated for 'chain 'C' and resid 109 through 111' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'D' and resid 9 through 14 Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 50 through 65 Processing helix chain 'D' and resid 69 through 81 Processing helix chain 'D' and resid 86 through 95 Processing helix chain 'D' and resid 98 through 105 Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 153 through 164 removed outlier: 4.961A pdb=" N GLN D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 205 removed outlier: 3.548A pdb=" N SER D 205 " --> pdb=" O VAL D 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 68 Processing helix chain 'E' and resid 109 through 118 removed outlier: 3.578A pdb=" N VAL E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 145 Processing helix chain 'E' and resid 150 through 157 Processing helix chain 'E' and resid 161 through 164 No H-bonds generated for 'chain 'E' and resid 161 through 164' Processing helix chain 'F' and resid 12 through 14 No H-bonds generated for 'chain 'F' and resid 12 through 14' Processing helix chain 'F' and resid 18 through 31 Processing helix chain 'F' and resid 68 through 80 Processing helix chain 'F' and resid 101 through 104 No H-bonds generated for 'chain 'F' and resid 101 through 104' Processing helix chain 'G' and resid 21 through 30 Processing helix chain 'G' and resid 36 through 54 removed outlier: 3.689A pdb=" N ARG G 53 " --> pdb=" O THR G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 67 Processing helix chain 'G' and resid 93 through 111 Processing helix chain 'G' and resid 117 through 128 Processing helix chain 'G' and resid 133 through 146 Processing helix chain 'G' and resid 149 through 151 No H-bonds generated for 'chain 'G' and resid 149 through 151' Processing helix chain 'H' and resid 6 through 19 Processing helix chain 'H' and resid 31 through 43 Processing helix chain 'H' and resid 89 through 91 No H-bonds generated for 'chain 'H' and resid 89 through 91' Processing helix chain 'H' and resid 96 through 98 No H-bonds generated for 'chain 'H' and resid 96 through 98' Processing helix chain 'H' and resid 113 through 119 Processing helix chain 'I' and resid 35 through 38 No H-bonds generated for 'chain 'I' and resid 35 through 38' Processing helix chain 'I' and resid 42 through 47 Processing helix chain 'I' and resid 50 through 55 Processing helix chain 'I' and resid 72 through 90 Processing helix chain 'I' and resid 95 through 101 Processing helix chain 'J' and resid 15 through 31 Processing helix chain 'J' and resid 81 through 89 removed outlier: 3.817A pdb=" N ASP J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 58 No H-bonds generated for 'chain 'K' and resid 56 through 58' Processing helix chain 'K' and resid 60 through 73 removed outlier: 3.704A pdb=" N ALA K 73 " --> pdb=" O ARG K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 77 No H-bonds generated for 'chain 'K' and resid 75 through 77' Processing helix chain 'K' and resid 94 through 101 Processing helix chain 'L' and resid 4 through 9 Processing helix chain 'L' and resid 22 through 24 No H-bonds generated for 'chain 'L' and resid 22 through 24' Processing helix chain 'L' and resid 114 through 116 No H-bonds generated for 'chain 'L' and resid 114 through 116' Processing helix chain 'M' and resid 15 through 21 removed outlier: 4.389A pdb=" N THR M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 37 Processing helix chain 'M' and resid 50 through 62 removed outlier: 4.137A pdb=" N GLU M 59 " --> pdb=" O THR M 55 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 83 removed outlier: 3.652A pdb=" N LEU M 80 " --> pdb=" O SER M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 93 Processing helix chain 'M' and resid 107 through 109 No H-bonds generated for 'chain 'M' and resid 107 through 109' Processing helix chain 'N' and resid 4 through 19 Processing helix chain 'N' and resid 21 through 31 Processing helix chain 'N' and resid 38 through 50 Processing helix chain 'N' and resid 53 through 55 No H-bonds generated for 'chain 'N' and resid 53 through 55' Processing helix chain 'N' and resid 57 through 59 No H-bonds generated for 'chain 'N' and resid 57 through 59' Processing helix chain 'N' and resid 81 through 89 Processing helix chain 'O' and resid 5 through 15 Processing helix chain 'O' and resid 25 through 45 removed outlier: 4.059A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU O 45 " --> pdb=" O GLY O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 73 Processing helix chain 'O' and resid 75 through 84 Processing helix chain 'P' and resid 54 through 63 removed outlier: 3.591A pdb=" N GLN P 63 " --> pdb=" O HIS P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 80 Processing helix chain 'Q' and resid 49 through 51 No H-bonds generated for 'chain 'Q' and resid 49 through 51' Processing helix chain 'R' and resid 12 through 16 Processing helix chain 'R' and resid 26 through 32 removed outlier: 4.177A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYR R 32 " --> pdb=" O THR R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 45 No H-bonds generated for 'chain 'R' and resid 42 through 45' Processing helix chain 'R' and resid 49 through 64 Processing helix chain 'S' and resid 13 through 25 Processing helix chain 'S' and resid 42 through 44 No H-bonds generated for 'chain 'S' and resid 42 through 44' Processing helix chain 'S' and resid 71 through 74 Processing helix chain 'T' and resid 5 through 41 removed outlier: 3.790A pdb=" N VAL T 35 " --> pdb=" O PHE T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 63 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 69 through 86 removed outlier: 3.525A pdb=" N LYS T 85 " --> pdb=" O ALA T 81 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU T 86 " --> pdb=" O GLN T 82 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 24 Processing helix chain 'V' and resid 62 through 87 removed outlier: 3.914A pdb=" N ALA V 67 " --> pdb=" O ASP V 63 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLY V 77 " --> pdb=" O GLN V 73 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N PHE V 78 " --> pdb=" O GLU V 74 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.696A pdb=" N ALA B 160 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL B 70 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE B 162 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N PHE B 198 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL B 187 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 31 through 35 removed outlier: 6.928A pdb=" N ILE B 40 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 98 through 105 Processing sheet with id= D, first strand: chain 'C' and resid 