Starting phenix.real_space_refine on Sun Feb 25 12:11:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nax_12251/02_2024/7nax_12251_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nax_12251/02_2024/7nax_12251.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nax_12251/02_2024/7nax_12251_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nax_12251/02_2024/7nax_12251_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nax_12251/02_2024/7nax_12251_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nax_12251/02_2024/7nax_12251.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nax_12251/02_2024/7nax_12251.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nax_12251/02_2024/7nax_12251_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nax_12251/02_2024/7nax_12251_neut_updated.pdb" } resolution = 2.96 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 1526 5.49 5 Mg 181 5.21 5 S 68 5.16 5 C 26126 2.51 5 N 9543 2.21 5 O 13900 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 PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 51345 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 32753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1526, 32753 Classifications: {'RNA': 1526} Modifications used: {'rna2p_pur': 118, 'rna2p_pyr': 91, 'rna3p': 8, 'rna3p_pur': 746, 'rna3p_pyr': 563} Link IDs: {'rna2p': 208, 'rna3p': 1317} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 4 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: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1156 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} 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: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1151 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 5, 'TRANS': 141} 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: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} 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: "A" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 181 Unusual residues: {' MG': 181} Classifications: {'undetermined': 181} Link IDs: {None: 180} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 26.96, per 1000 atoms: 0.53 Number of scatterers: 51345 At special positions: 0 Unit cell: (208.95, 210, 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 68 16.00 P 1526 15.00 Mg 181 11.99 O 13900 8.00 N 9543 7.00 C 26126 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: 30.63 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4332 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 20 sheets defined 39.1% alpha, 15.5% beta 502 base pairs and 860 stacking pairs defined. Time for finding SS restraints: 29.28 Creating SS restraints... Processing helix chain 'B' and resid 6 through 12 removed outlier: 3.707A 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 removed outlier: 3.505A pdb=" N GLN B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) 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 26 through 46 removed outlier: 4.706A pdb=" N ALA C 30 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ASP C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 82 through 95 Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 130 through 144 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 15 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 96 Processing helix chain 'D' and resid 98 through 105 Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 147 through 150 No H-bonds generated for 'chain 'D' and resid 147 through 150' Processing helix chain 'D' and resid 153 through 164 removed outlier: 3.677A pdb=" N LEU D 159 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 205 Processing helix chain 'E' and resid 56 through 68 Processing helix chain 'E' and resid 109 through 118 removed outlier: 3.575A pdb=" N ALA E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 145 Processing helix chain 'E' and resid 150 through 156 Processing helix chain 'E' and resid 161 through 165 Processing helix chain 'F' and resid 12 through 31 removed outlier: 4.657A pdb=" N GLU F 16 " --> pdb=" O ASP F 13 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL F 18 " --> pdb=" O SER F 15 " (cutoff:3.500A) Proline residue: F 19 - end of helix removed outlier: 4.892A pdb=" N ILE F 22 " --> pdb=" O PRO F 19 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR F 26 " --> pdb=" O GLU F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 80 Processing helix chain 'G' and resid 21 through 30 Processing helix chain 'G' and resid 36 through 53 removed outlier: 3.505A pdb=" N GLN G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 69 removed outlier: 3.959A pdb=" N GLU G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 110 Processing helix chain 'G' and resid 116 through 128 Processing helix chain 'G' and resid 134 through 143 Processing helix chain 'H' and resid 6 through 19 Processing helix chain 'H' and resid 31 through 42 Processing helix chain 'H' and resid 113 through 118 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 54 Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 72 through 90 Processing helix chain 'I' and resid 92 through 100 removed outlier: 3.888A pdb=" N SER I 96 " --> pdb=" O GLU I 92 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU I 97 " --> pdb=" O SER I 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 31 Processing helix chain 'J' and resid 81 through 88 removed outlier: 3.703A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 49 No H-bonds generated for 'chain 'K' and resid 47 through 49' Processing helix chain 'K' and resid 54 through 58 Processing helix chain 'K' and resid 60 through 74 removed outlier: 3.589A pdb=" N ALA K 73 " --> pdb=" O ARG K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 102 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: 4.135A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 36 Processing helix chain 'M' and resid 50 through 62 removed outlier: 3.677A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 82 Processing helix chain 'M' and resid 86 through 92 Processing helix chain 'M' and resid 107 through 110 No H-bonds generated for 'chain 'M' and resid 107 through 110' Processing helix chain 'N' and resid 4 through 19 Processing helix chain 'N' and resid 21 through 32 Processing helix chain 'N' and resid 40 through 50 removed outlier: 3.671A pdb=" N THR N 50 " --> pdb=" O LEU N 46 " (cutoff:3.500A) 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 90 removed outlier: 3.866A pdb=" N ARG N 85 " --> pdb=" O ARG N 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 15 Processing helix chain 'O' and resid 25 through 45 removed outlier: 4.117A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU O 45 " --> pdb=" O GLY O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 73 removed outlier: 4.082A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 85 Processing helix chain 'P' and resid 54 through 63 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 28 No H-bonds generated for 'chain 'R' and resid 26 through 28' Processing helix chain 'R' and resid 30 through 32 No H-bonds generated for 'chain 'R' and resid 30 through 32' 