Starting phenix.real_space_refine on Sun Feb 25 15:18:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nau_12248/02_2024/7nau_12248_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nau_12248/02_2024/7nau_12248.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nau_12248/02_2024/7nau_12248_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nau_12248/02_2024/7nau_12248_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nau_12248/02_2024/7nau_12248_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nau_12248/02_2024/7nau_12248.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nau_12248/02_2024/7nau_12248.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nau_12248/02_2024/7nau_12248_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nau_12248/02_2024/7nau_12248_neut_updated.pdb" } resolution = 3.78 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= 0.005 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 1522 5.49 5 Mg 57 5.21 5 S 73 5.16 5 C 26816 2.51 5 N 9713 2.21 5 O 14101 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 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 52283 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 32664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1522, 32664 Classifications: {'RNA': 1522} Modifications used: {'rna2p_pur': 118, 'rna2p_pyr': 92, 'rna3p': 8, 'rna3p_pur': 742, 'rna3p_pyr': 562} Link IDs: {'rna2p': 209, 'rna3p': 1312} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1653 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 7, 'TRANS': 203} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 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: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1143 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 5, 'TRANS': 140} 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: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 866 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 108} 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: "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: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Unusual residues: {' MG': 57} Classifications: {'undetermined': 57} Link IDs: {None: 56} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 28.15, per 1000 atoms: 0.54 Number of scatterers: 52283 At special positions: 0 Unit cell: (146.475, 239.785, 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 73 16.00 P 1522 15.00 Mg 57 11.99 O 14101 8.00 N 9713 7.00 C 26816 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 35.84 Conformation dependent library (CDL) restraints added in 3.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4612 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 91 helices and 22 sheets defined 39.1% alpha, 14.0% beta 462 base pairs and 730 stacking pairs defined. Time for finding SS restraints: 33.52 Creating SS restraints... Processing helix chain 'B' and resid 6 through 12 removed outlier: 3.707A pdb=" N ALA B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 43 through 63 Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.674A pdb=" N CYS B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 123 Processing helix chain 'B' and resid 131 through 148 Processing helix chain 'B' and resid 170 through 179 Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 207 through 226 Processing helix chain 'C' and resid 7 through 11 removed outlier: 3.781A 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: 5.628A 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 114 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 8 through 14 removed outlier: 3.922A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 40 through 42 No H-bonds generated for 'chain 'D' and resid 40 through 42' Processing helix chain 'D' and resid 50 through 64 removed outlier: 3.541A pdb=" N GLN D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 81 Processing helix chain 'D' and resid 86 through 95 Processing helix chain 'D' and resid 98 through 105 Processing helix chain 'D' and resid 111 through 120 removed outlier: 3.521A pdb=" N LEU D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 151 removed outlier: 3.774A pdb=" N LYS D 151 " --> pdb=" O LYS D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 164 removed outlier: 3.947A pdb=" N GLN D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 205 removed outlier: 3.558A pdb=" N SER D 205 " --> pdb=" O VAL D 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 66 Processing helix chain 'E' and resid 109 through 118 removed