Starting phenix.real_space_refine on Mon Mar 25 19:34:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nat_12247/03_2024/7nat_12247_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nat_12247/03_2024/7nat_12247.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nat_12247/03_2024/7nat_12247_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nat_12247/03_2024/7nat_12247_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nat_12247/03_2024/7nat_12247_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nat_12247/03_2024/7nat_12247.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nat_12247/03_2024/7nat_12247.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nat_12247/03_2024/7nat_12247_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nat_12247/03_2024/7nat_12247_neut_updated.pdb" } resolution = 3.59 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= 0.004 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 1430 5.49 5 Mg 65 5.21 5 S 74 5.16 5 C 26309 2.51 5 N 9486 2.21 5 O 13556 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 TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 50921 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 30694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1430, 30694 Classifications: {'RNA': 1430} Modifications used: {'rna2p_pur': 112, 'rna2p_pyr': 84, 'rna3p': 8, 'rna3p_pur': 697, 'rna3p_pyr': 529} Link IDs: {'rna2p': 195, 'rna3p': 1234} Chain breaks: 1 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: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "G" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 795 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "S" Number of atoms: 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: "U" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 551 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "X" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1174 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Unusual residues: {' MG': 64} Classifications: {'undetermined': 64} Link IDs: {None: 63} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 26.83, per 1000 atoms: 0.53 Number of scatterers: 50921 At special positions: 0 Unit cell: (146.475, 240.87, 194.215, 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 74 16.00 P 1430 15.00 Mg 65 11.99 O 13556 8.00 N 9486 7.00 C 26309 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 Atom "ATOM 23143 O4' U A1078 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 34.00 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4754 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 97 helices and 25 sheets defined 39.4% alpha, 14.0% beta 432 base pairs and 712 stacking pairs defined. Time for finding SS restraints: 26.72 Creating SS restraints... Processing helix chain 'B' and resid 6 through 12 removed outlier: 3.706A pdb=" N ALA B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 43 through 63 Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.674A pdb=" N CYS B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 123 Processing helix chain 'B' and resid 131 through 147 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 7 through 11 removed outlier: 3.932A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 7 through 11' Processing helix chain 'C' and resid 29 through 49 removed outlier: 3.985A pdb=" N ALA C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 82 through 94 Processing helix chain 'C' and resid 109 through 111 No H-bonds generated for 'chain 'C' and resid 109 through 111' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 130 through 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 31 No H-bonds generated for 'chain 'D' and resid 28 through 31' Processing helix chain 'D' and resid 40 through 43 removed outlier: 4.036A pdb=" N ALA D 43 " --> pdb=" O GLN D 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 40 through 43' Processing helix chain 'D' and resid 50 through 65 Processing helix chain 'D' and resid 69 through 79 Processing helix chain 'D' and resid 86 through 96 removed outlier: 3.533A pdb=" N LEU D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 104 Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 125 through 127 No H-bonds generated for 'chain 'D' and resid 125 through 127' 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 162 Processing helix chain 'D' and resid 197 through 204 removed outlier: 3.586A pdb=" N TYR D 204 " --> pdb=" O ILE D 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 68 removed outlier: 3.689A pdb=" N ARG E 68 " --> pdb=" O MET E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 118 removed outlier: 3.898A pdb=" N ALA E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 138 Processing helix chain 'E' and resid 141 through 145 Processing helix chain 'E' and resid 152 through 156 Processing helix chain 'E' and resid 161 through 164 No H-bonds generated for 'chain 'E' and resid 161 through 164' Processing helix chain 'F' and resid 12 through 31 removed outlier: 4.934A pdb=" N GLU F 16 " --> pdb=" O ASP F 13 " (cutoff:3.500A) Proline residue: F 19 - end of helix removed outlier: 4.913A pdb=" N GLU F 23 " --> pdb=" O GLY F 20 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR F 25 " --> pdb=" O ILE F 22 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA F 28 " --> pdb=" O TYR F 25 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE F 29 " --> pdb=" O THR F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 80 Processing helix chain 'F' and resid 103 through 105 No H-bonds generated for 'chain 'F' and resid 103 through 105' Processing helix chain 'G' and resid 16 through 18 No H-bonds generated for 'chain 'G' and resid 16 through 18' Processing helix chain 'G' and resid 22 through 30 Processing helix chain 'G' and resid 36 through 53 removed outlier: 4.209A pdb=" N THR G 49 " --> pdb=" O SER G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 69 removed outlier: 4.140A pdb=" N GLU G 63 " --> pdb=" O LEU G 59 " (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 144 Processing helix chain 'H' and resid 6 through 20 Processing helix chain 'H' and resid 31 through 42 removed outlier: 3.507A pdb=" N ALA H 35 " --> pdb=" O LYS H 31 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 119 Processing helix chain 'I' and resid 35 through 38 No H-bonds generated for 'chain 'I' and resid 35 through 38' Processing helix chain 'I' and resid 42 through 55 Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 58 through 60 No H-bonds generated for 'chain 'I' and resid 58 through 60' Processing helix chain 'I' and resid 72 through 91 Processing helix chain 'I' and resid 95 through 101 Processing helix chain 'J' and resid 15 through 31 Processing helix chain 'J' and resid 81 through 88 removed outlier: 4.525A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 50 No H-bonds generated for 'chain 'K' and resid 48 through 50' Processing helix chain 'K' and resid 54 through 56 No H-bonds generated for 'chain 'K' and resid 54 through 56' Processing helix chain 'K' and resid 60 through 74 removed outlier: 3.592A pdb=" N ALA K 66 " --> pdb=" O ALA K 62 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU K 68 " --> pdb=" O GLN K 64 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ALA K 73 " --> pdb=" O ARG K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 101 Processing helix chain 'L' and resid 4 through 9 removed outlier: 3.747A pdb=" N ARG L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) 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 117 Processing helix chain 'M' and resid 15 through 20 Processing helix chain 'M' and resid 27 through 37 Processing helix chain 'M' and resid 50 through 61 removed outlier: 4.503A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (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 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 83 through 89 Processing helix chain 'O' and resid 5 through 15 Processing