165 through 171 removed outlier: 3.639A pdb=" N GLY C 148 " --> pdb=" O PHE C 203 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 123 through 125 removed outlier: 3.835A pdb=" N GLU D 179 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 46 through 53 removed outlier: 6.517A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 85 through 89 Processing sheet with id= H, first strand: chain 'F' and resid 84 through 92 removed outlier: 7.009A pdb=" N MET F 9 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N SER F 87 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL F 7 " --> pdb=" O SER F 87 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL F 89 " --> pdb=" O GLU F 5 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU F 5 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ARG F 91 " --> pdb=" O HIS F 3 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N HIS F 3 " --> pdb=" O ARG F 91 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLU F 65 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE F 36 " --> pdb=" O GLU F 65 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 73 through 78 Processing sheet with id= J, first strand: chain 'H' and resid 24 through 28 Processing sheet with id= K, first strand: chain 'H' and resid 74 through 77 removed outlier: 6.816A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 6 through 11 Processing sheet with id= M, first strand: chain 'J' and resid 70 through 76 Processing sheet with id= N, first strand: chain 'J' and resid 45 through 52 Processing sheet with id= O, first strand: chain 'K' and resid 106 through 112 removed outlier: 7.772A pdb=" N VAL K 84 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE K 110 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL K 86 " --> pdb=" O ILE K 110 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASP K 112 " --> pdb=" O VAL K 86 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLY K 19 " --> pdb=" O GLU K 83 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N MET K 85 " --> pdb=" O GLY K 19 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA K 21 " --> pdb=" O MET K 85 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LYS K 87 " --> pdb=" O ALA K 21 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE K 23 " --> pdb=" O LYS K 87 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY K 43 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASP K 36 " --> pdb=" O ALA K 41 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ALA K 41 " --> pdb=" O ASP K 36 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'L' and resid 95 through 97 removed outlier: 6.844A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N THR L 39 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG L 50 " --> pdb=" O THR L 39 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'P' and resid 2 through 11 removed outlier: 3.673A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'Q' and resid 7 through 11 removed outlier: 9.267A pdb=" N SER Q 72 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N HIS Q 45 " --> pdb=" O SER Q 72 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N THR Q 74 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N HIS Q 47 " --> pdb=" O THR Q 74 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ALA Q 24 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL Q 12 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N GLU Q 26 " --> pdb=" O GLY Q 10 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLY Q 10 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'Q' and resid 58 through 60 removed outlier: 6.508A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL Q 78 " --> pdb=" O GLU Q 60 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'S' and resid 31 through 33 Processing sheet with id= U, first strand: chain 'V' and resid 94 through 99 removed outlier: 3.816A pdb=" N GLY V 40 " --> pdb=" O TYR V 53 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR V 55 " --> pdb=" O VAL V 38 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N VAL V 38 " --> pdb=" O THR V 55 " (cutoff:3.500A) 814 hydrogen bonds defined for protein. 2370 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1249 hydrogen bonds 1972 hydrogen bond angles 0 basepair planarities 500 basepair parallelities 894 stacking parallelities Total time for adding SS restraints: 56.30 Time building geometry restraints manager: 30.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8251 1.33 - 1.45: 22618 1.45 - 1.57: 22142 1.57 - 1.70: 3051 1.70 - 1.82: 132 Bond restraints: 56194 Sorted by residual: bond pdb=" C2 G7M A 527 " pdb=" N3 G7M A 527 " ideal model delta sigma weight residual 1.462 1.310 0.152 2.00e-02 2.50e+03 5.79e+01 bond pdb=" N3 2MG A1516 " pdb=" C4 2MG A1516 " ideal model delta sigma weight residual 1.496 1.348 0.148 2.00e-02 2.50e+03 5.45e+01 bond pdb=" N3 2MG A 966 " pdb=" C4 2MG A 966 " ideal model delta sigma weight residual 1.496 1.351 0.145 2.00e-02 2.50e+03 5.23e+01 bond pdb=" N3 2MG A1207 " pdb=" C4 2MG A1207 " ideal model delta sigma weight residual 1.496 1.352 0.144 2.00e-02 2.50e+03 5.22e+01 bond pdb=" C2 5MC A 967 " pdb=" N3 5MC A 967 " ideal model delta sigma weight residual 1.493 1.351 0.142 2.00e-02 2.50e+03 5.05e+01 ... (remaining 56189 not shown) Histogram of bond angle deviations from ideal: 97.00 - 104.95: 7054 104.95 - 112.89: 33886 112.89 - 120.84: 26141 120.84 - 128.79: 14714 128.79 - 136.74: 1621 Bond angle restraints: 83416 Sorted by residual: angle pdb=" C1' G7M A 527 " pdb=" N9 G7M A 527 " pdb=" C8 G7M A 527 " ideal model delta sigma weight residual 94.96 129.34 -34.38 3.00e+00 1.11e-01 1.31e+02 angle pdb=" C1' G7M A 527 " pdb=" N9 G7M A 527 " pdb=" C4 G7M A 527 " ideal model delta sigma weight residual 142.80 125.26 17.54 3.00e+00 1.11e-01 3.42e+01 angle pdb=" N LYS P 46 " pdb=" CA LYS P 46 " pdb=" C LYS P 46 " ideal model delta sigma weight residual 113.17 106.03 7.14 1.26e+00 6.30e-01 3.21e+01 angle pdb=" C4' G7M A 527 " pdb=" C3' G7M A 527 " pdb=" C2' G7M A 527 " ideal model delta sigma weight residual 102.60 97.00 5.60 1.00e+00 1.00e+00 3.14e+01 angle pdb=" C1' 2MG A1516 " pdb=" N9 2MG A1516 " pdb=" C8 2MG A1516 " ideal model delta sigma weight residual 110.07 126.36 -16.29 3.00e+00 1.11e-01 2.95e+01 ... (remaining 83411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 31926 35.62 - 71.23: 3572 71.23 - 106.85: 412 106.85 - 142.47: 3 142.47 - 178.09: 7 Dihedral angle restraints: 35920 sinusoidal: 28914 harmonic: 7006 Sorted by residual: dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 52.25 147.75 1 1.50e+01 4.44e-03 7.88e+01 dihedral pdb=" O4' C A 754 " pdb=" C1' C A 754 " pdb=" N1 C A 754 " pdb=" C2 C A 754 " ideal model