outlier: 3.858A pdb=" N VAL E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 146 Processing helix chain 'E' and resid 150 through 157 Processing helix chain 'E' and resid 161 through 164 No H-bonds generated for 'chain 'E' and resid 161 through 164' Processing helix chain 'F' and resid 12 through 32 removed outlier: 4.521A pdb=" N GLU F 16 " --> pdb=" O ASP F 13 " (cutoff:3.500A) Proline residue: F 19 - end of helix removed outlier: 4.008A pdb=" N GLU F 23 " --> pdb=" O GLY F 20 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG F 24 " --> pdb=" O MET F 21 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA F 27 " --> pdb=" O ARG F 24 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY F 31 " --> pdb=" O ALA F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 80 removed outlier: 3.698A pdb=" N ASP F 72 " --> pdb=" O GLN F 68 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU F 74 " --> pdb=" O VAL F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 105 Processing helix chain 'G' and resid 21 through 30 Processing helix chain 'G' and resid 36 through 53 removed outlier: 4.003A pdb=" N ILE G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR G 49 " --> pdb=" O SER G 45 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 69 removed outlier: 4.295A pdb=" N GLU G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 110 Processing helix chain 'G' and resid 116 through 128 Processing helix chain 'G' and resid 134 through 146 Processing helix chain 'H' and resid 6 through 20 Processing helix chain 'H' and resid 31 through 43 removed outlier: 3.688A pdb=" N VAL H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS H 41 " --> pdb=" O ALA H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 91 No H-bonds generated for 'chain 'H' and resid 89 through 91' Processing helix chain 'H' and resid 96 through 98 No H-bonds generated for 'chain 'H' and resid 96 through 98' Processing helix chain 'H' and resid 113 through 119 Processing helix chain 'I' and resid 35 through 38 No H-bonds generated for 'chain 'I' and resid 35 through 38' Processing helix chain 'I' and resid 42 through 55 Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 72 through 91 Processing helix chain 'I' and resid 95 through 100 Processing helix chain 'J' and resid 15 through 31 Processing helix chain 'J' and resid 81 through 89 removed outlier: 3.871A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 50 No H-bonds generated for 'chain 'K' and resid 47 through 50' Processing helix chain 'K' and resid 56 through 58 No H-bonds generated for 'chain 'K' and resid 56 through 58' Processing helix chain 'K' and resid 60 through 77 removed outlier: 3.629A pdb=" N LYS K 75 " --> pdb=" O ALA K 71 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLU K 76 " --> pdb=" O ASP K 72 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TYR K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 103 Processing helix chain 'L' and resid 4 through 9 Processing helix chain 'L' and resid 22 through 24 No H-bonds generated for 'chain 'L' and resid 22 through 24' Processing helix chain 'L' and resid 114 through 116 No H-bonds generated for 'chain 'L' and resid 114 through 116' Processing helix chain 'M' and resid 15 through 21 Processing helix chain 'M' and resid 27 through 37 Processing helix chain 'M' and resid 50 through 61 removed outlier: 4.498A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 82 Processing helix chain 'M' and resid 86 through 93 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 83 through 89 Processing helix chain 'O' and resid 5 through 14 Processing helix chain 'O' and resid 25 through 45 removed outlier: 3.566A pdb=" N GLN O 40 " --> pdb=" O ILE O 36 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE O 43 " --> pdb=" O LEU O 39 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 73 removed outlier: 3.552A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 85 removed outlier: 4.077A pdb=" N GLU O 83 " --> pdb=" O THR O 79 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARG O 84 " --> pdb=" O GLN O 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 54 through 62 Processing helix chain 'P' and resid 69 through 80 Processing helix chain 'Q' and resid 49 through 51 No H-bonds generated for 'chain 'Q' and resid 49 through 51' Processing helix chain 'R' and resid 12 through 16 Processing helix chain 'R' and resid 26 through 31 removed outlier: 3.915A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 45 No H-bonds generated for 'chain 'R' and resid 42 through 