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 24 Processing helix chain 'S' and resid 64 through 66 No H-bonds generated for 'chain 'S' and resid 64 through 66' Processing helix chain 'S' and resid 71 through 74 Processing helix chain 'T' and resid 5 through 41 Processing helix chain 'T' and resid 44 through 63 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 69 through 84 Processing sheet with id= A, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.697A pdb=" N ALA B 160 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL B 70 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE B 162 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 7.070A 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: 6.317A 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 103 through 105 removed outlier: 7.770A pdb=" N ALA C 104 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE C 68 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 166 through 170 Processing sheet with id= E, first strand: chain 'D' and resid 123 through 125 Processing sheet with id= F, first strand: chain 'E' and resid 71 through 73 removed outlier: 6.663A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.295A 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 38 through 41 removed outlier: 4.540A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET F 90 " --> pdb=" O GLU F 5 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 73 through 75 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: 6.750A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 5 through 11 Processing sheet with id= M, first strand: chain 'J' and resid 97 through 101 removed outlier: 4.640A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) 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 43 through 46 removed outlier: 3.929A pdb=" N GLY K 43 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL K 32 " --> pdb=" O ALA K 45 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASN K 81 " --> pdb=" O GLY K 19 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA K 21 " --> pdb=" O ASN K 81 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU K 83 " --> pdb=" O ALA K 21 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE K 23 " --> pdb=" O GLU K 83 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET K 85 " --> pdb=" O ILE K 23 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA K 25 " --> pdb=" O MET K 85 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS K 87 " --> pdb=" O ALA K 25 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG K 106 " --> pdb=" O LEU K 82 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N VAL K 84 " --> pdb=" O ARG K 106 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N THR K 108 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 12.115A pdb=" N VAL K 86 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N ILE K 110 " --> pdb=" O VAL K 86 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'L' and resid 95 through 97 removed outlier: 6.754A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR L 39 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 6.224A 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: 6.596A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'Q' and resid 73 through 75 removed outlier: 8.172A pdb=" N GLN Q 9 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLU Q 26 " --> pdb=" O GLN Q 9 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'Q' and resid 58 through 60 removed outlier: 6.637A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) removed outlier: 5.835A 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 33 775 hydrogen bonds defined for protein. 2205 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1250 hydrogen bonds 1950 hydrogen bond angles 0 basepair planarities 502 basepair parallelities 860 stacking parallelities Total time for adding SS restraints: 49.02 Time building geometry restraints manager: 32.34 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: 8925 1.33 - 1.45: 21910 1.45 - 1.57: 21343 1.57 - 1.70: 3049 1.70 - 1.82: 122 Bond restraints: 55349 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 5.75e+01 bond pdb=" N3 2MG A1207 " pdb=" C4 2MG A1207 " ideal model delta sigma weight residual 1.496 1.345 0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N3 2MG A1516 " pdb=" C4 2MG A1516 " ideal model delta sigma weight residual 1.496 1.349 0.147 2.00e-02 2.50e+03 5.41e+01 bond pdb=" N3 2MG A 966 " pdb=" C4 2MG A 966 " ideal model delta sigma weight residual 1.496 1.349 0.147 2.00e-02 2.50e+03 5.40e+01 bond pdb=" C2 5MC A 967 " pdb=" N3 5MC A 967 " ideal model delta sigma weight residual 1.493 1.346 0.147 2.00e-02 2.50e+03 5.39e+01 ... (remaining 55344 not shown) Histogram of bond angle deviations from ideal: 95.36 - 103.70: 4532 103.70 - 112.05: 33865 112.05 - 120.39: 25272 120.39 - 128.74: 16790 128.74 - 137.08: 1819 Bond angle restraints: 82278 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 94.96 130.11 -35.15 3.00e+00 1.11e-01 1.37e+02 angle pdb=" C THR B 125 " pdb=" CA THR B 125 " pdb=" CB THR B 125 " ideal model delta sigma weight residual 109.83 117.30 -7.47 9.90e-01 1.02e+00 5.70e+01 angle pdb=" CA D2T L 89 " pdb=" CB D2T L 89 " pdb=" SB D2T L 89 " ideal model delta sigma weight residual 114.38 95.36 19.02 3.00e+00 1.11e-01 4.02e+01 angle pdb=" N6 MA6 A1518 " pdb=" C6 MA6 A1518 " pdb=" N1 MA6 A1518 " ideal model delta sigma weight residual 104.44 122.58 -18.14 3.00e+00 1.11e-01 3.66e+01 angle pdb=" C1' G7M A 527 " pdb=" N9 G7M A 527 " pdb=" C4 G7M A 527 " ideal model delta sigma weight residual 142.80 124.85 17.95 3.00e+00 1.11e-01 3.58e+01 ... (remaining 82273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.36: 31213 34.36 - 68.73: 3718 68.73 - 103.09: 444 103.09 - 137.45: 9 137.45 - 171.82: 9 Dihedral angle restraints: 35393 sinusoidal: 28688 harmonic: 6705 Sorted by residual: dihedral pdb=" C5' U A1211 " pdb=" C4' U A1211 " pdb=" C3' U A1211 " pdb=" O3' U A1211 " ideal model delta sinusoidal sigma weight residual 147.00 77.30 69.70 1 8.00e+00 1.56e-02 9.80e+01 dihedral pdb=" C4' U A1211 " pdb=" C3' U A1211 " pdb=" C2' U A1211 " pdb=" C1' U A1211 " ideal model delta sinusoidal sigma weight residual -35.00 30.42 -65.42 1 8.00e+00 1.56e-02 8.76e+01 dihedral pdb=" O4' U A1008 " pdb=" C1' U A1008 " pdb=" N1 U A1008 " pdb=" C2 U A1008 " ideal model delta sinusoidal sigma weight residual 200.00 29.50 170.50 1 1.50e+01 4.44e-03 8.47e+01 ... (remaining 35390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 10123 0.104 - 0.207: 270 0.207 - 0.311: 14 0.311 - 0.414: 1 0.414 - 0.518: 3 Chirality restraints: 10411 Sorted by residual: chirality pdb=" C3' U A1211 " pdb=" C4' U A1211 " pdb=" O3' U A1211 " pdb=" C2' U A1211 " both_signs ideal model delta sigma weight residual False -2.74 -2.23 -0.52 2.00e-01 2.50e+01 6.70e+00 chirality pdb=" CB D2T L 89 " pdb=" CA D2T L 89 " pdb=" SB D2T L 89 " pdb=" CG D2T L 89 " both_signs ideal model delta sigma weight residual False -3.02 -3.49 0.47 2.00e-01 2.50e+01 5.55e+00 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 2.02 0.43 2.00e-01 2.50e+01 4.54e+00 ... (remaining 10408 not shown) Planarity restraints: 4777 