delta sinusoidal sigma weight residual 200.00 63.96 136.04 1 1.50e+01 4.44e-03 7.34e+01 dihedral pdb=" O4' C A1158 " pdb=" C1' C A1158 " pdb=" N1 C A1158 " pdb=" C2 C A1158 " ideal model delta sinusoidal sigma weight residual 200.00 66.70 133.30 1 1.50e+01 4.44e-03 7.19e+01 ... (remaining 35917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 9958 0.079 - 0.158: 482 0.158 - 0.238: 88 0.238 - 0.317: 7 0.317 - 0.396: 2 Chirality restraints: 10537 Sorted by residual: chirality pdb=" CA VAL J 57 " pdb=" N VAL J 57 " pdb=" C VAL J 57 " pdb=" CB VAL J 57 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" CA ASN N 35 " pdb=" N ASN N 35 " pdb=" C ASN N 35 " pdb=" CB ASN N 35 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA THR B 125 " pdb=" N THR B 125 " pdb=" C THR B 125 " pdb=" CB THR B 125 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 10534 not shown) Planarity restraints: 4920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A1407 " 0.045 2.00e-02 2.50e+03 5.77e-01 7.50e+03 pdb=" C4' 5MC A1407 " 0.434 2.00e-02 2.50e+03 pdb=" O4' 5MC A1407 " 0.605 2.00e-02 2.50e+03 pdb=" C3' 5MC A1407 " -0.592 2.00e-02 2.50e+03 pdb=" O3' 5MC A1407 " -0.597 2.00e-02 2.50e+03 pdb=" C2' 5MC A1407 " -0.194 2.00e-02 2.50e+03 pdb=" O2' 5MC A1407 " 0.940 2.00e-02 2.50e+03 pdb=" C1' 5MC A1407 " 0.232 2.00e-02 2.50e+03 pdb=" N1 5MC A1407 " -0.873 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1207 " -0.043 2.00e-02 2.50e+03 5.74e-01 7.41e+03 pdb=" C4' 2MG A1207 " -0.433 2.00e-02 2.50e+03 pdb=" O4' 2MG A1207 " -0.604 2.00e-02 2.50e+03 pdb=" C3' 2MG A1207 " 0.589 2.00e-02 2.50e+03 pdb=" O3' 2MG A1207 " 0.586 2.00e-02 2.50e+03 pdb=" C2' 2MG A1207 " 0.198 2.00e-02 2.50e+03 pdb=" O2' 2MG A1207 " -0.933 2.00e-02 2.50e+03 pdb=" C1' 2MG A1207 " -0.232 2.00e-02 2.50e+03 pdb=" N9 2MG A1207 " 0.870 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " 0.024 2.00e-02 2.50e+03 5.48e-01 6.74e+03 pdb=" C4' 2MG A1516 " 0.424 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " 0.577 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " -0.587 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " -0.530 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " -0.218 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " 0.886 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " 0.242 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " -0.818 2.00e-02 2.50e+03 ... (remaining 4917 not shown) Histogram of nonbonded interaction distances: 0.66 - 1.51: 3 1.51 - 2.35: 144 2.35 - 3.20: 44435 3.20 - 4.05: 171684 4.05 - 4.90: 264735 Warning: very small nonbonded interaction distances. Nonbonded interactions: 481001 Sorted by model distance: nonbonded pdb="MG MG A1702 " pdb="MG MG A1734 " model vdw 0.657 1.300 nonbonded pdb=" N1 U A 421 " pdb=" NH2 ARG C 127 " model vdw 0.855 3.200 nonbonded pdb=" C2 U A 421 " pdb=" NH2 ARG C 127 " model vdw 1.122 3.340 nonbonded pdb=" C6 U A 421 " pdb=" NH2 ARG C 127 " model vdw 1.758 3.420 nonbonded pdb=" O4 U A 180 " pdb="MG MG A1643 " model vdw 1.938 2.170 ... (remaining 480996 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 5.230 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: 16.980 Check model and map are aligned: 0.770 Set scattering table: 0.440 Process input model: 197.420 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 235.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 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 : 0.006 0.152 56194 Z= 0.377 Angle : 0.625 34.383 83416 Z= 0.370 Chirality : 0.039 0.396 10537 Planarity : 0.018 0.577 4920 Dihedral : 22.277 178.087 31392 Min Nonbonded Distance : 0.657 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Cbeta Deviations : 0.18 % 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: -1.47 (0.16), residues: 2402 helix: -0.30 (0.15), residues: 1010 sheet: -1.27 (0.24), residues: 394 loop : -1.43 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 201 HIS 0.012 0.001 HIS R 74 PHE 0.015 0.001 PHE F 8 TYR 0.012 0.001 TYR Q 34 ARG 0.008 0.000 ARG H 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 591 time to evaluate : 3.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 ILE cc_start: 0.4544 (mt) cc_final: 0.4284 (tt) REVERT: C 203 PHE cc_start: 0.7608 (t80) cc_final: 0.7209 (t80) REVERT: D 141 ASP cc_start: 0.8351 (m-30) cc_final: 0.8003 (m-30) REVERT: E 116 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7704 (tt0) REVERT: F 97 THR cc_start: 0.8189 (p) cc_final: 0.7804 (p) REVERT: H 113 ASP cc_start: 0.8756 (p0) cc_final: 0.8376 (p0) REVERT: H 114 ARG cc_start: 0.8074 (ttp-170) cc_final: 0.7797 (ttp80) REVERT: K 77 TYR cc_start: 0.7716 (m-80) cc_final: 0.7405 (m-80) REVERT: L 73 ASN cc_start: 0.8277 (p0) cc_final: 0.7834 (p0) REVERT: R 10 PHE cc_start: 0.6300 (m-10) cc_final: 0.6021 (m-10) REVERT: R 25 ASP cc_start: 0.8700 (t0) cc_final: 0.8472 (t70) REVERT: S 66 MET cc_start: 0.3930 (ptp) cc_final: 0.3397 (pp-130) REVERT: T 36 TYR cc_start: 0.8655 (m-80) cc_final: 0.8453 (m-80) REVERT: V 16 GLN cc_start: 0.9124 (tt0) cc_final: 0.8918 (tt0) REVERT: V 17 LYS cc_start: 0.8878 (mtpp) cc_final: 0.8529 (mtpp) REVERT: V 43 MET cc_start: 0.7154 (ptm) cc_final: 0.6861 (ptm) REVERT: V 45 ARG cc_start: 0.5543 (tmt170) cc_final: 0.5327 (ttt90) REVERT: V 51 LYS cc_start: 0.8762 (mtmt) cc_final: 0.8208 (mtpt) REVERT: V 76 SER cc_start: 0.8732 (m) cc_final: 0.8521 (p) REVERT: V 96 THR cc_start: 0.8566 (m) cc_final: 0.7879 (p) outliers start: 0 outliers final: 1 residues processed: 591 average time/residue: 1.8197 time to fit residues: 1324.1224 Evaluate side-chains 394 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 393 time to evaluate : 3.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 93 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 326 optimal weight: 5.9990 chunk 293 optimal weight: 4.9990 chunk 162 optimal weight: 8.9990 chunk 100 optimal weight: 40.0000 chunk 197 optimal weight: 0.1980 chunk 156 optimal weight: 6.9990 chunk 303 optimal weight: 4.9990 chunk 117 optimal weight: 30.0000 chunk 184 optimal weight: 6.9990 chunk 225 optimal weight: 2.9990 chunk 351 optimal weight: 5.