45' Processing helix chain 'R' and resid 49 through 64 removed outlier: 3.760A pdb=" N GLN R 54 " --> pdb=" O LYS R 50 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 24 Processing helix chain 'S' and resid 64 through 66 No H-bonds generated for 'chain 'S' and resid 64 through 66' Processing helix chain 'S' and resid 71 through 74 Processing helix chain 'T' and resid 5 through 41 removed outlier: 3.506A pdb=" N ILE T 12 " --> pdb=" O LYS T 8 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU T 15 " --> pdb=" O ALA T 11 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS T 20 " --> pdb=" O LYS T 16 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE T 32 " --> pdb=" O MET T 28 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL T 35 " --> pdb=" O PHE T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 63 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 69 through 84 Processing helix chain 'X' and resid 5 through 18 removed outlier: 3.578A pdb=" N ALA X 14 " --> pdb=" O GLU X 10 " (cutoff:3.500A) Proline residue: X 15 - end of helix Processing helix chain 'X' and resid 48 through 64 removed outlier: 4.292A pdb=" N VAL X 64 " --> pdb=" O ALA X 60 " (cutoff:3.500A) Processing helix chain 'X' and resid 88 through 93 Processing sheet with id= A, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.697A pdb=" N ALA B 160 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL B 70 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE B 162 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N PHE B 198 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL B 187 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 6.319A 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: 6.123A pdb=" N VAL B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 99 through 103 removed outlier: 6.745A pdb=" N ILE C 64 " --> pdb=" O GLN C 100 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASN C 102 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 5.807A 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 170 Processing sheet with id= E, first strand: chain 'D' and resid 123 through 125 Processing sheet with id= F, first strand: chain 'D' and resid 171 through 174 Processing sheet with id= G, first strand: chain 'E' and resid 46 through 53 removed outlier: 3.561A pdb=" N ALA E 17 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 85 through 89 removed outlier: 3.672A pdb=" N ARG E 93 " --> pdb=" O TYR E 128 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 89 through 91 removed outlier: 3.591A pdb=" N VAL F 64 " --> pdb=" O TYR F 4 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU F 65 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ILE F 36 " --> pdb=" O GLU F 65 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 73 through 75 Processing sheet with id= K, first strand: chain 'H' and resid 24 through 27 removed outlier: 3.602A pdb=" N VAL H 25 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU H 61 " --> pdb=" O VAL H 25 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 75 through 77 removed outlier: 6.859A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'I' and resid 6 through 11 removed outlier: 3.738A pdb=" N GLY I 10 " --> pdb=" O ALA I 17 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'J' and resid 98 through 101 removed outlier: 4.678A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'J' and resid 45 through 51 Processing sheet with id= P, first strand: chain 'K' and resid 110 through 112 removed outlier: 5.934A pdb=" N VAL K 84 " --> pdb=" O THR K 111 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ALA K 21 " --> pdb=" O MET K 85 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LYS K 87 " --> pdb=" O ALA K 21 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE K 23 " --> pdb=" O LYS K 87 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'L' and resid 79 through 83 removed outlier: 6.484A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR L 39 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ARG L 50 " --> pdb=" O THR L 39 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'P' and resid 2 through 11 removed outlier: 6.552A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'Q' and resid 58 through 61 removed outlier: 7.665A pdb=" N GLN Q 9 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLU Q 26 " --> pdb=" O GLN Q 9 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE Q 25 " --> pdb=" O THR Q 42 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR Q 42 " --> pdb=" O ILE Q 25 