helix chain 'O' and resid 25 through 43 removed outlier: 4.091A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE O 43 " --> pdb=" O LEU O 39 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 73 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 81 Processing helix chain 'Q' and resid 49 through 51 No H-bonds generated for 'chain 'Q' and resid 49 through 51' Processing helix chain 'R' and resid 12 through 16 Processing helix chain 'R' and resid 26 through 32 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 71 through 74 Processing helix chain 'T' and resid 5 through 41 removed outlier: 3.517A pdb=" N SER T 14 " --> pdb=" O ARG T 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU T 15 " --> pdb=" O ALA T 11 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS T 16 " --> pdb=" O ILE T 12 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N MET T 28 " --> pdb=" O ARG T 24 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE T 31 " --> pdb=" O MET T 27 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS T 34 " --> pdb=" O THR T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 63 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 69 through 86 Processing helix chain 'U' and resid 12 through 24 Processing helix chain 'U' and resid 28 through 36 removed outlier: 4.110A pdb=" N ARG U 34 " --> pdb=" O ALA U 30 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG U 35 " --> pdb=" O GLU U 31 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU U 36 " --> pdb=" O VAL U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 66 removed outlier: 3.682A pdb=" N ARG U 47 " --> pdb=" O THR U 43 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU U 63 " --> pdb=" O LYS U 59 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN U 64 " --> pdb=" O LEU U 60 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA U 65 " --> pdb=" O ALA U 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 19 Proline residue: X 15 - end of helix Processing helix chain 'X' and resid 48 through 64 removed outlier: 3.650A pdb=" N VAL X 64 " --> pdb=" O ALA X 60 " (cutoff:3.500A) Processing helix chain 'X' and resid 88 through 93 Processing helix chain 'X' and resid 138 through 140 No H-bonds generated for 'chain 'X' and resid 138 through 140' Processing sheet with id= A, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.696A pdb=" N ALA B 160 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL B 70 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 6.244A 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: 7.611A pdb=" N VAL B 187 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 6.319A 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: 6.124A pdb=" N VAL B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 99 through 103 removed outlier: 6.708A pdb=" N ILE C 64 " --> pdb=" O GLN C 100 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ASN C 102 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL C 66 " --> pdb=" O ASN C 102 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 166 through 171 Processing sheet with id= E, first strand: chain 'D' and resid 123 through 125 removed outlier: 4.718A pdb=" N ILE D 123 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 141 through 144 removed outlier: 3.693A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 12 through 15 Processing sheet with id= H, first strand: chain 'E' and resid 19 through 21 Processing sheet with id= I, first strand: chain 'E' and resid 85 through 89 Processing sheet with id= J, first strand: chain 'F' and resid 84 through 88 removed outlier: 6.666A pdb=" N MET F 9 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER F 87 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL F 7 " --> pdb=" O SER F 87 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE F 8 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU F 61 " --> pdb=" O ASP F 41 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ASP F 41 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ASN F 63 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LEU F 39 " --> pdb=" O ASN F 63 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 73 through 75 Processing sheet with id= L, first strand: chain 'H' and resid 24 through 28 removed outlier: 4.201A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 74 through 77 removed outlier: 6.847A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'I' and resid 6 through 10 removed outlier: 3.591A pdb=" N TYR I 6 " --> pdb=" O ILE I 21 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'I' and resid 28 through 30 removed outlier: 7.008A pdb=" N LEU I 63 " --> pdb=" O VAL I 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'J' and resid 97 through 101 removed outlier: 4.561A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'J' and resid 45 through 52 Processing sheet with id= R, first strand: chain 'K' and resid 106 through 112 removed outlier: 3.523A pdb=" N LEU K 82 " --> pdb=" O ARG K 106 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL K 84 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE K 110 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL K 86 " --> pdb=" O ILE K 110 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP K 112 " --> pdb=" O VAL K 86 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'L' and resid 79 through 82 removed outlier: 6.214A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR L 39 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ARG L 50 " --> pdb=" O THR L 39 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'P' and resid 2 through 11 removed outlier: 3.618A pdb=" N ARG P 51 " --> pdb=" O PHE P 38 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'Q' and resid 24 through 30 Processing sheet with id= V, first strand: chain 'Q' and resid 59 through 63 removed outlier: 3.557A pdb=" N ARG Q 77 " --> pdb=" O GLU Q 60 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ARG Q 62 " --> pdb=" O LEU Q 75 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU Q 75 " --> pdb=" O ARG Q 62 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'S' and resid 31 through 33 removed outlier: 3.629A pdb=" N LEU S 31 " --> pdb=" O THR S 48 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'X' and resid 75 through 78 removed outlier: 3.513A pdb=" N ILE X 40 " --> pdb=" O SER X 77 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ASP X 41 " --> pdb=" O LEU X 23 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LEU X 23 " --> pdb=" O ASP X 41 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'X' and resid 141 through 146 removed outlier: 6.954A pdb=" N VAL X 102 " --> pdb=" O GLN X 142 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA X 144 " --> pdb=" O THR X 100 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR X 100 " --> pdb=" O ALA X 144 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LEU X 146 " --> pdb=" O GLU X 98 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLU X 98 " --> pdb=" O LEU X 146 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL X 116 " --> pdb=" O THR X 128 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N THR X 126 " --> pdb=" O LYS X 118 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N VAL X 120 " --> pdb=" O MET X 124 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N MET X 124 " --> pdb=" O VAL X 120 " (cutoff:3.500A) 791 hydrogen bonds defined for protein. 