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN B 227 GLN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN C 139 GLN D 40 GLN D 41 HIS D 54 GLN D 126 ASN D 152 GLN E 83 HIS E 97 GLN E 122 ASN E 135 ASN F 3 HIS F 17 GLN F 37 HIS H 38 ASN I 4 ASN I 37 GLN I 50 GLN K 28 ASN L 5 ASN L 112 GLN M 52 GLN N 43 ASN O 28 GLN O 46 HIS O 80 GLN P 18 GLN P 26 ASN P 29 ASN T 70 ASN T 82 GLN T 84 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 56194 Z= 0.329 Angle : 0.663 12.521 83416 Z= 0.357 Chirality : 0.038 0.368 10537 Planarity : 0.007 0.185 4920 Dihedral : 22.935 178.918 26542 Min Nonbonded Distance : 1.026 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.11 % Allowed : 16.44 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.17), residues: 2402 helix: 0.48 (0.16), residues: 1004 sheet: -0.72 (0.25), residues: 406 loop : -1.00 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 22 HIS 0.006 0.001 HIS F 37 PHE 0.020 0.002 PHE C 37 TYR 0.015 0.002 TYR B 213 ARG 0.030 0.001 ARG C 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 415 time to evaluate : 3.212 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 41 ILE cc_start: 0.5230 (mt) cc_final: 0.4821 (tt) REVERT: B 116 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.8019 (t70) REVERT: B 143 LYS cc_start: 0.7189 (tppt) cc_final: 0.6637 (mttt) REVERT: B 154 MET cc_start: 0.6788 (ttm) cc_final: 0.6165 (tpp) REVERT: C 162 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8333 (pp) REVERT: C 211 MET cc_start: 0.2647 (OUTLIER) cc_final: 0.2154 (tpp) REVERT: D 141 ASP cc_start: 0.8198 (m-30) cc_final: 0.7892 (m-30) REVERT: E 14 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8541 (ttpt) REVERT: F 72 ASP cc_start: 0.8220 (p0) cc_final: 0.7607 (p0) REVERT: F 79 ARG cc_start: 0.8335 (mtp-110) cc_final: 0.8006 (mtm110) REVERT: G 31 MET cc_start: 0.4513 (ppp) cc_final: 0.3536 (ppp) REVERT: H 113 ASP cc_start: 0.8695 (p0) cc_final: 0.8380 (p0) REVERT: H 114 ARG cc_start: 0.8082 (ttp-170) cc_final: 0.7830 (ttp80) REVERT: I 12 ARG cc_start: 0.5989 (OUTLIER) cc_final: 0.5045 (tmt170) REVERT: K 77 TYR cc_start: 0.7949 (m-80) cc_final: 0.7627 (m-80) REVERT: O 58 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8387 (ttt90) REVERT: O 88 ARG cc_start: 0.7872 (mmp-170) cc_final: 0.7514 (mmm160) REVERT: P 45 GLU cc_start: 0.7574 (tp30) cc_final: 0.7342 (tp30) REVERT: R 25 ASP cc_start: 0.8793 (t0) cc_final: 0.8524 (t0) REVERT: R 61 ARG cc_start: 0.8732 (mtm180) cc_final: 0.8528 (mpt-90) REVERT: S 66 MET cc_start: 0.3884 (ptp) cc_final: 0.3312 (pp-130) REVERT: V 16 GLN cc_start: 0.9048 (tt0) cc_final: 0.8765 (tt0) REVERT: V 46 ASP cc_start: 0.8120 (t0) cc_final: 0.7791 (t0) REVERT: V 51 LYS cc_start: 0.8586 (mtmt) cc_final: 0.7518 (mtpt) REVERT: V 96 THR cc_start: 0.8640 (m) cc_final: 0.8378 (p) REVERT: V 98 PHE cc_start: 0.8283 (m-10) cc_final: 0.7930 (m-10) outliers start: 83 outliers final: 30 residues processed: 452 average time/residue: 1.7667 time to fit residues: 990.6983 Evaluate side-chains 401 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 365 time to evaluate : 3.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 92 ARG Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain V residue 55 THR Chi-restraints excluded: chain V residue 89 LEU Chi-restraints excluded: chain V residue 91 ILE Chi-restraints excluded: chain V residue 102 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 195 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 292 optimal weight: 8.9990 chunk 239 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 352 optimal weight: 6.9990 chunk 380 optimal weight: 4.9990 chunk 313 optimal weight: 4.9990 chunk 349 optimal weight: 3.9990 chunk 120 optimal weight: 30.0000 chunk 282 optimal weight: 50.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 ASN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN F 17 GLN H 38 ASN I 4 ASN I 5 GLN ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN T 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 56194 Z= 0.377 Angle : 0.663 12.730 83416 Z= 0.358 Chirality : 0.039 0.340 10537 Planarity : 0.006 0.125 4920 Dihedral : 22.941 179.006 26540 Min Nonbonded Distance : 1.133 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.69 % Allowed : 17.87 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.17), residues: 2402 helix: 0.63 (0.16), residues: 992 sheet: -0.66 (0.25), residues: 433 loop : -0.85 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 22 HIS 0.006 0.001 HIS K 118 PHE 0.023 0.002 PHE C 23 TYR 0.022 0.002 TYR R 51 ARG 0.025 0.001 ARG J 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 384 time to evaluate : 2.982 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 116 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8152 (t70) REVERT: D 141 ASP cc_start: 0.8131 (m-30) cc_final: 0.7798 (m-30) REVERT: E 69 ARG cc_start: 0.7790 (mpp80) cc_final: 0.7232 (mtm-85) REVERT: F 72 ASP cc_start: 0.8166 (p0) cc_final: 0.7434 (p0) REVERT: F 79 ARG cc_start: 0.8346 (mtp-110) cc_final: 0.8103 (mtm110) REVERT: G 31 MET cc_start: 0.4833 (OUTLIER) cc_final: 0.3730 (ppp) REVERT: H 113 ASP cc_start: 0.8665 (p0) cc_final: 0.8387 (p0) REVERT: I 5 GLN cc_start: 0.3236 (OUTLIER) cc_final: 0.2899 (mm110) REVERT: I 12 ARG cc_start: 0.6110 (OUTLIER) cc_final: 0.5156 (tmt170) REVERT: I 60 LYS cc_start: 0.4082 (ptpt) cc_final: 0.3595 (mppt) REVERT: J 44 THR cc_start: 0.6597 (p) cc_final: 0.6192 (t) REVERT: J 56 HIS cc_start: 0.4071 (OUTLIER) cc_final: 0.3767 (t-170) REVERT: K 77 TYR cc_start: 0.8106 (m-80) cc_final: 0.7744 (m-80) REVERT: K 97 ILE cc_start: 0.9503 (mp) cc_final: 0.9290 (pp) REVERT: O 88 ARG cc_start: 0.7945 (mmp-170) cc_final: 0.7571 (mmm-85) REVERT: Q 11 ARG cc_start: 0.8009 (mtp-110) cc_final: 0.7766 (mtp-110) REVERT: Q 40 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8001 (mmt180) REVERT: R 25 ASP cc_start: 0.8812 (t0) cc_final: 0.8508 (t0) REVERT: S 66 MET cc_start: 0.3778 (ptp) cc_final: 0.3413 (pp-130) REVERT: V 14 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8124 (tp30) REVERT: V 16 GLN cc_start: 0.9107 (tt0) cc_final: 0.8815 (tt0) REVERT: V 17 LYS cc_start: 0.8841 (mtpp) cc_final: 0.8597 (mttp) REVERT: V 45 ARG cc_start: 0.7555 (ttt90) cc_final: 0.7342 (ttt180) REVERT: V 51 LYS cc_start: 0.8698 (mtmt) cc_final: 0.8481 (mtpt) REVERT: V 66 LYS cc_start: 0.8963 (tppp) cc_final: 0.8646 (tmmm) outliers start: 115 outliers final: 42 residues processed: 441 average time/residue: 1.8436 time to fit residues: 1005.8283 Evaluate side-chains 406 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 357 time to evaluate : 3.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 31 MET Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 92 ARG Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 5 GLN Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain V residue 14 GLU Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 55 THR Chi-restraints excluded: chain V residue 89 LEU Chi-restraints excluded: chain V residue 91 ILE Chi-restraints excluded: chain V residue 102 SER Chi-restraints excluded: chain V residue 104 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 347 optimal weight: 0.8980 chunk 264 optimal weight: 2.9990 chunk 182 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 236 optimal weight: 0.9990 chunk 353 optimal weight: 3.9990 chunk 374 optimal weight: 1.9990 chunk 184 optimal weight: 40.0000 chunk 334 optimal weight: 6.9990 chunk 100 optimal weight: 40.