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL Q 29 " --> pdb=" O ILE Q 38 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'S' and resid 31 through 33 removed outlier: 3.984A pdb=" N LEU S 31 " --> pdb=" O THR S 48 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'X' and resid 74 through 77 removed outlier: 7.245A pdb=" N LEU X 36 " --> pdb=" O GLU X 75 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N SER X 77 " --> pdb=" O LEU X 36 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE X 38 " --> pdb=" O SER X 77 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY X 25 " --> pdb=" O TYR X 39 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'X' and resid 143 through 147 removed outlier: 4.221A pdb=" N GLU X 98 " --> pdb=" O VAL X 147 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL X 116 " --> pdb=" O THR X 128 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR X 126 " --> pdb=" O LYS X 118 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N VAL X 120 " --> pdb=" O MET X 124 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N MET X 124 " --> pdb=" O VAL X 120 " (cutoff:3.500A) 761 hydrogen bonds defined for protein. 2169 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1069 hydrogen bonds 1364 hydrogen bond angles 0 basepair planarities 462 basepair parallelities 730 stacking parallelities Total time for adding SS restraints: 50.57 Time building geometry restraints manager: 36.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5963 1.32 - 1.44: 23589 1.44 - 1.57: 23693 1.57 - 1.69: 3041 1.69 - 1.82: 131 Bond restraints: 56417 Sorted by residual: bond pdb=" N3 2MG A1207 " pdb=" C4 2MG A1207 " ideal model delta sigma weight residual 1.496 1.339 0.157 2.00e-02 2.50e+03 6.18e+01 bond pdb=" N3 2MG A 966 " pdb=" C4 2MG A 966 " ideal model delta sigma weight residual 1.496 1.341 0.155 2.00e-02 2.50e+03 6.00e+01 bond pdb=" C2 G7M A 527 " pdb=" N3 G7M A 527 " ideal model delta sigma weight residual 1.462 1.309 0.153 2.00e-02 2.50e+03 5.88e+01 bond pdb=" C2 5MC A 967 " pdb=" N3 5MC A 967 " ideal model delta sigma weight residual 1.493 1.340 0.153 2.00e-02 2.50e+03 5.84e+01 bond pdb=" N3 2MG A1516 " pdb=" C4 2MG A1516 " ideal model delta sigma weight residual 1.496 1.345 0.151 2.00e-02 2.50e+03 5.72e+01 ... (remaining 56412 not shown) Histogram of bond angle deviations from ideal: 97.17 - 105.18: 7442 105.18 - 113.20: 35271 113.20 - 121.22: 26861 121.22 - 129.24: 12557 129.24 - 137.25: 1578 Bond angle restraints: 83709 Sorted by residual: angle pdb=" C1' G7M A 527 " pdb=" N9 G7M A 527 " pdb=" C8 G7M A 527 " ideal model delta sigma weight residual 94.96 127.75 -32.79 3.00e+00 1.11e-01 1.19e+02 angle pdb=" CA PHE K 52 " pdb=" C PHE K 52 " pdb=" O PHE K 52 " ideal model delta sigma weight residual 121.05 111.14 9.91 1.14e+00 7.69e-01 7.56e+01 angle pdb=" C HIS Q 31 " pdb=" N PRO Q 32 " pdb=" CA PRO Q 32 " ideal model delta sigma weight residual 119.05 110.87 8.18 1.11e+00 8.12e-01 5.43e+01 angle pdb=" N ASN Q 51 " pdb=" CA ASN Q 51 " pdb=" C ASN Q 51 " ideal model delta sigma weight residual 111.39 101.79 9.60 1.38e+00 5.25e-01 4.84e+01 angle pdb=" C3' C A 528 " pdb=" C2' C A 528 " pdb=" O2' C A 528 " ideal model delta sigma weight residual 110.70 101.49 9.21 1.50e+00 4.44e-01 3.77e+01 ... (remaining 83704 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 31668 36.00 - 72.00: 3897 72.00 - 108.00: 458 108.00 - 143.99: 14 143.99 - 179.99: 9 Dihedral angle restraints: 36046 sinusoidal: 28911 harmonic: 7135 Sorted by residual: dihedral pdb=" C4' G A1279 " pdb=" C3' G A1279 " pdb=" C2' G A1279 " pdb=" C1' G A1279 " ideal model delta sinusoidal sigma weight residual -35.00 35.37 -70.37 1 8.00e+00 1.56e-02 9.96e+01 dihedral pdb=" C5' G A1279 " pdb=" C4' G A1279 " pdb=" C3' G A1279 " pdb=" O3' G A1279 " ideal model delta sinusoidal sigma weight residual 147.00 81.42 65.58 1 8.00e+00 1.56e-02 8.80e+01 dihedral pdb=" O4' U A1008 " pdb=" C1' U A1008 " pdb=" N1 U A1008 " pdb=" C2 U A1008 " ideal model delta sinusoidal sigma weight residual -160.00 16.02 -176.02 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 36043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 10093 0.122 - 0.243: 463 0.243 - 0.365: 23 0.365 - 0.486: 2 0.486 - 0.608: 2 Chirality restraints: 10583 Sorted by residual: chirality pdb=" CA ARG K 69 " pdb=" N ARG K 69 " pdb=" C ARG K 69 " pdb=" CB ARG K 69 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.23e+00 chirality pdb=" CA ASP K 72 " pdb=" N ASP K 72 " pdb=" C ASP K 72 " pdb=" CB ASP K 72 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" CA