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1207 " -0.062 2.00e-02 2.50e+03 5.94e-01 7.94e+03 pdb=" C4' 2MG A1207 " -0.440 2.00e-02 2.50e+03 pdb=" O4' 2MG A1207 " -0.620 2.00e-02 2.50e+03 pdb=" C3' 2MG A1207 " 0.595 2.00e-02 2.50e+03 pdb=" O3' 2MG A1207 " 0.627 2.00e-02 2.50e+03 pdb=" C2' 2MG A1207 " 0.181 2.00e-02 2.50e+03 pdb=" O2' 2MG A1207 " -0.964 2.00e-02 2.50e+03 pdb=" C1' 2MG A1207 " -0.228 2.00e-02 2.50e+03 pdb=" N9 2MG A1207 " 0.911 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A 966 " -0.005 2.00e-02 2.50e+03 5.25e-01 6.21e+03 pdb=" C4' 2MG A 966 " 0.428 2.00e-02 2.50e+03 pdb=" O4' 2MG A 966 " 0.587 2.00e-02 2.50e+03 pdb=" C3' 2MG A 966 " -0.573 2.00e-02 2.50e+03 pdb=" O3' 2MG A 966 " -0.470 2.00e-02 2.50e+03 pdb=" C2' 2MG A 966 " -0.250 2.00e-02 2.50e+03 pdb=" O2' 2MG A 966 " 0.820 2.00e-02 2.50e+03 pdb=" C1' 2MG A 966 " 0.245 2.00e-02 2.50e+03 pdb=" N9 2MG A 966 " -0.782 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A 967 " 0.015 2.00e-02 2.50e+03 5.13e-01 5.92e+03 pdb=" C4' 5MC A 967 " 0.417 2.00e-02 2.50e+03 pdb=" O4' 5MC A 967 " 0.510 2.00e-02 2.50e+03 pdb=" C3' 5MC A 967 " -0.576 2.00e-02 2.50e+03 pdb=" O3' 5MC A 967 " -0.475 2.00e-02 2.50e+03 pdb=" C2' 5MC A 967 " -0.240 2.00e-02 2.50e+03 pdb=" O2' 5MC A 967 " 0.841 2.00e-02 2.50e+03 pdb=" C1' 5MC A 967 " 0.250 2.00e-02 2.50e+03 pdb=" N1 5MC A 967 " -0.741 2.00e-02 2.50e+03 ... (remaining 4774 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 431 2.48 - 3.09: 34989 3.09 - 3.69: 99408 3.69 - 4.30: 146906 4.30 - 4.90: 197793 Nonbonded interactions: 479527 Sorted by model distance: nonbonded pdb=" OP2 C A1054 " pdb="MG MG A1751 " model vdw 1.876 2.170 nonbonded pdb=" OP1 G A 450 " pdb="MG MG A1663 " model vdw 1.894 2.170 nonbonded pdb=" OP2 G A 100 " pdb="MG MG A1642 " model vdw 1.916 2.170 nonbonded pdb=" OP2 G A 117 " pdb="MG MG A1701 " model vdw 1.922 2.170 nonbonded pdb=" OP2 A A1081 " pdb=" NZ LYS E 52 " model vdw 1.924 2.520 ... (remaining 479522 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: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 18.000 Check model and map are aligned: 0.860 Set scattering table: 0.450 Process input model: 196.100 Find NCS groups from input model: 1.050 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:14.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 234.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 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 : 0.008 0.152 55349 Z= 0.492 Angle : 0.690 35.154 82278 Z= 0.395 Chirality : 0.041 0.518 10411 Planarity : 0.016 0.594 4777 Dihedral : 22.726 171.817 31061 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.16), residues: 2301 helix: -0.67 (0.16), residues: 941 sheet: -2.11 (0.24), residues: 394 loop : -1.94 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 201 HIS 0.007 0.001 HIS N 71 PHE 0.018 0.002 PHE H 66 TYR 0.012 0.002 TYR R 51 ARG 0.009 0.001 ARG D 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 526 time to evaluate : 3.306 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 116 ASP cc_start: 0.6710 (m-30) cc_final: 0.5930 (t70) REVERT: B 221 VAL cc_start: 0.6716 (t) cc_final: 0.6474 (m) REVERT: C 138 VAL cc_start: 0.5896 (t) cc_final: 0.5678 (t) REVERT: D 44 ARG cc_start: 0.7295 (tmm160) cc_final: 0.7082 (tmt90) REVERT: E 13 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7769 (mt-10) REVERT: E 61 GLN cc_start: 0.8778 (tp-100) cc_final: 0.8383 (tp-100) REVERT: E 65 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8234 (tp30) REVERT: E 116 GLU cc_start: 0.8354 (tt0) cc_final: 0.8104 (tt0) REVERT: F 5 GLU cc_start: 0.8290 (tt0) cc_final: 0.7906 (tt0) REVERT: F 14 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7987 (mp10) REVERT: F 56 LYS cc_start: 0.8472 (ptmm) cc_final: 0.8030 (ttpp) REVERT: F 72 ASP cc_start: 0.8281 (t70) cc_final: 0.7479 (t0) REVERT: F 75 GLU cc_start: 0.8209 (pp20) cc_final: 0.7949 (pp20) REVERT: F 98 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7733 (tm-30) REVERT: G 95 ARG cc_start: 0.3070 (mmm160) cc_final: 0.2856 (mmm160) REVERT: H 47 GLU cc_start: 0.8237 (tm-30) cc_final: 0.8031 (tm-30) REVERT: H 69 LYS cc_start: 0.8346 (mmtm) cc_final: 0.8137 (mmpt) REVERT: H 74 SER cc_start: 0.8800 (t) cc_final: 0.8570 (p) REVERT: K 18 ASP cc_start: 0.8939 (p0) cc_final: 0.8657 (p0) REVERT: K 37 ARG cc_start: 0.7582 (mmp80) cc_final: 0.7212 (mmt-90) REVERT: K 64 GLN cc_start: 0.7651 (mm110) cc_final: 0.7128 (mm110) REVERT: K 86 VAL cc_start: 0.8528 (p) cc_final: 0.8256 (p) REVERT: L 62 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7893 (mt-10) REVERT: O 14 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7370 (tm-30) REVERT: P 76 LYS cc_start: 0.8815 (ttmm) cc_final: 0.8599 (ttmt) REVERT: Q 8 LEU cc_start: 0.8722 (mt) cc_final: 0.8422 (mm) REVERT: Q 11 ARG cc_start: 0.7729 (ttm-80) cc_final: 0.7490 (mtt-85) REVERT: Q 15 ASP cc_start: 0.8252 (p0) cc_final: 0.7639 (p0) REVERT: Q 18 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8234 (mt-10) REVERT: Q 55 ILE cc_start: 0.8905 (tt) cc_final: 0.8550 (mp) REVERT: Q 57 ASP cc_start: 0.8294 (m-30) cc_final: 0.7937 (m-30) REVERT: R 30 LYS cc_start: 0.9223 (mtpt) cc_final: 0.8839 (mtmt) outliers start: 0 outliers final: 1 residues processed: 526 average time/residue: 1.9715 time to fit residues: 1262.6316 Evaluate side-chains 291 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 290 time to evaluate : 3.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 5.9990 chunk 285 optimal weight: 6.9990 chunk 158 optimal weight: 20.0000 chunk 97 optimal weight: 30.0000 chunk 192 optimal weight: 5.9990 chunk 152 optimal weight: 0.4980 chunk 295 optimal weight: 2.9990 chunk 114 optimal weight: 30.0000 chunk 179 optimal weight: 10.0000 chunk 219 optimal weight: 4.9990 chunk 342 optimal weight: 0.6980 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN B 177 ASN B 227 GLN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN C 139 GLN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 HIS D 100 ASN D 126 ASN ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 GLN D 196 ASN E 73 ASN E 83 HIS E 89 HIS E 135 ASN G 68 ASN G 148 ASN ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 HIS K 29 ASN K 64 GLN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN L 6 GLN ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 66 GLN R 54 GLN R 74 HIS ** S 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 ASN T 78 ASN T 84 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 55349 Z= 0.270 Angle : 0.658 13.705 82278 Z= 0.350 Chirality : 0.037 0.400 10411 Planarity : 0.006 0.119 4777 Dihedral : 23.322 178.595 26418 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.88 % Allowed : 19.75 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.17), residues: 2301 helix: 0.41 (0.17), residues: 917 sheet: -1.74 (0.24), residues: 395 loop : -1.32 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 23 HIS 0.005 0.001 HIS P 59 PHE 0.023 0.002 PHE C 37 TYR 0.029 0.002 TYR C 168 ARG 0.010 0.001 ARG D 47 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 341 time to evaluate : 3.483 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 221 VAL cc_start: 0.7023 (t) cc_final: 0.6695 (m) REVERT: C 211 MET cc_start: 0.4349 (tpt) cc_final: 0.3234 (tpp) REVERT: D 44 ARG cc_start: 0.7489 (tmm160) cc_final: 0.7267 (tmt90) REVERT: E 61 GLN cc_start: 0.8859 (tp-100) cc_final: 0.8438 (tp-100) REVERT: E 65 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8165 (tp30) REVERT: E 116 GLU cc_start: 0.8366 (tt0) cc_final: 0.8122 (tt0) REVERT: F 5 GLU cc_start: 0.8339 (tt0) cc_final: 0.7949 (tt0) REVERT: F 14 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7894 (mp10) REVERT: F 72 ASP cc_start: 0.8535 (t70) cc_final: 0.8263 (t0) REVERT: F 90 MET cc_start: 0.8169 (ptm) cc_final: 0.7930 (ptm) REVERT: F 97 THR cc_start: 0.9158 (p) cc_final: 0.8900 (m) REVERT: F 98 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7721 (tm-30) REVERT: G 95 ARG cc_start: 0.3227 (mmm160) cc_final: 0.2914 (mmm160) REVERT: H 52 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7896 (mm-30) REVERT: H 54 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7638 (p0) REVERT: H 74 SER cc_start: 0.9073 (t) cc_final: 0.8656 (p) REVERT: I 72 ILE cc_start: 0.6572 (pt) cc_final: 0.6369 (mp) REVERT: K 27 PHE cc_start: 0.8262 (m-80) cc_final: 0.8028 (m-10) REVERT: K 64 GLN cc_start: 0.7391 (mm-40) cc_final: 0.7154 (mm110) REVERT: M 87 ARG cc_start: 0.4259 (mtp180) cc_final: 0.3879 (mpt-90) REVERT: N 49 GLN cc_start: 0.1938 (pt0) cc_final: 0.1608 (pp30) REVERT: O 14 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7412 (tm-30) REVERT: O 71 LYS cc_start: 0.8672 (ttpp) cc_final: 0.8223 (tttp) REVERT: O 74 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.7087 (p0) REVERT: P 76 LYS cc_start: 0.8910 (ttmm) cc_final: 0.8654 (ttmt) REVERT: Q 15 ASP cc_start: 0.8492 (p0) cc_final: 0.8017 (p0) REVERT: Q 55 ILE cc_start: 0.8990 (tt) cc_final: 0.8502 (mp) REVERT: Q 57 ASP cc_start: 0.8423 (m-30) cc_final: 0.7993 (m-30) REVERT: Q 72 SER cc_start: 0.9192 (p) cc_final: 0.8989 (t) REVERT: R 30 LYS cc_start: 0.9205 (mtpt) cc_final: 0.8807 (mtmt) REVERT: R 57 ARG cc_start: 0.8933 (mtm-85) cc_final: 0.8625 (mtm110) REVERT: T 43 ASP cc_start: 0.8088 (t0) cc_final: 0.7852 (t0) REVERT: T 59 ASP cc_start: 0.9091 (t70) cc_final: 0.8261 (t0) outliers start: 75 outliers final: 26 residues processed: 382 average time/residue: 1.9036 time to fit residues: 892.3375 Evaluate side-chains 328 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 299 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 31 ILE Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 74 ASP Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 71 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 284 optimal weight: 20.0000 chunk 233 optimal weight: 4.9990 chunk 94 optimal weight: 30.0000 chunk 342 optimal weight: 4.9990 chunk 370 optimal weight: 4.9990 chunk 305 optimal weight: 7.9990 chunk 340 optimal weight: 0.9980 chunk 116 optimal weight: 20.0000 chunk 275 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 69 HIS ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN G 148 ASN I 50 GLN ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 HIS K 29 ASN K 64 GLN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 46 HIS ** S 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 55349 Z= 0.320 Angle : 0.654 12.769 82278 Z= 0.351 Chirality : 0.037 0.392 10411 Planarity : 0.006 0.125 4777 Dihedral : 23.227 180.000 26418 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 5.95 % Allowed : 21.35 % Favored : 72.70 % 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: -0.80 (0.17), residues: 2301 helix: 0.64 (0.17), residues: 926 sheet: -1.61 (0.24), residues: 414 loop : -1.10 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 104 HIS 0.011 0.002 HIS M 91 PHE 0.027 0.002 PHE K 52 TYR 0.024 0.002 TYR C 168 ARG 0.010 0.001 ARG I 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 327 time to evaluate : 3.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 ASP cc_start: 0.4487 (OUTLIER) cc_final: 0.4241 (p0) REVERT: B 116 ASP cc_start: 0.7609 (m-30) cc_final: 0.6892 (t70) REVERT: D 44 ARG cc_start: 0.7629 (tmm160) cc_final: 0.7249 (ptm160) REVERT: D 164 GLN cc_start: 0.8826 (mm110) cc_final: 0.8535 (mp10) REVERT: E 61 GLN cc_start: 0.8836 (tp-100) cc_final: 0.8484 (tp-100) REVERT: E 65 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8344 (tp30) REVERT: E 159 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8788 (mttp) REVERT: F 5 GLU cc_start: 0.8504 (tt0) cc_final: 0.8095 (tt0) REVERT: F 14 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7929 (mp10) REVERT: F 69 GLU cc_start: 0.8903 (pm20) cc_final: 0.8562 (pm20) REVERT: F 72 ASP cc_start: 0.8883 (t70) cc_final: 0.8413 (t0) REVERT: F 75 GLU cc_start: 0.8366 (pp20) cc_final: 0.7925 (pp20) REVERT: F 90 MET cc_start: 0.8182 (ptm) cc_final: 0.7874 (ptm) REVERT: F 98 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7795 (tm-30) REVERT: G 95 ARG cc_start: 0.3252 (mmm160) cc_final: 0.2997 (mmm160) REVERT: G 131 LYS cc_start: 0.3782 (OUTLIER) cc_final: 0.3192 (tmmt) REVERT: H 52 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8056 (mm-30) REVERT: H 54 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7775 (p0) REVERT: H 69 LYS cc_start: 0.8724 (mmmm) cc_final: 0.8509 (mtmt) REVERT: H 74 SER cc_start: 0.8960 (t) cc_final: 0.8544 (p) REVERT: I 52 LEU cc_start: 0.4145 (tp) cc_final: 0.3501 (pp) REVERT: K 27 PHE cc_start: 0.8533 (m-80) cc_final: 0.8132 (m-10) REVERT: L 56 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7584 (ttm170) REVERT: M 7 ILE cc_start: 0.5487 (OUTLIER) cc_final: 0.5184 (mm) REVERT: N 6 MET cc_start: 0.3226 (OUTLIER) cc_final: 0.2982 (mmt) REVERT: N 49 GLN cc_start: 0.2448 (pt0) cc_final: 0.2164 (pt0) REVERT: N 84 VAL cc_start: 0.6351 (m) cc_final: 0.5575 (p) REVERT: O 14 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7844 (tm-30) REVERT: O 71 LYS cc_start: 0.8712 (ttpp) cc_final: 0.8414 (ttmm) REVERT: Q 55 ILE cc_start: 0.9013 (tt) cc_final: 0.8784 (mt) REVERT: Q 72 SER cc_start: 0.9271 (p) cc_final: 0.8842 (t) REVERT: R 30 LYS cc_start: 0.9203 (mtpt) cc_final: 0.8751 (mtmt) outliers start: 115 outliers final: 36 residues processed: 396 average time/residue: 1.7743 time to fit residues: 872.1082 Evaluate side-chains 320 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 276 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 185 LYS Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain G residue 79 ARG Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 131 LYS Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 70 CYS Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 56 ARG Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain N residue 6 MET Chi-restraints excluded: chain N residue 31 ILE Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain T residue 28 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 338 optimal weight: 2.9990 chunk 257 optimal weight: 0.8980 chunk 177 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 163 optimal weight: 10.0000 chunk 230 optimal weight: 0.9980 chunk 344 optimal weight: 1.9990 chunk 364 optimal weight: 40.0000 chunk 179 optimal weight: 10.0000 chunk 326 optimal weight: 50.0000 chunk 98 optimal weight: 30.