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 HIS E 97 GLN H 38 ASN I 32 GLN J 58 ASN K 101 ASN N 4 GLN T 82 GLN V 16 GLN V 58 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 56194 Z= 0.208 Angle : 0.596 12.965 83416 Z= 0.325 Chirality : 0.034 0.333 10537 Planarity : 0.006 0.123 4920 Dihedral : 22.909 179.668 26540 Min Nonbonded Distance : 1.139 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.90 % Allowed : 20.50 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.17), residues: 2402 helix: 0.88 (0.16), residues: 998 sheet: -0.42 (0.26), residues: 414 loop : -0.72 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 201 HIS 0.004 0.001 HIS K 118 PHE 0.015 0.001 PHE O 43 TYR 0.024 0.002 TYR B 213 ARG 0.017 0.001 ARG J 89 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 400 time to evaluate : 2.986 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 90 PHE cc_start: 0.5264 (m-80) cc_final: 0.4774 (m-80) REVERT: B 116 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8097 (t70) REVERT: C 29 PHE cc_start: 0.5398 (OUTLIER) cc_final: 0.4894 (t80) REVERT: C 87 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7485 (pt) REVERT: E 69 ARG cc_start: 0.7705 (mpp80) cc_final: 0.7168 (mtm-85) REVERT: F 72 ASP cc_start: 0.8141 (p0) cc_final: 0.7542 (p0) REVERT: F 79 ARG cc_start: 0.8357 (mtp-110) cc_final: 0.8068 (mtm110) REVERT: G 31 MET cc_start: 0.4749 (OUTLIER) cc_final: 0.3785 (ppp) REVERT: G 129 GLU cc_start: 0.6050 (pm20) cc_final: 0.5237 (pp20) REVERT: H 113 ASP cc_start: 0.8615 (p0) cc_final: 0.8339 (p0) REVERT: I 60 LYS cc_start: 0.4121 (ptpt) cc_final: 0.3663 (mppt) REVERT: J 44 THR cc_start: 0.6675 (p) cc_final: 0.6332 (t) REVERT: K 77 TYR cc_start: 0.8017 (m-80) cc_final: 0.7812 (m-80) REVERT: O 48 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8140 (ptpp) REVERT: O 88 ARG cc_start: 0.7871 (mmp-170) cc_final: 0.7564 (mmm-85) REVERT: Q 40 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.7999 (mmt180) REVERT: R 25 ASP cc_start: 0.8818 (t0) cc_final: 0.8482 (t0) REVERT: R 61 ARG cc_start: 0.8680 (mtm180) cc_final: 0.8446 (mtt-85) REVERT: R 74 HIS cc_start: 0.5979 (OUTLIER) cc_final: 0.5456 (p-80) REVERT: S 66 MET cc_start: 0.3956 (ptp) cc_final: 0.3095 (ppp) REVERT: V 16 GLN cc_start: 0.8959 (tt0) cc_final: 0.8735 (tt0) REVERT: V 17 LYS cc_start: 0.8740 (mtpp) cc_final: 0.8506 (mtpp) REVERT: V 45 ARG cc_start: 0.7641 (ttt90) cc_final: 0.7363 (ttt90) REVERT: V 66 LYS cc_start: 0.8969 (tppp) cc_final: 0.8624 (tmmm) outliers start: 99 outliers final: 44 residues processed: 453 average time/residue: 1.8146 time to fit residues: 1016.6573 Evaluate side-chains 421 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 370 time to evaluate : 3.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 31 MET Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 74 HIS Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 89 LEU Chi-restraints excluded: chain V residue 91 ILE Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain V residue 102 SER Chi-restraints excluded: chain V residue 104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 311 optimal weight: 0.0770 chunk 212 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 278 optimal weight: 7.9990 chunk 154 optimal weight: 7.9990 chunk 319 optimal weight: 6.9990 chunk 258 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 191 optimal weight: 0.0870 chunk 335 optimal weight: 0.8980 chunk 94 optimal weight: 30.0000 overall best weight: 2.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN C 190 HIS E 97 GLN F 17 GLN H 38 ASN I 32 GLN L 73 ASN T 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 56194 Z= 0.196 Angle : 0.583 12.957 83416 Z= 0.319 Chirality : 0.033 0.314 10537 Planarity : 0.006 0.121 4920 Dihedral : 22.852 179.272 26540 Min Nonbonded Distance : 1.152 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.80 % Allowed : 21.68 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.17), residues: 2402 helix: 1.05 (0.16), residues: 991 sheet: -0.27 (0.26), residues: 414 loop : -0.66 (0.20), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 22 HIS 0.004 0.001 HIS K 118 PHE 0.019 0.001 PHE C 130 TYR 0.033 0.001 TYR B 213 ARG 0.011 0.000 ARG Q 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 396 time to evaluate : 3.162 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 90 PHE cc_start: 0.5725 (m-80) cc_final: 0.5380 (m-80) REVERT: B 116 ASP cc_start: 0.8438 (m-30) cc_final: 0.8127 (t70) REVERT: B 173 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7546 (tp) REVERT: E 69 ARG cc_start: 0.7767 (mpp80) cc_final: 0.7348 (mtm-85) REVERT: F 72 ASP cc_start: 0.8141 (p0) cc_final: 0.7534 (p0) REVERT: G 31 MET cc_start: 0.4843 (OUTLIER) cc_final: 0.3589 (ppp) REVERT: G 53 ARG cc_start: -0.0018 (OUTLIER) cc_final: -0.1617 (ptt90) REVERT: G 56 LYS cc_start: 0.1446 (OUTLIER) cc_final: 0.0486 (tttm) REVERT: G 92 ARG cc_start: 0.4343 (OUTLIER) cc_final: 0.3767 (ptm160) REVERT: G 129 GLU cc_start: 0.6075 (pm20) cc_final: 0.5182 (pp20) REVERT: H 113 ASP cc_start: 0.8576 (p0) cc_final: 0.8308 (p0) REVERT: I 60 LYS cc_start: 0.4145 (ptpt) cc_final: 0.3694 (mppt) REVERT: I 64 TYR cc_start: 0.1207 (OUTLIER) cc_final: 0.0978 (t80) REVERT: J 44 THR cc_start: 0.6497 (p) cc_final: 0.6258 (t) REVERT: J 56 HIS cc_start: 0.3864 (OUTLIER) cc_final: 0.3582 (t-170) REVERT: O 88 ARG cc_start: 0.7848 (mmp-170) cc_final: 0.7581 (mmm-85) REVERT: Q 11 ARG cc_start: 0.7918 (mtp-110) cc_final: 0.7677 (mtp85) REVERT: Q 40 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8016 (mmt180) REVERT: R 25 ASP cc_start: 0.8807 (t0) cc_final: 0.8470 (t0) REVERT: S 66 MET cc_start: 0.3908 (ptp) cc_final: 0.3073 (ppp) REVERT: V 17 LYS cc_start: 0.8738 (mtpp) cc_final: 0.8325 (mtpp) REVERT: V 34 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7824 (pmm) REVERT: V 35 MET cc_start: 0.7755 (ttt) cc_final: 0.7347 (tmm) REVERT: V 66 LYS cc_start: 0.8957 (tppp) cc_final: 0.8647 (tmmm) outliers start: 97 outliers final: 43 residues processed: 448 average time/residue: 1.7662 time to fit residues: 982.3770 Evaluate side-chains 423 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 371 time to evaluate : 3.