2244 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1011 hydrogen bonds 1362 hydrogen bond angles 0 basepair planarities 432 basepair parallelities 712 stacking parallelities Total time for adding SS restraints: 45.58 Time building geometry restraints manager: 35.34 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: 9058 1.33 - 1.45: 21168 1.45 - 1.57: 21605 1.57 - 1.70: 2858 1.70 - 1.82: 132 Bond restraints: 54821 Sorted by residual: bond pdb=" N3 2MG A1207 " pdb=" C4 2MG A1207 " ideal model delta sigma weight residual 1.496 1.336 0.160 2.00e-02 2.50e+03 6.41e+01 bond pdb=" N3 2MG A1516 " pdb=" C4 2MG A1516 " ideal model delta sigma weight residual 1.496 1.338 0.158 2.00e-02 2.50e+03 6.23e+01 bond pdb=" N3 2MG A 966 " pdb=" C4 2MG A 966 " ideal model delta sigma weight residual 1.496 1.340 0.156 2.00e-02 2.50e+03 6.10e+01 bond pdb=" C2 5MC A 967 " pdb=" N3 5MC A 967 " ideal model delta sigma weight residual 1.493 1.341 0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" C2 G7M A 527 " pdb=" N3 G7M A 527 " ideal model delta sigma weight residual 1.462 1.312 0.150 2.00e-02 2.50e+03 5.62e+01 ... (remaining 54816 not shown) Histogram of bond angle deviations from ideal: 97.26 - 105.29: 7065 105.29 - 113.32: 34432 113.32 - 121.35: 26286 121.35 - 129.38: 12037 129.38 - 137.41: 1259 Bond angle restraints: 81079 Sorted by residual: angle pdb=" N ASN U 9 " pdb=" CA ASN U 9 " pdb=" C ASN U 9 " ideal model delta sigma weight residual 114.12 101.77 12.35 1.39e+00 5.18e-01 7.89e+01 angle pdb=" C VAL X 24 " pdb=" N GLY X 25 " pdb=" CA GLY X 25 " ideal model delta sigma weight residual 122.33 115.86 6.47 7.30e-01 1.88e+00 7.85e+01 angle pdb=" N ASN S 53 " pdb=" CA ASN S 53 " pdb=" C ASN S 53 " ideal model delta sigma weight residual 110.53 101.71 8.82 1.32e+00 5.74e-01 4.46e+01 angle pdb=" C1' 2MG A1516 " pdb=" N9 2MG A1516 " pdb=" C8 2MG A1516 " ideal model delta sigma weight residual 110.07 128.78 -18.71 3.00e+00 1.11e-01 3.89e+01 angle pdb=" C1' 2MG A1207 " pdb=" N9 2MG A1207 " pdb=" C8 2MG A1207 " ideal model delta sigma weight residual 110.07 128.22 -18.15 3.00e+00 1.11e-01 3.66e+01 ... (remaining 81074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 30954 35.86 - 71.72: 3604 71.72 - 107.58: 431 107.58 - 143.43: 10 143.43 - 179.29: 10 Dihedral angle restraints: 35009 sinusoidal: 27660 harmonic: 7349 Sorted by residual: 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 25.72 174.28 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 52.24 147.76 1 1.50e+01 4.44e-03 7.88e+01 dihedral pdb=" O4' C A 754 " pdb=" C1' C A 754 " pdb=" N1 C A 754 " pdb=" C2 C A 754 " ideal model delta sinusoidal sigma weight residual 200.00 55.91 144.09 1 1.50e+01 4.44e-03 7.72e+01 ... (remaining 35006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 9760 0.104 - 0.208: 400 0.208 - 0.311: 39 0.311 - 0.415: 5 0.415 - 0.519: 2 Chirality restraints: 10206 Sorted by residual: chirality pdb=" CA D2T L 89 " pdb=" N D2T L 89 " pdb=" C D2T L 89 " pdb=" CB D2T L 89 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.74e+00 chirality pdb=" C3' A A 523 " pdb=" C4' A A 523 " pdb=" O3' A A 523 " pdb=" C2' A A 523 " both_signs ideal model delta sigma weight residual False -2.48 -2.05 -0.43 2.00e-01 2.50e+01 4.67e+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 2.06 0.38 2.00e-01 2.50e+01 3.59e+00 ... (remaining 10203 not shown) Planarity restraints: 4991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A 966 " 0.032 2.00e-02 2.50e+03 5.90e-01 7.83e+03 pdb=" C4' 2MG A 966 " 0.451 2.00e-02 2.50e+03 pdb=" O4' 2MG A 966 " 0.706 2.00e-02 2.50e+03 pdb=" C3' 2MG A 966 " -0.585 2.00e-02 2.50e+03 pdb=" O3' 2MG A 966 " -0.573 2.00e-02 2.50e+03 pdb=" C2' 2MG A 966 " -0.221 2.00e-02 2.50e+03 pdb=" O2' 2MG A 966 " 0.899 2.00e-02 2.50e+03 pdb=" C1' 2MG A 966 " 0.215 2.00e-02 2.50e+03 pdb=" N9 2MG A 966 " -0.925 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1207 " -0.058 2.00e-02 2.50e+03 5.84e-01 7.68e+03 pdb=" C4' 2MG A1207 " -0.433 2.00e-02 2.50e+03 pdb=" O4' 2MG A1207 " -0.576 2.00e-02 2.50e+03 pdb=" C3' 2MG A1207 " 0.595 2.00e-02 2.50e+03 pdb=" O3' 2MG A1207 " 0.623 2.00e-02 2.50e+03 pdb=" C2' 2MG A1207 " 0.175 2.00e-02 2.50e+03 pdb=" O2' 2MG A1207 " -0.971 2.00e-02 2.50e+03 pdb=" C1' 2MG A1207 " -0.238 2.00e-02 2.50e+03 pdb=" N9 2MG A1207 " 0.882 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A 967 " 0.016 2.00e-02 2.50e+03 5.65e-01 7.19e+03 pdb=" C4' 5MC A 967 " 0.437 2.00e-02 2.50e+03 pdb=" O4' 5MC A 967 " 0.631 2.00e-02 2.50e+03 pdb=" C3' 5MC A 967 " -0.586 2.00e-02 2.50e+03 pdb=" O3' 5MC A 967 " -0.549 2.00e-02 2.50e+03 pdb=" C2' 5MC A 967 " -0.218 2.00e-02 2.50e+03 pdb=" O2' 5MC A 967 " 0.897 2.00e-02 2.50e+03 pdb=" C1' 5MC A 967 " 0.231 2.00e-02 2.50e+03 pdb=" N1 5MC A 967 " -0.858 2.00e-02 2.50e+03 ... (remaining 4988 not shown) Histogram of nonbonded interaction distances: 0.62 - 1.47: 7 1.47 - 2.33: 450 2.33 - 3.19: 51720 3.19 - 4.04: 177048 4.04 - 4.90: 263659 Warning: very small nonbonded interaction distances. Nonbonded interactions: 492884 Sorted by model distance: nonbonded pdb=" O3' U A1078 " pdb=" NH2 ARG E 138 " model vdw 0.616 2.520 nonbonded pdb=" C3' U A1078 " pdb=" NH2 ARG E 138 " model vdw 0.903 3.550 nonbonded pdb=" C1' U A1078 " pdb=" NH1 ARG E 138 " model vdw 0.967 3.550 nonbonded pdb=" OP2 A A1081 " pdb=" NZ LYS E 52 " model vdw 0.985 2.520 nonbonded pdb=" C2' U A1078 " pdb=" NH1 ARG E 138 " model vdw 1.212 3.550 ... (remaining 492879 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.860 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: 0.040 Extract box with map and model: 14.470 Check model and map are aligned: 0.740 Set scattering table: 0.420 Process input model: 189.230 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.160 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 214.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.160 54821 Z= 0.543 Angle : 0.837 18.709 81079 Z= 0.494 Chirality : 0.049 0.519 10206 Planarity : 0.017 0.590 4991 Dihedral : 23.254 179.292 30255 Min Nonbonded Distance : 0.616 Molprobity Statistics. All-atom Clashscore : 27.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.15), residues: 2517 helix: -2.01 (0.14), residues: 1012 sheet: -2.25 (0.23), residues: 438 loop : -2.12 (0.17), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 201 HIS 0.010 0.001 HIS S 14 PHE 0.015 0.002 PHE X 94 TYR 0.017 0.002 TYR I 90 ARG 0.011 0.001 ARG I 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 560 time to evaluate : 3.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 71 GLN cc_start: 0.9018 (tt0) cc_final: 0.8603 (tt0) REVERT: D 74 ASN cc_start: 0.9469 (m110) cc_final: 0.9264 (m110) REVERT: D 75 TYR cc_start: 0.9277 (m-10) cc_final: 0.8844 (m-80) REVERT: D 194 ASP cc_start: 0.8923 (p0) cc_final: 0.8564 (p0) REVERT: E 12 GLN cc_start: 0.8921 (tt0) cc_final: 0.8468 (pt0) REVERT: E 13 GLU cc_start: 0.8607 (mp0) cc_final: 0.8279 (mp0) REVERT: E 23 LYS cc_start: 0.9000 (ttpt) cc_final: 0.8685 (tppt) REVERT: E 60 ILE cc_start: 0.9675 (tt) cc_final: 0.9323 (pt) REVERT: E 64 MET cc_start: 0.9069 (tpp) cc_final: 0.8308 (tpp) REVERT: E 66 LYS cc_start: 0.9470 (mtmt) cc_final: 0.8770 (mtmm) REVERT: E 90 THR cc_start: 0.7524 (p) cc_final: 0.6856 (p) REVERT: E 96 MET cc_start: 0.8650 (mtm) cc_final: 0.8420 (mtp) REVERT: F 72 ASP cc_start: 0.9040 (m-30) cc_final: 0.8830 (m-30) REVERT: F 82 ASP cc_start: 0.9440 (p0) cc_final: 0.9119 (p0) REVERT: G 31 MET cc_start: 0.2931 (ttm) cc_final: 0.1884 (mtp) REVERT: H 54 ASP cc_start: 0.8892 (p0) cc_final: 0.8683 (p0) REVERT: H 73 GLU cc_start: 0.8001 (pp20) cc_final: 0.7782 (pp20) REVERT: H 99 LEU cc_start: 0.9509 (mt) cc_final: 0.9269 (mm) REVERT: J 47 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6536 (mm-30) REVERT: K 77 TYR cc_start: 0.8777 (m-80) cc_final: 0.8391 (m-80) REVERT: K 94 GLU cc_start: 0.8613 (pm20) cc_final: 0.8110 (pm20) REVERT: M 42 ASP cc_start: 0.4680 (m-30) cc_final: 0.4393 (p0) REVERT: N 6 MET cc_start: 0.5768 (mmt) cc_final: 0.5043 (mmt) REVERT: P 46 LYS cc_start: 0.8694 (mmtm) cc_final: 0.8492 (mtmt) REVERT: Q 8 LEU cc_start: 0.9468 (mt) cc_final: 0.9237 (mt) REVERT: Q 26 GLU cc_start: 0.8351 (tp30) cc_final: 0.7983 (tp30) REVERT: Q 80 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7782 (tm-30) REVERT: Q 81 LYS cc_start: 0.8378 (tppt) cc_final: 0.8172 (tppt) REVERT: T 18 ARG cc_start: 0.9249 (ttp80) cc_final: 0.8916 (ttp80) REVERT: X 41 ASP cc_start: 0.8464 (t0) cc_final: 0.8054 (t0) outliers start: 0 outliers final: 0 residues processed: 560 average time/residue: 0.7549 time to fit residues: 651.5877 Evaluate side-chains 342 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 342 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 329 optimal weight: 0.9990 chunk 295 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 100 optimal weight: 30.0000 chunk 199 optimal weight: 4.9990 chunk 157 optimal weight: 8.9990 chunk 305 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 185 optimal weight: 6.9990 chunk 227 optimal weight: 7.9990 chunk 354 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 HIS B 109 GLN ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN C 139 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN I 32 GLN ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN T 3 ASN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 ASN T 78 ASN X 140 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 54821 Z= 0.295 Angle : 0.692 13.229 81079 Z= 0.367 Chirality : 0.037 0.329 10206 Planarity : 0.006 0.122 4991 Dihedral : 24.061 178.719 25172 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 27.