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN ** S 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 55349 Z= 0.205 Angle : 0.589 13.882 82278 Z= 0.318 Chirality : 0.034 0.387 10411 Planarity : 0.005 0.123 4777 Dihedral : 23.167 178.594 26418 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.08 % Allowed : 25.59 % Favored : 70.32 % 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: -0.39 (0.17), residues: 2301 helix: 0.86 (0.17), residues: 925 sheet: -1.22 (0.25), residues: 400 loop : -0.83 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 201 HIS 0.006 0.001 HIS K 118 PHE 0.021 0.002 PHE N 77 TYR 0.014 0.001 TYR C 42 ARG 0.009 0.001 ARG D 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 326 time to evaluate : 3.417 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 82 ASP cc_start: 0.4643 (OUTLIER) cc_final: 0.4388 (p0) REVERT: B 116 ASP cc_start: 0.7436 (m-30) cc_final: 0.6840 (t70) REVERT: C 211 MET cc_start: 0.4646 (tpt) cc_final: 0.4420 (tpp) REVERT: D 44 ARG cc_start: 0.7630 (tmm160) cc_final: 0.7194 (ptm160) REVERT: D 164 GLN cc_start: 0.8813 (mm110) cc_final: 0.8488 (mp10) REVERT: E 13 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8145 (mt-10) REVERT: E 61 GLN cc_start: 0.8849 (tp-100) cc_final: 0.8494 (tp-100) REVERT: E 65 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8310 (tp30) REVERT: F 5 GLU cc_start: 0.8482 (tt0) cc_final: 0.8086 (tt0) REVERT: F 69 GLU cc_start: 0.8816 (pm20) cc_final: 0.8615 (pm20) REVERT: F 72 ASP cc_start: 0.8890 (t70) cc_final: 0.8409 (t0) REVERT: F 90 MET cc_start: 0.8170 (ptm) cc_final: 0.7775 (ptm) REVERT: F 98 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7836 (tm-30) REVERT: H 74 SER cc_start: 0.8989 (t) cc_final: 0.8616 (p) REVERT: I 52 LEU cc_start: 0.3991 (tp) cc_final: 0.3558 (pp) REVERT: K 27 PHE cc_start: 0.8607 (m-80) cc_final: 0.8169 (m-10) REVERT: K 126 LYS cc_start: 0.7942 (mppt) cc_final: 0.7633 (mppt) REVERT: M 7 ILE cc_start: 0.5475 (OUTLIER) cc_final: 0.5180 (mm) REVERT: M 87 ARG cc_start: 0.4001 (mtp180) cc_final: 0.3489 (mmt180) REVERT: N 49 GLN cc_start: 0.2350 (pt0) cc_final: 0.2138 (pt0) REVERT: O 14 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7800 (tm-30) REVERT: O 71 LYS cc_start: 0.8686 (ttpp) cc_final: 0.8450 (ttmm) REVERT: P 76 LYS cc_start: 0.9051 (ttmm) cc_final: 0.8717 (ttmt) REVERT: Q 55 ILE cc_start: 0.8960 (tt) cc_final: 0.8695 (mt) REVERT: Q 72 SER cc_start: 0.9247 (p) cc_final: 0.8830 (t) REVERT: R 30 LYS cc_start: 0.9181 (mtpt) cc_final: 0.8714 (mtmt) outliers start: 79 outliers final: 35 residues processed: 370 average time/residue: 1.7961 time to fit residues: 825.8818 Evaluate side-chains 329 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 292 time to evaluate : 3.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 131 LYS Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain I residue 53 GLU Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 70 CYS Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 31 ILE Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain T residue 14 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 303 optimal weight: 8.9990 chunk 206 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 271 optimal weight: 20.0000 chunk 150 optimal weight: 10.0000 chunk 310 optimal weight: 0.0000 chunk 251 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 186 optimal weight: 20.0000 chunk 327 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 overall best weight: 5.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 ASN I 81 HIS K 109 ASN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN P 9 HIS ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 55349 Z= 0.423 Angle : 0.696 13.859 82278 Z= 0.369 Chirality : 0.040 0.406 10411 Planarity : 0.006 0.125 4777 Dihedral : 23.218 178.545 26418 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 5.38 % Allowed : 25.75 % Favored : 68.87 % 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: -0.64 (0.17), residues: 2301 helix: 0.55 (0.17), residues: 931 sheet: -1.27 (0.25), residues: 404 loop : -0.88 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 23 HIS 0.011 0.001 HIS M 91 PHE 0.026 0.002 PHE F 8 TYR 0.018 0.002 TYR C 168 ARG 0.017 0.001 ARG G 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 300 time to evaluate : 3.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 MET cc_start: 0.4645 (mtt) cc_final: 0.4350 (mtp) REVERT: B 82 ASP cc_start: 0.4723 (OUTLIER) cc_final: 0.4427 (p0) REVERT: B 116 ASP cc_start: 0.7685 (m-30) cc_final: 0.7009 (t70) REVERT: C 132 ARG cc_start: 0.5211 (OUTLIER) cc_final: 0.4810 (ptp90) REVERT: D 44 ARG cc_start: 0.7667 (tmm160) cc_final: 0.7254 (ptm160) REVERT: D 164 GLN cc_start: 0.8855 (mm110) cc_final: 0.8524 (mp10) REVERT: E 61 GLN cc_start: 0.8845 (tp-100) cc_final: 0.8508 (tp-100) REVERT: E 65 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8339 (tp30) REVERT: E 162 GLU cc_start: 0.8653 (pm20) cc_final: 0.8372 (pm20) REVERT: F 5 GLU cc_start: 0.8515 (tt0) cc_final: 0.8067 (tt0) REVERT: F 69 GLU cc_start: 0.8746 (pm20) cc_final: 0.8515 (pm20) REVERT: F 72 ASP cc_start: 0.8837 (t70) cc_final: 0.8392 (t0) REVERT: F 88 MET cc_start: 0.8654 (ttp) cc_final: 0.8329 (ttt) REVERT: F 90 MET cc_start: 0.8241 (ptm) cc_final: 0.7839 (ptm) REVERT: F 98 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7894 (tm-30) REVERT: G 131 LYS cc_start: 0.4092 (OUTLIER) cc_final: 0.3487 (tmmt) REVERT: H 74 SER cc_start: 0.8970 (t) cc_final: 0.8402 (p) REVERT: H 114 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7971 (ptp90) REVERT: I 52 LEU cc_start: 0.4291 (tp) cc_final: 0.3738 (pp) REVERT: K 27 PHE cc_start: 0.8613 (m-80) cc_final: 0.8356 (m-10) REVERT: K 126 LYS cc_start: 0.7909 (mppt) cc_final: 0.7634 (mppt) REVERT: L 56 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7699 (ttm170) REVERT: M 7 ILE cc_start: 0.5585 (OUTLIER) cc_final: 0.5348 (mm) REVERT: M 87 ARG cc_start: 0.4370 (mtp180) cc_final: 0.3935 (mpt-90) REVERT: N 93 ILE cc_start: 0.6937 (OUTLIER) cc_final: 0.6722 (mp) REVERT: O 14 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7830 (tm-30) REVERT: O 71 LYS cc_start: 0.8637 (ttpp) cc_final: 0.8372 (ttmm) REVERT: R 30 LYS cc_start: 0.9196 (mtpt) cc_final: 0.8742 (mtmt) REVERT: S 44 MET cc_start: 0.2444 (mtp) cc_final: 0.0343 (mmt) REVERT: T 59 ASP cc_start: 0.9075 (OUTLIER) cc_final: 0.8544 (t70) outliers start: 104 outliers final: 48 residues processed: 373 average time/residue: 1.7674 time to fit residues: 823.4707 Evaluate side-chains 336 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 280 time to evaluate : 3.