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 31 MET Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 92 ARG Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 64 TYR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain V residue 34 MET Chi-restraints excluded: chain V residue 91 ILE Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain V residue 102 SER Chi-restraints excluded: chain V residue 104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 125 optimal weight: 40.0000 chunk 336 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 219 optimal weight: 0.2980 chunk 92 optimal weight: 10.0000 chunk 374 optimal weight: 6.9990 chunk 310 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 123 optimal weight: 40.0000 chunk 196 optimal weight: 5.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 HIS H 38 ASN K 101 ASN L 73 ASN T 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 56194 Z= 0.412 Angle : 0.694 12.684 83416 Z= 0.370 Chirality : 0.040 0.337 10537 Planarity : 0.006 0.123 4920 Dihedral : 22.931 179.705 26540 Min Nonbonded Distance : 1.118 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 5.45 % Allowed : 22.28 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2402 helix: 0.78 (0.16), residues: 985 sheet: -0.41 (0.25), residues: 429 loop : -0.77 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 22 HIS 0.006 0.001 HIS J 15 PHE 0.019 0.002 PHE O 43 TYR 0.024 0.002 TYR R 51 ARG 0.008 0.001 ARG V 88 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 378 time to evaluate : 4.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 PHE cc_start: 0.6441 (m-80) cc_final: 0.5995 (m-80) REVERT: B 116 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8160 (t70) REVERT: B 154 MET cc_start: 0.6869 (mmm) cc_final: 0.6245 (mtp) REVERT: B 173 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7834 (tp) REVERT: D 178 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7397 (mtt) REVERT: F 72 ASP cc_start: 0.8173 (p0) cc_final: 0.7638 (p0) REVERT: G 31 MET cc_start: 0.5403 (OUTLIER) cc_final: 0.5082 (ppp) REVERT: G 53 ARG cc_start: 0.0486 (OUTLIER) cc_final: -0.1091 (ptt90) REVERT: G 56 LYS cc_start: 0.1425 (OUTLIER) cc_final: 0.0450 (tttm) REVERT: G 92 ARG cc_start: 0.4489 (OUTLIER) cc_final: 0.3873 (ptm160) REVERT: G 129 GLU cc_start: 0.5920 (pm20) cc_final: 0.5335 (pp20) REVERT: H 113 ASP cc_start: 0.8703 (p0) cc_final: 0.8400 (p0) REVERT: I 60 LYS cc_start: 0.4599 (ptpt) cc_final: 0.4200 (mppt) REVERT: J 56 HIS cc_start: 0.4272 (OUTLIER) cc_final: 0.3924 (t-170) REVERT: O 88 ARG cc_start: 0.8048 (mmp-170) cc_final: 0.7739 (mmm-85) REVERT: Q 40 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8023 (mmt180) REVERT: R 25 ASP cc_start: 0.8843 (t0) cc_final: 0.8525 (t0) REVERT: R 61 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8282 (mtt180) REVERT: R 73 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7763 (mpp80) REVERT: S 66 MET cc_start: 0.3953 (ptp) cc_final: 0.2920 (ppp) REVERT: V 17 LYS cc_start: 0.8839 (mtpp) cc_final: 0.8531 (mtpp) REVERT: V 25 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7607 (mtm-85) REVERT: V 34 MET cc_start: 0.8122 (pmm) cc_final: 0.7809 (pmm) REVERT: V 66 LYS cc_start: 0.9002 (tppp) cc_final: 0.8595 (tmmm) outliers start: 110 outliers final: 48 residues processed: 439 average time/residue: 1.8317 time to fit residues: 996.3713 Evaluate side-chains 427 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 367 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 31 MET Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 92 ARG Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 5 GLN Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 61 ARG Chi-restraints excluded: chain R residue 73 ARG Chi-restraints excluded: chain S residue 3 ARG Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain V residue 25 ARG Chi-restraints excluded: chain V residue 89 LEU Chi-restraints excluded: chain V residue 91 ILE Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain V residue 102 SER Chi-restraints excluded: chain V residue 104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 361 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 213 optimal weight: 5.9990 chunk 273 optimal weight: 1.9990 chunk 211 optimal weight: 6.9990 chunk 315 optimal weight: 0.0570 chunk 209 optimal weight: 0.9990 chunk 373 optimal weight: 0.9980 chunk 233 optimal weight: 5.9990 chunk 227 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 overall best weight: 0.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 HIS ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 HIS F 17 GLN H 38 ASN O 80 GLN T 82 GLN V 16 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 56194 Z= 0.146 Angle : 0.587 13.017 83416 Z= 0.319 Chirality : 0.032 0.302 10537 Planarity : 0.006 0.120 4920 Dihedral : 22.850 179.731 26540 Min Nonbonded Distance : 1.213 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.51 % Allowed : 24.80 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.17), residues: 2402 helix: 1.03 (0.16), residues: 990 sheet: -0.31 (0.26), residues: 421 loop : -0.58 (0.20), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 22 HIS 0.008 0.001 HIS B 170 PHE 0.017 0.001 PHE F 8 TYR 0.015 0.001 TYR I 6 ARG 0.024 0.001 ARG J 89 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 402 time to evaluate : 3.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 MET cc_start: 0.5706 (mmm) cc_final: 0.4289 (mpt) REVERT: B 90 PHE cc_start: 0.6353 (m-80) cc_final: 0.5855 (m-80) REVERT: B 116 ASP cc_start: 0.8418 (m-30) cc_final: 0.8057 (t70) REVERT: B 154 MET cc_start: 0.6840 (mmm) cc_final: 0.6217 (mtp) REVERT: E 69 ARG cc_start: 0.7866 (mpp80) cc_final: 0.7386 (mtm-85) REVERT: F 72 ASP cc_start: 0.8073 (p0) cc_final: 0.7736 (p0) REVERT: G 31 MET cc_start: 0.5266 (OUTLIER) cc_final: 0.4048 (ppp) REVERT: G 53 ARG cc_start: 0.0109 (OUTLIER) cc_final: -0.1342 (ptt90) REVERT: G 56 LYS cc_start: 0.1335 (OUTLIER) cc_final: 0.0420 (tttm) REVERT: G 92 ARG cc_start: 0.4486 (OUTLIER) cc_final: 0.3858 (ptm160) REVERT: G 116 MET cc_start: 0.2824 (OUTLIER) cc_final: 0.2491 (ppp) REVERT: G 129 GLU cc_start: 0.5779 (pm20) cc_final: 0.5253 (pp20) REVERT: H 113 ASP cc_start: 0.8566 (p0) cc_final: 0.8294 (p0) REVERT: I 5 GLN cc_start: 0.4123 (OUTLIER) cc_final: 0.3896 (tp40) REVERT: I 60 LYS cc_start: 0.4584 (ptpt) cc_final: 0.4187 (mppt) REVERT: K 64 GLN cc_start: 0.8699 (pt0) cc_final: 0.8195 (tm-30) REVERT: O 88 ARG cc_start: 0.7849 (mmp-170) cc_final: 0.7578 (mmm-85) REVERT: Q 11 ARG cc_start: 0.7987 (mtp-110) cc_final: 0.7785 (mtp-110) REVERT: Q 40 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.7985 (mmt180) REVERT: R 25 ASP cc_start: 0.8799 (t0) cc_final: 0.8505 (t0) REVERT: S 66 MET cc_start: 0.3796 (ptp) cc_final: 0.3010 (ppp) REVERT: V 16 GLN cc_start: 0.8720 (tt0) cc_final: 0.8484 (tt0) REVERT: V 34 MET cc_start: 0.7944 (pmm) cc_final: 0.7707 (pmm) REVERT: V 35 MET cc_start: 0.7833 (ttt) cc_final: 0.7417 (tmm) REVERT: V 45 ARG cc_start: 0.7679 (ptm160) cc_final: 0.7474 (ptm160) REVERT: V 66 LYS cc_start: 0.8880 (tppp) cc_final: 0.8592 (tmmm) outliers start: 71 outliers final: 30 residues processed: 443 average time/residue: 1.8028 time to fit residues: 982.9674 Evaluate side-chains 412 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 375 time to evaluate : 2.