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.20 % Allowed : 20.12 % Favored : 76.67 % 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: -1.89 (0.16), residues: 2517 helix: -0.65 (0.15), residues: 1029 sheet: -1.81 (0.24), residues: 426 loop : -1.46 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP X 113 HIS 0.009 0.001 HIS B 170 PHE 0.028 0.002 PHE X 94 TYR 0.034 0.002 TYR B 213 ARG 0.016 0.001 ARG E 138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 383 time to evaluate : 3.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: D 73 ARG cc_start: 0.9248 (ptm-80) cc_final: 0.9029 (ttp80) REVERT: D 74 ASN cc_start: 0.9252 (m110) cc_final: 0.8909 (m-40) REVERT: D 75 TYR cc_start: 0.9180 (m-10) cc_final: 0.8772 (m-80) REVERT: D 194 ASP cc_start: 0.9070 (p0) cc_final: 0.8472 (p0) REVERT: E 12 GLN cc_start: 0.9091 (tt0) cc_final: 0.8655 (pt0) REVERT: E 23 LYS cc_start: 0.8975 (ttpt) cc_final: 0.8685 (tptt) REVERT: E 26 LYS cc_start: 0.9206 (tptp) cc_final: 0.8946 (tppt) REVERT: E 55 GLU cc_start: 0.8791 (pm20) cc_final: 0.8509 (pm20) REVERT: E 60 ILE cc_start: 0.9717 (tt) cc_final: 0.9113 (pt) REVERT: E 64 MET cc_start: 0.8972 (tpp) cc_final: 0.8373 (tpp) REVERT: F 82 ASP cc_start: 0.9500 (p0) cc_final: 0.9196 (p0) REVERT: H 54 ASP cc_start: 0.8743 (p0) cc_final: 0.8529 (p0) REVERT: I 65 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7901 (tt) REVERT: K 77 TYR cc_start: 0.9019 (m-80) cc_final: 0.8580 (m-80) REVERT: M 42 ASP cc_start: 0.5549 (m-30) cc_final: 0.5042 (p0) REVERT: N 6 MET cc_start: 0.5976 (mmt) cc_final: 0.5131 (mmt) REVERT: N 14 VAL cc_start: 0.8435 (t) cc_final: 0.8149 (p) REVERT: N 89 MET cc_start: 0.9020 (mmp) cc_final: 0.8751 (mmm) REVERT: O 62 GLN cc_start: 0.9419 (tp-100) cc_final: 0.9212 (tp40) REVERT: Q 80 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7766 (tm-30) REVERT: Q 81 LYS cc_start: 0.8396 (tppt) cc_final: 0.8166 (tppt) REVERT: R 16 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8722 (mp0) REVERT: S 20 GLU cc_start: 0.6576 (pt0) cc_final: 0.6135 (mm-30) REVERT: X 41 ASP cc_start: 0.8682 (t0) cc_final: 0.8261 (t0) outliers start: 68 outliers final: 42 residues processed: 427 average time/residue: 0.7026 time to fit residues: 479.5390 Evaluate side-chains 372 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 329 time to evaluate : 3.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain I residue 65 ILE Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain T residue 78 ASN Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 53 ASP Chi-restraints excluded: chain X residue 95 VAL Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 133 ASP Chi-restraints excluded: chain X residue 149 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 196 optimal weight: 7.9990 chunk 109 optimal weight: 20.0000 chunk 294 optimal weight: 8.9990 chunk 241 optimal weight: 5.9990 chunk 97 optimal weight: 40.0000 chunk 354 optimal weight: 6.9990 chunk 383 optimal weight: 8.9990 chunk 315 optimal weight: 20.0000 chunk 351 optimal weight: 4.9990 chunk 120 optimal weight: 20.0000 chunk 284 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN C 139 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN E 146 ASN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 15 HIS ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN K 101 ASN ** M 14 HIS ** 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 35 GLN S 69 HIS ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 54821 Z= 0.311 Angle : 0.671 12.953 81079 Z= 0.358 Chirality : 0.036 0.263 10206 Planarity : 0.006 0.126 4991 Dihedral : 24.003 179.447 25172 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 28.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.34 % Allowed : 21.82 % Favored : 73.85 % 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: -1.47 (0.16), residues: 2517 helix: -0.25 (0.15), residues: 1044 sheet: -1.69 (0.24), residues: 426 loop : -1.25 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 42 HIS 0.006 0.001 HIS S 83 PHE 0.018 0.002 PHE B 184 TYR 0.026 0.002 TYR B 213 ARG 0.010 0.001 ARG I 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 347 time to evaluate : 3.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: D 74 ASN cc_start: 0.9326 (m-40) cc_final: 0.8951 (m110) REVERT: D 75 TYR cc_start: 0.9097 (m-10) cc_final: 0.8725 (m-80) REVERT: D 194 ASP cc_start: 0.9103 (p0) cc_final: 0.8468 (p0) REVERT: E 12 GLN cc_start: 0.9113 (tt0) cc_final: 0.8672 (pt0) REVERT: E 23 LYS cc_start: 0.8991 (ttpt) cc_final: 0.8672 (tptt) REVERT: E 26 LYS cc_start: 0.9190 (tptp) cc_final: 0.8751 (tptp) REVERT: E 60 ILE cc_start: 0.9720 (tt) cc_final: 0.9326 (pt) REVERT: E 64 MET cc_start: 0.8696 (tpp) cc_final: 0.8147 (tpp) REVERT: F 1 MET cc_start: 0.8802 (ttm) cc_final: 0.8519 (ttm) REVERT: F 9 MET cc_start: 0.8361 (mmp) cc_final: 0.8065 (mmp) REVERT: F 93 LYS cc_start: 0.9061 (tptt) cc_final: 0.8781 (tptt) REVERT: J 52 LEU cc_start: 0.7610 (mt) cc_final: 0.7252 (tp) REVERT: M 42 ASP cc_start: 0.6034 (OUTLIER) cc_final: 0.5565 (p0) REVERT: N 6 MET cc_start: 0.6056 (mmt) cc_final: 0.5209 (mmt) REVERT: O 28 GLN cc_start: 0.9299 (OUTLIER) cc_final: 0.8626 (mp10) REVERT: O 62 GLN cc_start: 0.9321 (tp-100) cc_final: 0.8952 (tp-100) REVERT: O 71 LYS cc_start: 0.9573 (ttpt) cc_final: 0.9282 (ttpt) REVERT: P 1 MET cc_start: 0.8341 (ptm) cc_final: 0.7997 (ptm) REVERT: R 16 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8785 (mp0) REVERT: S 20 GLU cc_start: 0.6986 (pt0) cc_final: 0.6282 (mm-30) REVERT: S 44 MET cc_start: 0.4656 (mpp) cc_final: 0.4430 (mpp) REVERT: X 41 ASP cc_start: 0.8453 (t0) cc_final: 0.8015 (t0) REVERT: X 105 MET cc_start: 0.7905 (ptp) cc_final: 0.7511 (ptp) outliers start: 92 outliers final: 58 residues processed: 413 average time/residue: 0.6807 time to fit residues: 455.2956 Evaluate side-chains 364 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 304 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 37 PHE Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain O residue 28 GLN Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain U residue 9 ASN Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 47 ASN Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 53 ASP Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 112 LYS Chi-restraints excluded: chain X residue 121 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 350 optimal weight: 0.0980 chunk 266 optimal weight: 10.0000 chunk 184 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 238 optimal weight: 4.9990 chunk 356 optimal weight: 7.9990 chunk 376 optimal weight: 5.9990 chunk 186 optimal weight: 8.9990 chunk 337 optimal weight: 8.9990 chunk 101 optimal weight: 20.0000 overall best weight: 5.