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 185 LYS Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain G residue 3 ARG Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 131 LYS Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 114 ARG Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 70 CYS Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 56 ARG Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 31 ILE Chi-restraints excluded: chain N residue 93 ILE Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 59 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 122 optimal weight: 40.0000 chunk 328 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 213 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 364 optimal weight: 50.0000 chunk 302 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 120 optimal weight: 30.0000 chunk 191 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN C 139 GLN F 14 GLN K 109 ASN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 55349 Z= 0.293 Angle : 0.625 12.506 82278 Z= 0.336 Chirality : 0.036 0.392 10411 Planarity : 0.006 0.124 4777 Dihedral : 23.190 178.689 26418 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 5.22 % Allowed : 26.99 % Favored : 67.79 % 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: -0.50 (0.17), residues: 2301 helix: 0.72 (0.17), residues: 929 sheet: -1.13 (0.25), residues: 401 loop : -0.91 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 201 HIS 0.008 0.001 HIS M 91 PHE 0.026 0.002 PHE F 8 TYR 0.016 0.002 TYR C 42 ARG 0.011 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 299 time to evaluate : 3.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 ASP cc_start: 0.4607 (OUTLIER) cc_final: 0.4305 (p0) REVERT: B 116 ASP cc_start: 0.7710 (m-30) cc_final: 0.6884 (t70) REVERT: C 127 ARG cc_start: 0.2727 (OUTLIER) cc_final: 0.1771 (ttm-80) REVERT: D 44 ARG cc_start: 0.7695 (tmm160) cc_final: 0.7257 (ptm160) REVERT: D 164 GLN cc_start: 0.8921 (mm110) cc_final: 0.8609 (mp10) REVERT: E 61 GLN cc_start: 0.8830 (tp-100) cc_final: 0.8484 (tp-100) REVERT: E 65 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8362 (OUTLIER) REVERT: E 162 GLU cc_start: 0.8584 (pm20) cc_final: 0.8300 (pm20) REVERT: F 5 GLU cc_start: 0.8539 (tt0) cc_final: 0.8125 (tt0) REVERT: F 69 GLU cc_start: 0.8711 (pm20) cc_final: 0.8472 (pm20) REVERT: F 72 ASP cc_start: 0.8853 (t70) cc_final: 0.8455 (t0) REVERT: F 88 MET cc_start: 0.8574 (ttp) cc_final: 0.8294 (ttt) REVERT: F 90 MET cc_start: 0.8203 (ptm) cc_final: 0.7758 (ptm) REVERT: F 98 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7921 (tm-30) REVERT: G 131 LYS cc_start: 0.4156 (OUTLIER) cc_final: 0.3593 (tmmt) REVERT: H 74 SER cc_start: 0.9007 (t) cc_final: 0.8437 (p) REVERT: H 114 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8042 (ptp90) REVERT: I 52 LEU cc_start: 0.4122 (tp) cc_final: 0.3633 (pp) REVERT: K 27 PHE cc_start: 0.8624 (m-80) cc_final: 0.8351 (m-10) REVERT: K 126 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7605 (mppt) REVERT: L 56 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7724 (ttm110) REVERT: M 7 ILE cc_start: 0.5704 (OUTLIER) cc_final: 0.5383 (mm) REVERT: M 87 ARG cc_start: 0.4370 (mtp180) cc_final: 0.3887 (mpt-90) REVERT: O 14 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7803 (tm-30) REVERT: O 71 LYS cc_start: 0.8651 (ttpp) cc_final: 0.8401 (ttmm) REVERT: Q 16 LYS cc_start: 0.9067 (mtpm) cc_final: 0.8829 (mtpm) REVERT: Q 55 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8690 (mt) REVERT: R 30 LYS cc_start: 0.9176 (mtpt) cc_final: 0.8730 (mtmt) REVERT: S 44 MET cc_start: 0.2341 (mtp) cc_final: 0.0170 (mmt) REVERT: T 59 ASP cc_start: 0.9084 (OUTLIER) cc_final: 0.8587 (t70) outliers start: 101 outliers final: 53 residues processed: 369 average time/residue: 1.7498 time to fit residues: 810.7070 Evaluate side-chains 343 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 282 time to evaluate : 3.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 ARG Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain G residue 3 ARG Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 131 LYS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 114 ARG Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 70 CYS Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 126 LYS Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 56 ARG Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 31 ILE Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 59 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 351 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 207 optimal weight: 0.5980 chunk 266 optimal weight: 30.0000 chunk 206 optimal weight: 7.9990 chunk 307 optimal weight: 0.7980 chunk 203 optimal weight: 0.4980 chunk 363 optimal weight: 0.3980 chunk 227 optimal weight: 0.9990 chunk 221 optimal weight: 7.9990 chunk 167 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 ASN K 28 ASN K 109 ASN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN T 20 HIS ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.100 55349 Z= 0.135 Angle : 0.574 12.780 82278 Z= 0.310 Chirality : 0.032 0.371 10411 Planarity : 0.005 0.122 4777 Dihedral : 23.126 179.367 26418 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.57 % Allowed : 28.90 % Favored : 67.53 % 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 (0.18), residues: 2301 helix: 0.99 (0.17), residues: 923 sheet: -0.96 (0.25), residues: 403 loop : -0.67 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 201 HIS 0.009 0.001 HIS M 91 PHE 0.023 0.001 PHE F 8 TYR 0.016 0.001 TYR F 4 ARG 0.013 0.000 ARG D 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 321 time to evaluate : 3.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 MET cc_start: 0.3663 (OUTLIER) cc_final: 0.3015 (ptp) REVERT: B 82 ASP cc_start: 0.4863 (OUTLIER) cc_final: 0.4531 (p0) REVERT: B 116 ASP cc_start: 0.7584 (m-30) cc_final: 0.6925 (t70) REVERT: B 170 HIS cc_start: 0.6951 (p90) cc_final: 0.6466 (p90) REVERT: C 127 ARG cc_start: 0.2654 (OUTLIER) cc_final: 0.1680 (ttm-80) REVERT: C 211 MET cc_start: 0.4739 (tpt) cc_final: 0.4406 (tpp) REVERT: D 44 ARG cc_start: 0.7627 (tmm160) cc_final: 0.7132 (ptm160) REVERT: D 141 ASP cc_start: 0.7814 (m-30) cc_final: 0.7175 (m-30) REVERT: D 164 GLN cc_start: 0.8947 (mm110) cc_final: 0.8623 (mp10) REVERT: E 13 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7813 (mt-10) REVERT: E 61 GLN cc_start: 0.8849 (tp-100) cc_final: 0.8441 (tp-100) REVERT: E 65 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8366 (OUTLIER) REVERT: E 162 GLU cc_start: 0.8478 (pm20) cc_final: 0.8177 (pm20) REVERT: F 5 GLU cc_start: 0.8482 (tt0) cc_final: 0.8184 (tt0) REVERT: F 8 PHE cc_start: 0.8524 (p90) cc_final: 0.8261 (p90) REVERT: F 62 MET cc_start: 0.8828 (ptm) cc_final: 0.8338 (ptp) REVERT: F 69 GLU cc_start: 0.8676 (pm20) cc_final: 0.8387 (pm20) REVERT: F 72 ASP cc_start: 0.8854 (t70) cc_final: 0.8622 (t70) REVERT: F 90 MET cc_start: 0.8157 (ptm) cc_final: 0.7768 (ptm) REVERT: G 131 LYS cc_start: 0.4042 (OUTLIER) cc_final: 0.3597 (tmmt) REVERT: H 43 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8408 (mp0) REVERT: H 74 SER cc_start: 0.8985 (t) cc_final: 0.8421 (p) REVERT: H 114 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.8048 (ptp90) REVERT: I 52 LEU cc_start: 0.4053 (tp) cc_final: 0.3519 (pp) REVERT: K 27 PHE cc_start: 0.8593 (m-80) cc_final: 0.8299 (m-10) REVERT: K 126 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7625 (mppt) REVERT: L 44 LYS cc_start: 0.8449 (tptm) cc_final: 0.8088 (ttpt) REVERT: M 87 ARG cc_start: 0.4195 (mtp180) cc_final: 0.3991 (mpt-90) REVERT: N 77 PHE cc_start: 0.4712 (OUTLIER) cc_final: 0.4435 (p90) REVERT: O 14 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7776 (tm-30) REVERT: O 71 LYS cc_start: 0.8609 (ttpp) cc_final: 0.8382 (ttmm) REVERT: Q 15 ASP cc_start: 0.8818 (p0) cc_final: 0.8495 (p0) REVERT: Q 55 ILE cc_start: 0.8993 (tt) cc_final: 0.8195 (mp) REVERT: Q 72 SER cc_start: 0.9118 (p) cc_final: 0.8761 (t) REVERT: R 30 LYS cc_start: 0.9083 (mtpt) cc_final: 0.8677 (mtmt) REVERT: S 44 MET cc_start: 0.2125 (mtp) cc_final: 0.0582 (mmt) outliers start: 69 outliers final: 29 residues processed: 364 average time/residue: 1.7935 time to fit residues: 813.3021 Evaluate side-chains 328 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 292 time to evaluate : 3.