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 31 MET Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 92 ARG Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 5 GLN Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain S residue 3 ARG Chi-restraints excluded: chain V residue 89 LEU Chi-restraints excluded: chain V residue 91 ILE Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain V residue 104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 230 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 222 optimal weight: 5.9990 chunk 112 optimal weight: 30.0000 chunk 73 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 237 optimal weight: 1.9990 chunk 254 optimal weight: 10.0000 chunk 184 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 293 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 HIS ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN C 190 HIS E 148 ASN H 38 ASN K 101 ASN L 73 ASN N 62 ASN T 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 56194 Z= 0.483 Angle : 0.729 13.215 83416 Z= 0.385 Chirality : 0.041 0.336 10537 Planarity : 0.007 0.122 4920 Dihedral : 22.907 179.529 26540 Min Nonbonded Distance : 1.116 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.55 % Allowed : 24.60 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.17), residues: 2402 helix: 0.70 (0.16), residues: 990 sheet: -0.38 (0.25), residues: 424 loop : -0.67 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 22 HIS 0.018 0.001 HIS B 170 PHE 0.019 0.002 PHE O 43 TYR 0.038 0.003 TYR B 213 ARG 0.014 0.001 ARG J 89 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 380 time to evaluate : 3.008 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 90 PHE cc_start: 0.6643 (m-80) cc_final: 0.6173 (m-80) REVERT: B 116 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8169 (t70) REVERT: B 154 MET cc_start: 0.6842 (mmm) cc_final: 0.6195 (mtp) REVERT: F 72 ASP cc_start: 0.8150 (p0) cc_final: 0.7784 (p0) REVERT: G 31 MET cc_start: 0.5465 (OUTLIER) cc_final: 0.4150 (ppp) REVERT: G 53 ARG cc_start: 0.0830 (OUTLIER) cc_final: -0.0752 (ptt90) REVERT: G 56 LYS cc_start: 0.1374 (OUTLIER) cc_final: 0.0399 (tttm) REVERT: G 92 ARG cc_start: 0.4561 (OUTLIER) cc_final: 0.3984 (ptm160) REVERT: G 116 MET cc_start: 0.2815 (OUTLIER) cc_final: 0.2569 (ppp) REVERT: G 129 GLU cc_start: 0.5637 (pm20) cc_final: 0.5277 (pp20) REVERT: H 113 ASP cc_start: 0.8701 (p0) cc_final: 0.8402 (p0) REVERT: I 5 GLN cc_start: 0.4323 (OUTLIER) cc_final: 0.4057 (tp40) REVERT: I 60 LYS cc_start: 0.4623 (ptpt) cc_final: 0.4303 (mppt) REVERT: M 50 GLU cc_start: 0.5275 (OUTLIER) cc_final: 0.4693 (mp0) REVERT: O 88 ARG cc_start: 0.8038 (mmp-170) cc_final: 0.7751 (mmm-85) REVERT: Q 40 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8023 (mmt180) REVERT: R 25 ASP cc_start: 0.8850 (t0) cc_final: 0.8538 (t0) REVERT: R 61 ARG cc_start: 0.8780 (mtm180) cc_final: 0.8529 (mtt-85) REVERT: S 11 ILE cc_start: 0.4051 (OUTLIER) cc_final: 0.3268 (tp) REVERT: S 66 MET cc_start: 0.3852 (ptp) cc_final: 0.2935 (ppp) REVERT: V 10 ARG cc_start: 0.8472 (mtp85) cc_final: 0.8159 (mmm-85) REVERT: V 34 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7936 (pmm) REVERT: V 45 ARG cc_start: 0.7492 (ptm160) cc_final: 0.7149 (ptm160) REVERT: V 66 LYS cc_start: 0.9008 (tppp) cc_final: 0.8649 (tmmm) outliers start: 92 outliers final: 43 residues processed: 432 average time/residue: 1.7648 time to fit residues: 939.2858 Evaluate side-chains 415 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 361 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 31 MET Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 92 ARG Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 5 GLN Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 50 GLU Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 73 ARG Chi-restraints excluded: chain S residue 3 ARG Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain V residue 34 MET Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 89 LEU Chi-restraints excluded: chain V residue 91 ILE Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain V residue 102 SER Chi-restraints excluded: chain V residue 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 339 optimal weight: 3.9990 chunk 357 optimal weight: 6.9990 chunk 326 optimal weight: 5.9990 chunk 347 optimal weight: 0.8980 chunk 209 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 272 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 314 optimal weight: 20.0000 chunk 328 optimal weight: 0.2980 chunk 346 optimal weight: 0.7980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 HIS ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 HIS F 17 GLN G 142 HIS H 38 ASN L 73 ASN O 80 GLN T 82 GLN V 16 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 56194 Z= 0.180 Angle : 0.613 12.970 83416 Z= 0.332 Chirality : 0.033 0.307 10537 Planarity : 0.006 0.120 4920 Dihedral : 22.877 179.773 26540 Min Nonbonded Distance : 1.196 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.56 % Allowed : 26.34 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.17), residues: 2402 helix: 0.85 (0.16), residues: 991 sheet: -0.31 (0.25), residues: 429 loop : -0.58 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP C 22 HIS 0.019 0.001 HIS B 94 PHE 0.020 0.001 PHE F 78 TYR 0.039 0.002 TYR B 213 ARG 0.015 0.000 ARG Q 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 383 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 MET cc_start: 0.5809 (mmm) cc_final: 0.4348 (mpt) REVERT: B 90 PHE cc_start: 0.6618 (m-80) cc_final: 0.6168 (m-80) REVERT: B 113 ARG cc_start: 0.6392 (ttp80) cc_final: 0.6177 (ttp80) REVERT: B 116 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8118 (t70) REVERT: B 154 MET cc_start: 0.6806 (mmm) cc_final: 0.6164 (mtp) REVERT: C 144 LEU cc_start: 0.6803 (mm) cc_final: 0.6223 (tp) REVERT: F 72 ASP cc_start: 0.8109 (p0) cc_final: 0.7832 (p0) REVERT: G 31 MET cc_start: 0.5262 (OUTLIER) cc_final: 0.4122 (ppp) REVERT: G 53 ARG cc_start: 0.0506 (OUTLIER) cc_final: -0.1066 (ptt90) REVERT: G 56 LYS cc_start: 0.1337 (OUTLIER) cc_final: 0.0428 (tttm) REVERT: G 92 ARG cc_start: 0.4588 (OUTLIER) cc_final: 0.3995 (ptm160) REVERT: G 129 GLU cc_start: 0.5632 (pm20) cc_final: 0.5260 (pp20) REVERT: H 113 ASP cc_start: 0.8592 (p0) cc_final: 0.8304 (p0) REVERT: I 60 LYS cc_start: 0.4432 (ptpt) cc_final: 0.4079 (mppt) REVERT: I 115 LYS cc_start: 0.7286 (mttm) cc_final: 0.7039 (mppt) REVERT: K 64 GLN cc_start: 