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN B 120 GLN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN C 102 ASN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN G 148 ASN ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 15 HIS ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 HIS K 64 GLN ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 ASN P 79 ASN S 52 HIS ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 52 ASN ** T 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 ASN ** X 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 54821 Z= 0.289 Angle : 0.651 12.976 81079 Z= 0.349 Chirality : 0.035 0.260 10206 Planarity : 0.006 0.118 4991 Dihedral : 23.959 179.684 25172 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 28.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.25 % Favored : 95.71 % Rotamer: Outliers : 5.14 % Allowed : 24.32 % Favored : 70.55 % 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: -1.21 (0.16), residues: 2517 helix: -0.03 (0.16), residues: 1022 sheet: -1.54 (0.24), residues: 420 loop : -1.13 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP F 42 HIS 0.026 0.002 HIS J 15 PHE 0.016 0.002 PHE B 90 TYR 0.032 0.002 TYR B 213 ARG 0.015 0.001 ARG X 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 333 time to evaluate : 3.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.2883 (mtp) cc_final: 0.2503 (mtt) REVERT: D 75 TYR cc_start: 0.9054 (m-10) cc_final: 0.8608 (m-80) REVERT: D 194 ASP cc_start: 0.9116 (p0) cc_final: 0.8504 (p0) REVERT: E 12 GLN cc_start: 0.9138 (tt0) cc_final: 0.8643 (pt0) REVERT: E 23 LYS cc_start: 0.8985 (ttpt) cc_final: 0.8672 (tptt) REVERT: E 26 LYS cc_start: 0.9243 (tptp) cc_final: 0.8929 (tptp) REVERT: E 64 MET cc_start: 0.8680 (tpp) cc_final: 0.8397 (tpp) REVERT: F 1 MET cc_start: 0.8701 (ttm) cc_final: 0.8295 (ttm) REVERT: F 82 ASP cc_start: 0.9498 (p0) cc_final: 0.9187 (p0) REVERT: F 93 LYS cc_start: 0.9059 (tptt) cc_final: 0.8834 (tptt) REVERT: I 65 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7482 (tt) REVERT: J 98 VAL cc_start: 0.7709 (t) cc_final: 0.7460 (p) REVERT: L 38 TYR cc_start: 0.9383 (p90) cc_final: 0.8929 (p90) REVERT: L 56 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8647 (ttm-80) REVERT: M 42 ASP cc_start: 0.6066 (OUTLIER) cc_final: 0.5671 (p0) REVERT: N 6 MET cc_start: 0.5961 (mmt) cc_final: 0.5084 (mmt) REVERT: N 89 MET cc_start: 0.8904 (mmm) cc_final: 0.8467 (mmm) REVERT: O 28 GLN cc_start: 0.9302 (OUTLIER) cc_final: 0.8502 (mp10) REVERT: O 62 GLN cc_start: 0.9303 (tp-100) cc_final: 0.8931 (tp-100) REVERT: O 71 LYS cc_start: 0.9550 (ttpt) cc_final: 0.9120 (ttpt) REVERT: P 18 GLN cc_start: 0.8694 (mm110) cc_final: 0.8389 (mm110) REVERT: R 16 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8771 (mp0) REVERT: S 20 GLU cc_start: 0.6959 (pt0) cc_final: 0.6185 (mm-30) REVERT: S 44 MET cc_start: 0.4210 (mpp) cc_final: 0.3862 (mpp) REVERT: X 41 ASP cc_start: 0.8192 (t0) cc_final: 0.7780 (t0) outliers start: 109 outliers final: 73 residues processed: 411 average time/residue: 0.6775 time to fit residues: 454.8894 Evaluate side-chains 373 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 296 time to evaluate : 3.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 37 PHE Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 185 LYS Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain I residue 65 ILE Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 56 ARG Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 63 PHE Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain O residue 28 GLN Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain U residue 9 ASN Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 47 ASN Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 53 ASP Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 112 LYS Chi-restraints excluded: chain X residue 114 GLN Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 124 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 313 optimal weight: 20.0000 chunk 213 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 280 optimal weight: 10.0000 chunk 155 optimal weight: 20.0000 chunk 321 optimal weight: 6.9990 chunk 260 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 192 optimal weight: 4.9990 chunk 338 optimal weight: 0.8980 chunk 95 optimal weight: 30.0000 overall best weight: 6.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS B 109 GLN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN ** M 14 HIS ** 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 35 GLN P 79 ASN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 52 ASN ** T 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 ASN ** X 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 54821 Z= 0.331 Angle : 0.681 12.912 81079 Z= 0.362 Chirality : 0.036 0.262 10206 Planarity : 0.006 0.119 4991 Dihedral : 23.993 178.606 25172 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 30.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.85 % Favored : 95.11 % Rotamer: Outliers : 5.23 % Allowed : 25.78 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.16), residues: 2517 helix: -0.11 (0.16), residues: 1020 sheet: -1.48 (0.25), residues: 426 loop : -1.21 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP F 42 HIS 0.007 0.001 HIS B 18 PHE 0.016 0.002 PHE U 37 TYR 0.035 0.002 TYR B 213 ARG 0.011 0.001 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 322 time to evaluate : 3.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.3160 (mtp) cc_final: 0.2701 (mtt) REVERT: B 154 MET cc_start: 0.6779 (mmm) cc_final: 0.6278 (mmm) REVERT: C 149 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8545 (mp) REVERT: D 75 TYR cc_start: 0.9067 (m-10) cc_final: 0.8656 (m-80) REVERT: D 194 ASP cc_start: 0.9166 (p0) cc_final: 0.8558 (p0) REVERT: E 12 GLN cc_start: 0.9108 (tt0) cc_final: 0.8685 (pt0) REVERT: E 23 LYS cc_start: 0.8984 (ttpt) cc_final: 0.8730 (tptt) REVERT: E 64 MET cc_start: 0.8690 (tpp) cc_final: 0.8217 (tpp) REVERT: E 66 LYS cc_start: 0.9489 (mtmm) cc_final: 0.9287 (mtmm) REVERT: F 1 MET cc_start: 0.8719 (ttm) cc_final: 0.8264 (ttm) REVERT: F 9 MET cc_start: 0.8330 (mmp) cc_final: 0.7931 (mmp) REVERT: F 82 ASP cc_start: 0.9507 (p0) cc_final: 0.9209 (p0) REVERT: F 93 LYS cc_start: 0.9114 (tptt) cc_final: 0.8898 (tptt) REVERT: I 65 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7555 (tt) REVERT: J 98 VAL cc_start: 0.7917 (t) cc_final: 0.7708 (p) REVERT: K 64 GLN cc_start: 0.9630 (OUTLIER) cc_final: 0.9425 (pp30) REVERT: L 62 GLU cc_start: 0.9268 (mm-30) cc_final: 0.8700 (tp30) REVERT: M 42 ASP cc_start: 0.6333 (OUTLIER) cc_final: 0.5953 (p0) REVERT: N 6 MET cc_start: 0.5869 (mmt) cc_final: 0.4956 (mmt) REVERT: N 89 MET cc_start: 0.9013 (mmm) cc_final: 0.8797 (mmm) REVERT: O 28 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.8438 (mp10) REVERT: O 62 GLN cc_start: 0.9312 (tp-100) cc_final: 0.8947 (tp-100) REVERT: P 18 GLN cc_start: 0.8729 (mm110) cc_final: 0.8412 (mm110) REVERT: R 16 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8881 (mp0) REVERT: R 38 LYS cc_start: 0.9121 (mmmm) cc_final: 0.8821 (mmmt) REVERT: S 20 GLU cc_start: 0.6851 (pt0) cc_final: 0.5885 (mm-30) REVERT: S 44 MET cc_start: 0.4309 (mpp) cc_final: 0.3936 (mpp) REVERT: U 37 PHE cc_start: 0.8958 (m-10) cc_final: 0.8521 (m-80) REVERT: U 59 LYS cc_start: 0.9316 (tppt) cc_final: 0.9071 (mttt) REVERT: X 1 MET cc_start: 0.4872 (tpt) cc_final: 0.4273 (tmm) REVERT: X 41 ASP cc_start: 0.8028 (t0) cc_final: 0.7637 (t0) outliers start: 111 outliers final: 85 residues processed: 405 average time/residue: 0.6749 time to fit residues: 445.2208 Evaluate side-chains 393 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 303 time to evaluate : 3.