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 ARG Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain G residue 3 ARG Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 131 LYS Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 114 ARG Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 70 CYS Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 126 LYS Chi-restraints excluded: chain N residue 77 PHE Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 82 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 224 optimal weight: 0.8980 chunk 145 optimal weight: 10.0000 chunk 217 optimal weight: 0.8980 chunk 109 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 231 optimal weight: 0.0980 chunk 247 optimal weight: 8.9990 chunk 179 optimal weight: 20.0000 chunk 33 optimal weight: 7.9990 chunk 285 optimal weight: 30.0000 overall best weight: 3.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN K 109 ASN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 55349 Z= 0.295 Angle : 0.636 14.005 82278 Z= 0.338 Chirality : 0.036 0.350 10411 Planarity : 0.006 0.121 4777 Dihedral : 23.109 179.918 26418 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.77 % Allowed : 29.47 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.17), residues: 2301 helix: 0.96 (0.17), residues: 923 sheet: -1.01 (0.25), residues: 409 loop : -0.70 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 201 HIS 0.007 0.001 HIS M 91 PHE 0.018 0.002 PHE F 8 TYR 0.014 0.002 TYR D 76 ARG 0.013 0.001 ARG D 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 295 time to evaluate : 3.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 ASP cc_start: 0.4942 (OUTLIER) cc_final: 0.4603 (p0) REVERT: B 116 ASP cc_start: 0.7680 (m-30) cc_final: 0.6896 (t70) REVERT: C 127 ARG cc_start: 0.2702 (OUTLIER) cc_final: 0.1752 (ttm-80) REVERT: C 134 MET cc_start: 0.5506 (mtp) cc_final: 0.5113 (mtm) REVERT: D 164 GLN cc_start: 0.8951 (mm110) cc_final: 0.8610 (mp10) REVERT: E 61 GLN cc_start: 0.8854 (tp-100) cc_final: 0.8519 (tp-100) REVERT: E 65 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8373 (tp30) REVERT: E 116 GLU cc_start: 0.8505 (tt0) cc_final: 0.8245 (pt0) REVERT: E 162 GLU cc_start: 0.8572 (pm20) cc_final: 0.8330 (pm20) REVERT: F 5 GLU cc_start: 0.8508 (tt0) cc_final: 0.8133 (tt0) REVERT: F 69 GLU cc_start: 0.8650 (pm20) cc_final: 0.8433 (pm20) REVERT: F 90 MET cc_start: 0.8122 (ptm) cc_final: 0.7814 (ptm) REVERT: F 91 ARG cc_start: 0.8946 (ttt180) cc_final: 0.8731 (ttt-90) REVERT: G 31 MET cc_start: 0.1205 (OUTLIER) cc_final: 0.0887 (tpt) REVERT: G 131 LYS cc_start: 0.4082 (OUTLIER) cc_final: 0.3555 (tmmt) REVERT: H 74 SER cc_start: 0.8991 (t) cc_final: 0.8409 (p) REVERT: H 114 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.8055 (ptp90) REVERT: K 27 PHE cc_start: 0.8620 (m-80) cc_final: 0.8320 (m-10) REVERT: K 126 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7639 (mppt) REVERT: M 87 ARG cc_start: 0.4384 (mtp180) cc_final: 0.3966 (mpt90) REVERT: O 14 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7855 (tm-30) REVERT: O 71 LYS cc_start: 0.8675 (ttpp) cc_final: 0.8426 (ttmm) REVERT: R 30 LYS cc_start: 0.9089 (mtpt) cc_final: 0.8661 (mtmt) REVERT: S 44 MET cc_start: 0.2371 (mtp) cc_final: 0.0483 (mmt) outliers start: 73 outliers final: 45 residues processed: 339 average time/residue: 1.7673 time to fit residues: 748.2334 Evaluate side-chains 334 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 283 time to evaluate : 2.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 ARG Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain G residue 3 ARG Chi-restraints excluded: chain G residue 31 MET Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 131 LYS Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 114 ARG Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 70 CYS Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 126 LYS Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain N residue 6 MET Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain R residue 25 ASP Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 82 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 330 optimal weight: 20.0000 chunk 348 optimal weight: 1.9990 chunk 317 optimal weight: 3.9990 chunk 338 optimal weight: 6.9990 chunk 203 optimal weight: 0.3980 chunk 147 optimal weight: 30.0000 chunk 265 optimal weight: 3.9990 chunk 103 optimal weight: 30.0000 chunk 305 optimal weight: 8.9990 chunk 320 optimal weight: 20.0000 chunk 337 optimal weight: 0.9980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 109 ASN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 55349 Z= 0.202 Angle : 0.608 13.539 82278 Z= 0.325 Chirality : 0.034 0.346 10411 Planarity : 0.005 0.121 4777 Dihedral : 23.116 179.778 26418 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.36 % Allowed : 30.61 % Favored : 66.03 % 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 (0.18), residues: 2301 helix: 0.95 (0.17), residues: 920 sheet: -0.97 (0.25), residues: 407 loop : -0.64 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 201 HIS 0.006 0.001 HIS M 91 PHE 0.017 0.002 PHE C 37 TYR 0.017 0.001 TYR F 59 ARG 0.014 0.001 ARG D 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 293 time to evaluate : 3.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 MET cc_start: 0.3844 (OUTLIER) cc_final: 0.3252 (ptp) REVERT: B 82 ASP cc_start: 0.4870 (OUTLIER) cc_final: 0.4548 (p0) REVERT: B 116 ASP cc_start: 0.7613 (m-30) cc_final: 0.6884 (t70) REVERT: C 127 ARG cc_start: 0.2689 (OUTLIER) cc_final: 0.1724 (ttm-80) REVERT: C 134 MET cc_start: 0.5389 (mtp) cc_final: 0.5020 (mtm) REVERT: D 44 ARG cc_start: 0.7670 (tmm160) cc_final: 0.7239 (ptm160) REVERT: D 141 ASP cc_start: 0.7821 (m-30) cc_final: 0.7161 (m-30) REVERT: D 164 GLN cc_start: 0.8977 (mm110) cc_final: 0.8631 (mp10) REVERT: E 61 GLN cc_start: 0.8869 (tp-100) cc_final: 0.8520 (tp-100) REVERT: E 65 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8353 (OUTLIER) REVERT: E 162 GLU cc_start: 0.8542 (pm20) cc_final: 0.8303 (pm20) REVERT: F 5 GLU cc_start: 0.8443 (tt0) cc_final: 0.8083 (tt0) REVERT: F 90 MET cc_start: 0.8057 (ptm) cc_final: 0.7701 (ptm) REVERT: G 31 MET cc_start: 0.1204 (OUTLIER) cc_final: 0.0988 (tpt) REVERT: G 131 LYS cc_start: 0.3950 (OUTLIER) cc_final: 0.3472 (tmmt) REVERT: H 74 SER cc_start: 0.9042 (t) cc_final: 0.8525 (p) REVERT: H 114 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8091 (ptp90) REVERT: K 27 PHE cc_start: 0.8603 (m-80) cc_final: 0.8301 (m-10) REVERT: K 85 MET cc_start: 0.8074 (mmm) cc_final: 0.7697 (mmt) REVERT: K 126 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7520 (mppt) REVERT: L 44 LYS cc_start: 0.8457 (tptm) cc_final: 0.8066 (ttpt) REVERT: M 87 ARG cc_start: 0.4359 (mtp180) cc_final: 0.3958 (mpt90) REVERT: N 77 PHE cc_start: 0.4872 (OUTLIER) cc_final: 0.4479 (p90) REVERT: O 14 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7837 (tm-30) REVERT: O 47 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8657 (mtmm) REVERT: O 71 LYS cc_start: 0.8628 (ttpp) cc_final: 0.8388 (ttmm) REVERT: R 30 LYS cc_start: 0.9029 (mtpt) cc_final: 0.8667 (mtmt) REVERT: S 44 MET cc_start: 0.1980 (mtp) cc_final: 0.0329 (mmt) REVERT: T 40 GLU cc_start: 0.8626 (tt0) cc_final: 0.8372 (tm-30) outliers start: 65 outliers final: 43 residues processed: 338 average time/residue: 1.7325 time to fit residues: 733.4588 Evaluate side-chains 333 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 282 time to evaluate : 2.