0.8668 (pt0) cc_final: 0.8180 (tm-30) REVERT: M 50 GLU cc_start: 0.5444 (OUTLIER) cc_final: 0.4617 (mp0) REVERT: O 88 ARG cc_start: 0.7882 (mmp-170) cc_final: 0.7605 (mmm-85) REVERT: Q 11 ARG cc_start: 0.7953 (mtp-110) cc_final: 0.7679 (mtp-110) REVERT: Q 40 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8019 (mmt180) REVERT: R 25 ASP cc_start: 0.8807 (t0) cc_final: 0.8480 (t0) REVERT: S 11 ILE cc_start: 0.3909 (tp) cc_final: 0.3286 (tp) REVERT: S 66 MET cc_start: 0.3673 (ptp) cc_final: 0.2794 (ppp) REVERT: V 10 ARG cc_start: 0.8356 (mtp85) cc_final: 0.7940 (mmm-85) REVERT: V 16 GLN cc_start: 0.8767 (tt0) cc_final: 0.8563 (tt0) REVERT: V 35 MET cc_start: 0.7830 (ttt) cc_final: 0.7428 (tmm) REVERT: V 45 ARG cc_start: 0.7503 (ptm160) cc_final: 0.7033 (ptm160) REVERT: V 66 LYS cc_start: 0.8937 (tppp) cc_final: 0.8528 (tmmm) outliers start: 72 outliers final: 40 residues processed: 424 average time/residue: 1.6244 time to fit residues: 852.7223 Evaluate side-chains 418 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 371 time to evaluate : 3.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 31 MET Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 92 ARG Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 50 GLU Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain P residue 44 SER Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain R residue 73 ARG Chi-restraints excluded: chain S residue 3 ARG Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 89 LEU Chi-restraints excluded: chain V residue 91 ILE Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain V residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 228 optimal weight: 0.9990 chunk 367 optimal weight: 7.9990 chunk 224 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 chunk 255 optimal weight: 0.6980 chunk 385 optimal weight: 6.9990 chunk 354 optimal weight: 5.9990 chunk 307 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 237 optimal weight: 1.9990 chunk 188 optimal weight: 10.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 HIS ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 HIS G 9 GLN H 38 ASN K 81 ASN K 101 ASN L 73 ASN T 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 56194 Z= 0.224 Angle : 0.626 14.001 83416 Z= 0.337 Chirality : 0.034 0.298 10537 Planarity : 0.006 0.120 4920 Dihedral : 22.837 179.359 26540 Min Nonbonded Distance : 1.184 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.97 % Allowed : 27.08 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.17), residues: 2402 helix: 0.86 (0.16), residues: 987 sheet: -0.26 (0.25), residues: 427 loop : -0.58 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.002 TRP C 22 HIS 0.015 0.001 HIS B 94 PHE 0.024 0.002 PHE C 23 TYR 0.038 0.002 TYR B 213 ARG 0.013 0.001 ARG Q 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 383 time to evaluate : 3.072 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 49 MET cc_start: 0.6042 (mmm) cc_final: 0.4424 (mpt) REVERT: B 90 PHE cc_start: 0.6641 (m-80) cc_final: 0.6123 (m-80) REVERT: B 113 ARG cc_start: 0.6398 (ttp80) cc_final: 0.6186 (ttp80) REVERT: B 116 ASP cc_start: 0.8524 (m-30) cc_final: 0.8139 (t70) REVERT: B 127 ASP cc_start: 0.6263 (OUTLIER) cc_final: 0.5977 (m-30) REVERT: B 137 ARG cc_start: 0.7857 (mmm160) cc_final: 0.7628 (mtp180) REVERT: B 154 MET cc_start: 0.6747 (mmm) cc_final: 0.6141 (mtp) REVERT: G 31 MET cc_start: 0.5451 (OUTLIER) cc_final: 0.4308 (ppp) REVERT: G 53 ARG cc_start: 0.0524 (OUTLIER) cc_final: -0.1044 (ptt90) REVERT: G 56 LYS cc_start: 0.1303 (OUTLIER) cc_final: 0.0404 (tttm) REVERT: G 92 ARG cc_start: 0.4671 (OUTLIER) cc_final: 0.4043 (ptm160) REVERT: G 129 GLU cc_start: 0.5662 (pm20) cc_final: 0.5297 (pp20) REVERT: H 113 ASP cc_start: 0.8595 (p0) cc_final: 0.8314 (p0) REVERT: I 60 LYS cc_start: 0.4558 (ptpt) cc_final: 0.4236 (mppt) REVERT: I 115 LYS cc_start: 0.7271 (mttm) cc_final: 0.7027 (mppt) REVERT: K 64 GLN cc_start: 0.8655 (pt0) cc_final: 0.8155 (tm-30) REVERT: M 50 GLU cc_start: 0.5440 (OUTLIER) cc_final: 0.4620 (mp0) REVERT: N 89 MET cc_start: 0.5299 (mmm) cc_final: 0.5049 (mmp) REVERT: O 88 ARG cc_start: 0.7921 (mmp-170) cc_final: 0.7646 (mmm-85) REVERT: Q 11 ARG cc_start: 0.7966 (mtp-110) cc_final: 0.7676 (mtp-110) REVERT: Q 40 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8018 (mmt180) REVERT: R 25 ASP cc_start: 0.8811 (t0) cc_final: 0.8489 (t0) REVERT: S 66 MET cc_start: 0.3666 (ptp) cc_final: 0.2855 (ppp) REVERT: V 14 GLU cc_start: 0.8412 (tp30) cc_final: 0.7918 (mp0) REVERT: V 16 GLN cc_start: 0.8725 (tt0) cc_final: 0.8452 (tt0) REVERT: V 45 ARG cc_start: 0.7519 (ptm160) cc_final: 0.7031 (ptm160) outliers start: 60 outliers final: 37 residues processed: 422 average time/residue: 1.5646 time to fit residues: 815.9639 Evaluate side-chains 417 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 373 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 31 MET Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 92 ARG Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain M residue 50 GLU Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain P residue 44 SER Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 89 LEU Chi-restraints excluded: chain V residue 91 ILE Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain V residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 243 optimal weight: 2.9990 chunk 327 optimal weight: 9.9990 chunk 94 optimal weight: 30.0000 chunk 283 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 307 optimal weight: 2.9990 chunk 128 optimal weight: 30.0000 chunk 315 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN B 93 ASN B 94 HIS ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN C 190 HIS H 38 ASN K 81 ASN T 52 ASN T 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.102100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.057084 restraints weight = 140205.733| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 1.52 r_work: 0.2718 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 56194 Z= 0.421 Angle : 0.721 13.166 83416 Z= 0.382 Chirality : 0.040 0.332 10537 Planarity : 0.007 0.122 4920 Dihedral : 22.946 180.000 26540 Min Nonbonded Distance : 1.149 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.22 % Allowed : 27.38 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.17), residues: 2402 helix: 0.64 (0.16), residues: 974 sheet: -0.43 (0.25), residues: 422 loop : -0.70 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP C 22 HIS 0.008 0.001 HIS B 94 PHE 0.019 0.002 PHE C 23 TYR 0.038 0.003 TYR B 213 ARG 0.012 0.001 ARG Q 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16966.17 seconds wall clock time: 299 minutes 51.93 seconds (17991.93 seconds total)