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 37 PHE Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain I residue 65 ILE Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain M residue 8 ASN Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 28 GLN Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 57 HIS Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 9 ASN Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 47 ASN Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 53 ASP Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 112 LYS Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 124 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 126 optimal weight: 30.0000 chunk 339 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 221 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 chunk 377 optimal weight: 2.9990 chunk 313 optimal weight: 9.9990 chunk 174 optimal weight: 30.0000 chunk 31 optimal weight: 10.0000 chunk 124 optimal weight: 30.0000 chunk 198 optimal weight: 10.0000 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 91 HIS ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 ASN ** O 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 52 ASN ** T 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 54821 Z= 0.408 Angle : 0.745 12.878 81079 Z= 0.392 Chirality : 0.039 0.263 10206 Planarity : 0.006 0.119 4991 Dihedral : 24.116 178.134 25172 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 36.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.60 % Favored : 94.36 % Rotamer: Outliers : 5.89 % Allowed : 25.87 % Favored : 68.24 % 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: -1.52 (0.16), residues: 2517 helix: -0.33 (0.16), residues: 1021 sheet: -1.61 (0.26), residues: 397 loop : -1.29 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.004 TRP F 42 HIS 0.011 0.002 HIS C 190 PHE 0.023 0.002 PHE B 32 TYR 0.036 0.002 TYR B 213 ARG 0.010 0.001 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 310 time to evaluate : 4.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 MET cc_start: 0.4048 (mtp) cc_final: 0.3467 (mtp) REVERT: D 75 TYR cc_start: 0.9098 (m-10) cc_final: 0.8640 (m-80) REVERT: D 194 ASP cc_start: 0.9152 (p0) cc_final: 0.8507 (p0) REVERT: E 12 GLN cc_start: 0.9128 (tt0) cc_final: 0.8676 (pt0) REVERT: E 23 LYS cc_start: 0.9033 (ttpt) cc_final: 0.8789 (tptt) REVERT: E 26 LYS cc_start: 0.9222 (tptp) cc_final: 0.8965 (tppt) REVERT: E 64 MET cc_start: 0.8733 (tpp) cc_final: 0.8389 (tpp) REVERT: E 69 ARG cc_start: 0.8793 (ptp90) cc_final: 0.8561 (ptp90) REVERT: E 71 MET cc_start: 0.8592 (mmm) cc_final: 0.7599 (tmm) REVERT: F 1 MET cc_start: 0.8735 (ttm) cc_final: 0.8258 (ttm) REVERT: F 9 MET cc_start: 0.8186 (mmp) cc_final: 0.7833 (mmp) REVERT: F 41 ASP cc_start: 0.9006 (t0) cc_final: 0.8759 (t0) REVERT: F 93 LYS cc_start: 0.9108 (tptt) cc_final: 0.8885 (tptt) REVERT: J 52 LEU cc_start: 0.7782 (mt) cc_final: 0.7426 (tp) REVERT: J 67 ILE cc_start: 0.7266 (mm) cc_final: 0.6926 (mm) REVERT: L 62 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8624 (tp30) REVERT: M 42 ASP cc_start: 0.6500 (OUTLIER) cc_final: 0.6165 (p0) REVERT: N 6 MET cc_start: 0.5854 (mmt) cc_final: 0.4903 (mmt) REVERT: N 62 ASN cc_start: 0.6890 (OUTLIER) cc_final: 0.6211 (p0) REVERT: N 89 MET cc_start: 0.9045 (mmm) cc_final: 0.8823 (mmm) REVERT: O 62 GLN cc_start: 0.9344 (tp-100) cc_final: 0.9017 (tp-100) REVERT: P 18 GLN cc_start: 0.8854 (mm110) cc_final: 0.8559 (mm110) REVERT: R 16 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8945 (mp0) REVERT: R 38 LYS cc_start: 0.9057 (mmmm) cc_final: 0.8827 (mmmm) REVERT: R 70 TYR cc_start: 0.8050 (m-10) cc_final: 0.7820 (m-10) REVERT: S 20 GLU cc_start: 0.6958 (pt0) cc_final: 0.5738 (mm-30) REVERT: S 55 ARG cc_start: 0.6594 (OUTLIER) cc_final: 0.6210 (ptp-110) REVERT: T 28 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8339 (tpp) REVERT: U 37 PHE cc_start: 0.8933 (m-10) cc_final: 0.8498 (m-80) REVERT: U 46 LYS cc_start: 0.8367 (mmtm) cc_final: 0.8156 (mmtm) REVERT: U 59 LYS cc_start: 0.9304 (tppt) cc_final: 0.9065 (mttt) REVERT: X 41 ASP cc_start: 0.8006 (t0) cc_final: 0.7663 (t0) outliers start: 125 outliers final: 94 residues processed: 402 average time/residue: 0.7082 time to fit residues: 468.5225 Evaluate side-chains 389 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 291 time to evaluate : 3.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 23 TRP Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 37 PHE Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 193 TYR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain M residue 8 ASN Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 55 ARG Chi-restraints excluded: chain S residue 57 HIS Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain T residue 28 MET Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 9 ASN Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 36 LEU Chi-restraints excluded: chain X residue 47 ASN Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 53 ASP Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 112 LYS Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 124 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 363 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 214 optimal weight: 6.9990 chunk 275 optimal weight: 0.7980 chunk 213 optimal weight: 7.9990 chunk 317 optimal weight: 6.9990 chunk 210 optimal weight: 10.0000 chunk 375 optimal weight: 0.9990 chunk 235 optimal weight: 7.9990 chunk 229 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN B 120 GLN ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 ASN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 HIS K 64 GLN ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 ASN P 79 ASN Q 45 HIS T 52 ASN ** T 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 ASN ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 54821 Z= 0.218 Angle : 0.635 13.130 81079 Z= 0.339 Chirality : 0.034 0.294 10206 Planarity : 0.005 0.117 4991 Dihedral : 23.966 177.024 25172 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 27.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.89 % Favored : 96.07 % Rotamer: Outliers : 4.85 % Allowed : 27.47 % Favored : 67.67 % 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: -1.17 (0.17), residues: 2517 helix: 0.03 (0.16), residues: 1026 sheet: -1.53 (0.26), residues: 400 loop : -1.14 (0.19), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP F 42 HIS 0.006 0.001 HIS B 18 PHE 0.018 0.002 PHE N 77 TYR 0.036 0.002 TYR B 213 ARG 0.010 0.001 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 332 time to evaluate : 3.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.4043 (mtp) cc_final: 0.3489 (mtp) REVERT: B 154 MET cc_start: 0.6545 (mmm) cc_final: 0.6110 (mmm) REVERT: C 211 MET cc_start: 0.4630 (OUTLIER) cc_final: 0.3973 (mmm) REVERT: D 75 TYR cc_start: 0.8945 (m-10) cc_final: 0.8518 (m-80) REVERT: D 194 ASP cc_start: 0.9204 (p0) cc_final: 0.8511 (p0) REVERT: E 12 GLN cc_start: 0.9159 (tt0) cc_final: 0.8707 (pt0) REVERT: E 23 LYS cc_start: 0.8983 (ttpt) cc_final: 0.8739 (tptt) REVERT: E 26 LYS cc_start: 0.9201 (tptp) cc_final: 0.8914 (tppt) REVERT: E 45 ARG cc_start: 0.8752 (ttt90) cc_final: 0.8246 (ttt90) REVERT: E 64 MET cc_start: 0.8796 (tpp) cc_final: 0.8273 (tpp) REVERT: F 1 MET cc_start: 0.8639 (ttm) cc_final: 0.8099 (ttm) REVERT: F 9 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7914 (mmp) REVERT: F 41 ASP cc_start: 0.8959 (t0) cc_final: 0.8700 (t0) REVERT: F 80 PHE cc_start: 0.9386 (m-10) cc_final: 0.9157 (m-80) REVERT: F 82 ASP cc_start: 0.9506 (p0) cc_final: 0.9248 (p0) REVERT: F 93 LYS cc_start: 0.9100 (tptt) cc_final: 0.8895 (tptt) REVERT: J 52 LEU cc_start: 0.7636 (mt) cc_final: 0.7241 (tp) REVERT: J 67 ILE cc_start: 0.7228 (mm) cc_final: 0.6901 (mm) REVERT: L 62 GLU cc_start: 0.9297 (mm-30) cc_final: 0.8684 (tp30) REVERT: N 6 MET cc_start: 0.5903 (mmt) cc_final: 0.4928 (mmt) REVERT: N 89 MET cc_start: 0.8942 (mmm) cc_final: 0.8732 (mmm) REVERT: O 28 GLN cc_start: 0.9248 (OUTLIER) cc_final: 0.8476 (mp10) REVERT: O 62 GLN cc_start: 0.9259 (tp-100) cc_final: 0.8857 (tp-100) REVERT: P 18 GLN cc_start: 0.8757 (mm110) cc_final: 0.8414 (mm110) REVERT: R 16 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8949 (mp0) REVERT: S 20 GLU cc_start: 0.6907 (pt0) cc_final: 0.5807 (mm-30) REVERT: T 15 GLU cc_start: 0.9018 (pm20) cc_final: 0.8494 (pm20) REVERT: T 18 ARG cc_start: 0.9211 (ttp80) cc_final: 0.8851 (ttp80) REVERT: U 37 PHE cc_start: 0.8946 (m-10) cc_final: 0.8549 (m-80) REVERT: U 59 LYS cc_start: 0.9309 (tppt) cc_final: 0.9084 (mttt) REVERT: X 41 ASP cc_start: 0.7953 (t0) cc_final: 0.7607 (t0) outliers start: 103 outliers final: 78 residues processed: 403 average time/residue: 0.6478 time to fit residues: 428.6914 Evaluate side-chains 389 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 308 time to evaluate : 3.