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 ARG Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain G residue 3 ARG Chi-restraints excluded: chain G residue 31 MET Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 131 LYS Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 114 ARG Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 70 CYS Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 126 LYS Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain N residue 77 PHE Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 82 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 222 optimal weight: 3.9990 chunk 358 optimal weight: 6.9990 chunk 218 optimal weight: 0.6980 chunk 169 optimal weight: 9.9990 chunk 248 optimal weight: 0.9990 chunk 375 optimal weight: 2.9990 chunk 345 optimal weight: 3.9990 chunk 299 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 231 optimal weight: 0.0870 chunk 183 optimal weight: 8.9990 overall best weight: 1.7564 ------------------------------------------------------------------------------- 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 177 ASN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN K 28 ASN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 109 ASN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 55349 Z= 0.177 Angle : 0.598 13.855 82278 Z= 0.320 Chirality : 0.033 0.332 10411 Planarity : 0.005 0.120 4777 Dihedral : 23.082 179.649 26416 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.84 % Allowed : 31.08 % Favored : 66.08 % 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 (0.18), residues: 2301 helix: 0.98 (0.17), residues: 917 sheet: -0.91 (0.25), residues: 403 loop : -0.64 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 201 HIS 0.019 0.001 HIS S 69 PHE 0.013 0.001 PHE K 52 TYR 0.023 0.001 TYR C 168 ARG 0.014 0.000 ARG D 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 298 time to evaluate : 3.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 MET cc_start: 0.4029 (OUTLIER) cc_final: 0.3523 (ptp) REVERT: B 116 ASP cc_start: 0.7636 (m-30) cc_final: 0.6890 (t70) REVERT: C 127 ARG cc_start: 0.2661 (OUTLIER) cc_final: 0.1641 (ttm-80) REVERT: C 134 MET cc_start: 0.5342 (mtp) cc_final: 0.4949 (mtm) REVERT: D 44 ARG cc_start: 0.7654 (tmm160) cc_final: 0.7199 (ptm160) REVERT: D 141 ASP cc_start: 0.7812 (m-30) cc_final: 0.7178 (m-30) REVERT: D 164 GLN cc_start: 0.8982 (mm110) cc_final: 0.8669 (mp10) REVERT: D 178 MET cc_start: 0.8356 (ptp) cc_final: 0.8122 (ptt) REVERT: E 13 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7612 (mt-10) REVERT: E 61 GLN cc_start: 0.8864 (tp-100) cc_final: 0.8517 (tp-100) REVERT: E 65 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8350 (OUTLIER) REVERT: E 93 ARG cc_start: 0.8639 (mtm-85) cc_final: 0.8299 (mpp80) REVERT: E 162 GLU cc_start: 0.8517 (pm20) cc_final: 0.8302 (pm20) REVERT: F 5 GLU cc_start: 0.8401 (tt0) cc_final: 0.8100 (tt0) REVERT: F 56 LYS cc_start: 0.8542 (ptmt) cc_final: 0.7748 (ttpp) REVERT: F 90 MET cc_start: 0.8058 (ptm) cc_final: 0.7700 (ptm) REVERT: G 31 MET cc_start: 0.1184 (tpt) cc_final: 0.0969 (tpt) REVERT: G 131 LYS cc_start: 0.4070 (OUTLIER) cc_final: 0.3611 (tmmt) REVERT: H 74 SER cc_start: 0.9110 (t) cc_final: 0.8595 (p) REVERT: H 114 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.8088 (ptp90) REVERT: K 27 PHE cc_start: 0.8591 (m-80) cc_final: 0.8267 (m-10) REVERT: K 84 VAL cc_start: 0.8339 (m) cc_final: 0.8084 (p) REVERT: K 85 MET cc_start: 0.8103 (mmm) cc_final: 0.7725 (mmt) REVERT: L 44 LYS cc_start: 0.8488 (tptm) cc_final: 0.8105 (ttpt) REVERT: M 87 ARG cc_start: 0.4257 (mtp180) cc_final: 0.3914 (mpt90) REVERT: N 77 PHE cc_start: 0.4693 (p90) cc_final: 0.4330 (p90) REVERT: O 14 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7842 (tm-30) REVERT: O 71 LYS cc_start: 0.8589 (ttpp) cc_final: 0.8354 (ttmm) REVERT: Q 55 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8677 (mt) REVERT: Q 57 ASP cc_start: 0.8501 (m-30) cc_final: 0.8245 (m-30) REVERT: R 30 LYS cc_start: 0.9009 (mtpt) cc_final: 0.8652 (mtmt) REVERT: S 44 MET cc_start: 0.1913 (mtp) cc_final: 0.0340 (mmt) REVERT: T 40 GLU cc_start: 0.8564 (tt0) cc_final: 0.8344 (tm-30) outliers start: 55 outliers final: 39 residues processed: 336 average time/residue: 1.7825 time to fit residues: 747.7291 Evaluate side-chains 329 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 286 time to evaluate : 3.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 ARG Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain G residue 3 ARG Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 131 LYS Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 114 ARG Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 70 CYS Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain R residue 25 ASP Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 82 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 237 optimal weight: 6.9990 chunk 318 optimal weight: 0.0370 chunk 91 optimal weight: 7.9990 chunk 275 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 299 optimal weight: 0.9990 chunk 125 optimal weight: 30.0000 chunk 307 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- 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 177 ASN H 38 ASN I 50 GLN K 28 ASN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 109 ASN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.100345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.059063 restraints weight = 159517.628| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.56 r_work: 0.2829 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 55349 Z= 0.250 Angle : 0.622 14.120 82278 Z= 0.332 Chirality : 0.035 0.329 10411 Planarity : 0.006 0.120 4777 Dihedral : 23.062 179.741 26416 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.21 % Allowed : 30.97 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2301 helix: 0.94 (0.17), residues: 917 sheet: -0.96 (0.25), residues: 408 loop : -0.63 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 167 HIS 0.007 0.001 HIS M 91 PHE 0.028 0.002 PHE N 73 TYR 0.020 0.002 TYR C 168 ARG 0.014 0.001 ARG D 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16570.63 seconds wall clock time: 297 minutes 48.99 seconds (17868.99 seconds total)