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 TRP Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain C residue 37 PHE Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 24 HIS Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 72 HIS Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain O residue 28 GLN Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 57 HIS Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain T residue 52 ASN Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 9 ASN Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 9 THR Chi-restraints excluded: chain X residue 36 LEU Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 95 VAL Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 100 THR Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 112 LYS Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 124 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 232 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 224 optimal weight: 2.9990 chunk 113 optimal weight: 30.0000 chunk 73 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 238 optimal weight: 8.9990 chunk 256 optimal weight: 10.0000 chunk 185 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 295 optimal weight: 7.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 ASN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 HIS M 14 HIS ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 ASN ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 ASN ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 54821 Z= 0.281 Angle : 0.665 13.093 81079 Z= 0.352 Chirality : 0.035 0.261 10206 Planarity : 0.006 0.118 4991 Dihedral : 23.954 177.676 25172 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 30.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.69 % Favored : 95.27 % Rotamer: Outliers : 4.90 % Allowed : 27.76 % Favored : 67.34 % 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: -1.22 (0.16), residues: 2517 helix: -0.01 (0.16), residues: 1025 sheet: -1.66 (0.26), residues: 406 loop : -1.12 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.003 TRP F 42 HIS 0.014 0.001 HIS K 24 PHE 0.018 0.002 PHE N 77 TYR 0.036 0.002 TYR B 213 ARG 0.009 0.001 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 317 time to evaluate : 3.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.4349 (mtp) cc_final: 0.3759 (mtp) REVERT: B 154 MET cc_start: 0.6774 (mmm) cc_final: 0.6335 (mmm) REVERT: C 211 MET cc_start: 0.4642 (OUTLIER) cc_final: 0.4023 (mmm) REVERT: D 75 TYR cc_start: 0.8976 (m-10) cc_final: 0.8543 (m-80) REVERT: D 194 ASP cc_start: 0.9213 (p0) cc_final: 0.8486 (p0) REVERT: E 12 GLN cc_start: 0.9185 (tt0) cc_final: 0.8703 (pt0) REVERT: E 13 GLU cc_start: 0.8446 (mp0) cc_final: 0.8224 (mp0) REVERT: E 23 LYS cc_start: 0.8987 (ttpt) cc_final: 0.8733 (tptt) REVERT: E 26 LYS cc_start: 0.9241 (tptp) cc_final: 0.8718 (tptp) REVERT: E 64 MET cc_start: 0.8942 (tpp) cc_final: 0.8674 (tpp) REVERT: F 9 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7833 (mmp) REVERT: F 41 ASP cc_start: 0.8952 (t0) cc_final: 0.8683 (t0) REVERT: F 80 PHE cc_start: 0.9394 (m-10) cc_final: 0.9163 (m-80) REVERT: F 82 ASP cc_start: 0.9509 (p0) cc_final: 0.9244 (p0) REVERT: J 25 ILE cc_start: 0.6955 (tp) cc_final: 0.6751 (tt) REVERT: J 67 ILE cc_start: 0.7232 (mm) cc_final: 0.6923 (mm) REVERT: L 62 GLU cc_start: 0.9345 (mm-30) cc_final: 0.8700 (tp30) REVERT: N 6 MET cc_start: 0.5605 (mmt) cc_final: 0.4504 (mmt) REVERT: N 89 MET cc_start: 0.8966 (mmm) cc_final: 0.8756 (mmm) REVERT: O 28 GLN cc_start: 0.9290 (OUTLIER) cc_final: 0.8418 (mp10) REVERT: O 62 GLN cc_start: 0.9266 (tp-100) cc_final: 0.8866 (tp-100) REVERT: P 18 GLN cc_start: 0.8789 (mm110) cc_final: 0.8461 (mm110) REVERT: R 16 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8966 (mp0) REVERT: R 38 LYS cc_start: 0.8994 (mmmm) cc_final: 0.8791 (mmmm) REVERT: S 20 GLU cc_start: 0.7030 (pt0) cc_final: 0.5857 (mm-30) REVERT: T 18 ARG cc_start: 0.9215 (ttp80) cc_final: 0.8840 (ttp80) REVERT: U 37 PHE cc_start: 0.8976 (m-10) cc_final: 0.8578 (m-80) REVERT: U 59 LYS cc_start: 0.9287 (tppt) cc_final: 0.9058 (mttt) REVERT: X 41 ASP cc_start: 0.7971 (t0) cc_final: 0.7655 (t0) outliers start: 104 outliers final: 87 residues processed: 385 average time/residue: 0.6598 time to fit residues: 416.5218 Evaluate side-chains 389 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 299 time to evaluate : 3.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 23 TRP Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 37 PHE Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 59 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 72 HIS Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain M residue 8 ASN Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain O residue 28 GLN Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 57 HIS Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 9 ASN Chi-restraints excluded: chain U residue 20 LYS Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 9 THR Chi-restraints excluded: chain X residue 36 LEU Chi-restraints excluded: chain X residue 46 ILE Chi-restraints excluded: chain X residue 47 ASN Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 100 THR Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 112 LYS Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 124 MET Chi-restraints excluded: chain X residue 149 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 341 optimal weight: 0.0980 chunk 360 optimal weight: 7.9990 chunk 328 optimal weight: 6.9990 chunk 350 optimal weight: 1.9990 chunk 210 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 275 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 316 optimal weight: 1.9990 chunk 331 optimal weight: 9.9990 chunk 349 optimal weight: 4.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN B 120 GLN ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 ASN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 ASN ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 54821 Z= 0.170 Angle : 0.621 13.269 81079 Z= 0.331 Chirality : 0.033 0.354 10206 Planarity : 0.005 0.117 4991 Dihedral : 23.816 179.334 25172 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 24.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.93 % Favored : 96.03 % Rotamer: Outliers : 3.86 % Allowed : 28.75 % Favored : 67.39 % 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: -1.01 (0.17), residues: 2517 helix: 0.17 (0.16), residues: 1021 sheet: -1.48 (0.26), residues: 407 loop : -1.03 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP F 42 HIS 0.006 0.001 HIS B 18 PHE 0.018 0.001 PHE N 77 TYR 0.038 0.002 TYR B 213 ARG 0.014 0.001 ARG N 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 346 time to evaluate : 3.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 27 MET cc_start: 0.4010 (mtp) cc_final: 0.3522 (mtp) REVERT: B 154 MET cc_start: 0.6572 (mmm) cc_final: 0.5816 (mmm) REVERT: D 75 TYR cc_start: 0.8909 (m-10) cc_final: 0.8535 (m-80) REVERT: D 194 ASP cc_start: 0.9201 (p0) cc_final: 0.8495 (p0) REVERT: E 12 GLN cc_start: 0.9159 (tt0) cc_final: 0.8615 (pt0) REVERT: E 13 GLU cc_start: 0.8388 (mp0) cc_final: 0.8165 (mp0) REVERT: E 23 LYS cc_start: 0.8943 (ttpt) cc_final: 0.8710 (tptt) REVERT: E 26 LYS cc_start: 0.9149 (tptp) cc_final: 0.8903 (tppt) REVERT: E 64 MET cc_start: 0.8923 (tpp) cc_final: 0.8673 (tpp) REVERT: E 93 ARG cc_start: 0.7799 (mtm-85) cc_final: 0.7115 (mtm-85) REVERT: F 5 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8292 (mm-30) REVERT: F 80 PHE cc_start: 0.9363 (m-10) cc_final: 0.9109 (m-80) REVERT: F 82 ASP cc_start: 0.9419 (p0) cc_final: 0.9193 (p0) REVERT: J 52 LEU cc_start: 0.7565 (mt) cc_final: 0.7141 (tp) REVERT: J 67 ILE cc_start: 0.7256 (mm) cc_final: 0.6965 (mm) REVERT: L 62 GLU cc_start: 0.9294 (mm-30) cc_final: 0.8669 (tp30) REVERT: N 6 MET cc_start: 0.5669 (mmt) cc_final: 0.4557 (mmt) REVERT: O 28 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.8449 (mp10) REVERT: O 62 GLN cc_start: 0.9182 (tp-100) cc_final: 0.8768 (tp-100) REVERT: P 18 GLN cc_start: 0.8653 (mm110) cc_final: 0.8273 (mm110) REVERT: R 38 LYS cc_start: 0.9047 (mmmm) cc_final: 0.8811 (mmmm) REVERT: S 20 GLU cc_start: 0.7182 (pt0) cc_final: 0.6148 (mm-30) REVERT: T 15 GLU cc_start: 0.9024 (pm20) cc_final: 0.8473 (pm20) REVERT: T 18 ARG cc_start: 0.9153 (ttp80) cc_final: 0.8831 (ttp80) REVERT: U 59 LYS cc_start: 0.9305 (tppt) cc_final: 0.9058 (mttt) REVERT: X 41 ASP cc_start: 0.7993 (t0) cc_final: 0.7696 (t0) outliers start: 82 outliers final: 67 residues processed: 404 average time/residue: 0.6757 time to fit residues: 443.3304 Evaluate side-chains 385 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 317 time to evaluate : 3.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 TRP Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain C residue 37 PHE Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 72 HIS Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain M residue 8 ASN Chi-restraints excluded: chain M residue 63 PHE Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain O residue 28 GLN Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain S residue 57 HIS Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 9 ASN Chi-restraints excluded: chain U residue 20 LYS Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 36 LEU Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 95 VAL Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 124 MET Chi-restraints excluded: chain X residue 149 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 230 optimal weight: 9.9990 chunk 370 optimal weight: 0.9990 chunk 226 optimal weight: 9.9990 chunk 175 optimal weight: 30.0000 chunk 257 optimal weight: 0.0270 chunk 388 optimal weight: 5.9990 chunk 357 optimal weight: 30.0000 chunk 309 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 238 optimal weight: 0.0670 chunk 189 optimal weight: 20.0000 overall best weight: 3.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN B 120 GLN ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 ASN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 29 ASN ** T 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 140 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 54821 Z= 0.208 Angle : 0.638 13.206 81079 Z= 0.339 Chirality : 0.033 0.293 10206 Planarity : 0.006 0.117 4991 Dihedral : 23.790 178.315 25172 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 25.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.29 % Favored : 95.67 % Rotamer: Outliers : 3.77 % Allowed : 29.50 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.17), residues: 2517 helix: 0.11 (0.16), residues: 1027 sheet: -1.48 (0.26), residues: 408 loop : -1.00 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP F 42 HIS 0.007 0.001 HIS B 18 PHE 0.018 0.001 PHE N 77 TYR 0.042 0.002 TYR B 213 ARG 0.014 0.001 ARG F 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 320 time to evaluate : 3.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.4215 (mtp) cc_final: 0.3757 (mtp) REVERT: D 75 TYR cc_start: 0.8923 (m-10) cc_final: 0.8555 (m-80) REVERT: D 194 ASP cc_start: 0.9214 (p0) cc_final: 0.8503 (p0) REVERT: E 12 GLN cc_start: 0.9125 (tt0) cc_final: 0.8591 (pt0) REVERT: E 13 GLU cc_start: 0.8385 (mp0) cc_final: 0.8172 (mp0) REVERT: E 23 LYS cc_start: 0.8941 (ttpt) cc_final: 0.8694 (tptt) REVERT: E 26 LYS cc_start: 0.9202 (tptp) cc_final: 0.8750 (tptp) REVERT: E 64 MET cc_start: 0.8977 (tpp) cc_final: 0.8725 (tpp) REVERT: F 1 MET cc_start: 0.8610 (ttm) cc_final: 0.8227 (ttm) REVERT: F 9 MET cc_start: 0.8621 (mmp) cc_final: 0.8312 (mmp) REVERT: F 80 PHE cc_start: 0.9404 (m-10) cc_final: 0.9150 (m-80) REVERT: F 82 ASP cc_start: 0.9418 (p0) cc_final: 0.9212 (p0) REVERT: J 67 ILE cc_start: 0.7209 (mm) cc_final: 0.6900 (mm) REVERT: L 62 GLU cc_start: 0.9287 (mm-30) cc_final: 0.8673 (tp30) REVERT: L 70 GLU cc_start: 0.7932 (pm20) cc_final: 0.7502 (pm20) REVERT: L 90 LEU cc_start: 0.8342 (mp) cc_final: 0.8136 (mp) REVERT: N 6 MET cc_start: 0.5719 (mmt) cc_final: 0.4612 (mmt) REVERT: O 28 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.8473 (mp10) REVERT: O 62 GLN cc_start: 0.9194 (tp-100) cc_final: 0.8775 (tp-100) REVERT: P 18 GLN cc_start: 0.8694 (mm110) cc_final: 0.8325 (mm110) REVERT: R 38 LYS cc_start: 0.9036 (mmmm) cc_final: 0.8789 (mmmm) REVERT: S 20 GLU cc_start: 0.7228 (pt0) cc_final: 0.6113 (mm-30) REVERT: T 15 GLU cc_start: 0.9038 (pm20) cc_final: 0.8499 (pm20) REVERT: T 18 ARG cc_start: 0.9154 (ttp80) cc_final: 0.8843 (ttp80) REVERT: U 37 PHE cc_start: 0.8927 (m-10) cc_final: 0.8601 (m-80) REVERT: U 54 LYS cc_start: 0.9173 (ttpp) cc_final: 0.8913 (pttm) REVERT: U 59 LYS cc_start: 0.9307 (tppt) cc_final: 0.9069 (mttt) REVERT: X 41 ASP cc_start: 0.8063 (t0) cc_final: 0.7810 (t0) outliers start: 80 outliers final: 68 residues processed: 372 average time/residue: 0.6510 time to fit residues: 397.4420 Evaluate side-chains 376 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 307 time to evaluate : 3.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 23 TRP Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 37 PHE Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 72 HIS Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain M residue 8 ASN Chi-restraints excluded: chain M residue 63 PHE Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain O residue 28 GLN Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain S residue 57 HIS Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 9 ASN Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 36 LEU Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 95 VAL Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 124 MET Chi-restraints excluded: chain X residue 149 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 245 optimal weight: 0.9990 chunk 329 optimal weight: 3.9990 chunk 94 optimal weight: 40.0000 chunk 285 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 309 optimal weight: 6.9990 chunk 129 optimal weight: 30.0000 chunk 318 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 ASN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 29 ASN T 20 HIS ** T 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.036485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.024263 restraints weight = 565269.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.025045 restraints weight = 214004.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.025544 restraints weight = 128445.838| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.4919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 54821 Z= 0.226 Angle : 0.647 13.195 81079 Z= 0.343 Chirality : 0.034 0.262 10206 Planarity : 0.006 0.117 4991 Dihedral : 23.789 178.275 25172 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 27.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.45 % Favored : 95.51 % Rotamer: Outliers : 4.10 % Allowed : 29.08 % Favored : 66.82 % 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: -1.03 (0.17), residues: 2517 helix: 0.12 (0.16), residues: 1029 sheet: -1.53 (0.25), residues: 417 loop : -0.98 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP F 42 HIS 0.008 0.001 HIS B 18 PHE 0.018 0.002 PHE N 77 TYR 0.042 0.002 TYR B 213 ARG 0.012 0.001 ARG F 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9768.64 seconds wall clock time: 180 minutes 36.03 seconds (10836.03 seconds total)