GLU K 68 " pdb=" N GLU K 68 " pdb=" C GLU K 68 " pdb=" CB GLU K 68 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.23e+00 ... (remaining 10580 not shown) Planarity restraints: 4978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " 0.056 2.00e-02 2.50e+03 6.15e-01 8.50e+03 pdb=" C4' 2MG A1516 " 0.451 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " 0.692 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " -0.593 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " -0.644 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " -0.184 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " 0.974 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " 0.206 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " -0.959 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A 966 " 0.024 2.00e-02 2.50e+03 5.84e-01 7.68e+03 pdb=" C4' 2MG A 966 " 0.451 2.00e-02 2.50e+03 pdb=" O4' 2MG A 966 " 0.715 2.00e-02 2.50e+03 pdb=" C3' 2MG A 966 " -0.585 2.00e-02 2.50e+03 pdb=" O3' 2MG A 966 " -0.554 2.00e-02 2.50e+03 pdb=" C2' 2MG A 966 " -0.231 2.00e-02 2.50e+03 pdb=" O2' 2MG A 966 " 0.876 2.00e-02 2.50e+03 pdb=" C1' 2MG A 966 " 0.218 2.00e-02 2.50e+03 pdb=" N9 2MG A 966 " -0.915 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A 967 " 0.012 2.00e-02 2.50e+03 5.66e-01 7.21e+03 pdb=" C4' 5MC A 967 " 0.441 2.00e-02 2.50e+03 pdb=" O4' 5MC A 967 " 0.659 2.00e-02 2.50e+03 pdb=" C3' 5MC A 967 " -0.584 2.00e-02 2.50e+03 pdb=" O3' 5MC A 967 " -0.540 2.00e-02 2.50e+03 pdb=" C2' 5MC A 967 " -0.228 2.00e-02 2.50e+03 pdb=" O2' 5MC A 967 " 0.877 2.00e-02 2.50e+03 pdb=" C1' 5MC A 967 " 0.226 2.00e-02 2.50e+03 pdb=" N1 5MC A 967 " -0.864 2.00e-02 2.50e+03 ... (remaining 4975 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 45 1.99 - 2.72: 6963 2.72 - 3.44: 86217 3.44 - 4.17: 178407 4.17 - 4.90: 238189 Nonbonded interactions: 509821 Sorted by model distance: nonbonded pdb=" OP2 A A1081 " pdb=" NZ LYS E 52 " model vdw 1.262 2.520 nonbonded pdb=" O3' G A1365 " pdb="MG MG A1652 " model vdw 1.752 2.170 nonbonded pdb=" O3' G A1242 " pdb="MG MG A1656 " model vdw 1.796 2.170 nonbonded pdb=" OP2 A A 560 " pdb="MG MG A1603 " model vdw 1.837 2.170 nonbonded pdb=" OP1 U A1199 " pdb="MG MG A1655 " model vdw 1.842 2.170 ... (remaining 509816 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: 4.890 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: 0.060 Extract box with map and model: 14.560 Check model and map are aligned: 0.730 Set scattering table: 0.460 Process input model: 208.400 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 233.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 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 : 0.010 0.157 56417 Z= 0.619 Angle : 0.956 32.788 83709 Z= 0.579 Chirality : 0.056 0.608 10583 Planarity : 0.018 0.615 4978 Dihedral : 23.826 179.993 31434 Min Nonbonded Distance : 1.262 Molprobity Statistics. All-atom Clashscore : 33.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 0.05 % Allowed : 12.90 % Favored : 87.05 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.16), residues: 2447 helix: -1.65 (0.16), residues: 951 sheet: -1.86 (0.24), residues: 398 loop : -1.89 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP Q 73 HIS 0.009 0.002 HIS X 56 PHE 0.020 0.002 PHE K 61 TYR 0.016 0.002 TYR I 64 ARG 0.013 0.001 ARG I 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 601 time to evaluate : 4.185 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: symmetry clash REVERT: B 9 MET cc_start: -0.2787 (mtt) cc_final: -0.3202 (ptp) REVERT: B 146 ASN cc_start: 0.8073 (m-40) cc_final: 0.7421 (m-40) REVERT: C 41 GLN cc_start: 0.8674 (tt0) cc_final: 0.8232 (tt0) REVERT: C 193 TYR cc_start: 0.6615 (m-80) cc_final: 0.6298 (m-80) REVERT: D 71 GLN cc_start: 0.9323 (tt0) cc_final: 0.8980 (tt0) REVERT: D 75 TYR cc_start: 0.8993 (m-80) cc_final: 0.8152 (m-80) REVERT: E 12 GLN cc_start: 0.8987 (mp10) cc_final: 0.7879 (pm20) REVERT: E 14 LYS cc_start: 0.8908 (mttm) cc_final: 0.8690 (mmtm) REVERT: E 43 ASN cc_start: 0.8764 (t0) cc_final: 0.8384 (p0) REVERT: E 60 ILE cc_start: 0.9671 (mt) cc_final: 0.9470 (mt) REVERT: E 96 MET cc_start: 0.8931 (mpp) cc_final: 0.8613 (mpp) REVERT: E 116 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8294 (tm-30) REVERT: F 9 MET cc_start: 0.8615 (mtm) cc_final: 0.8329 (mtp) REVERT: F 35 LYS cc_start: 0.9517 (mptt) cc_final: 0.9239 (mmtt) REVERT: F 88 MET cc_start: 0.9105 (tpt) cc_final: 0.8457 (tmm) REVERT: F 90 MET cc_start: 0.9013 (mtm) cc_final: 0.8315 (mtp) REVERT: F 93 LYS cc_start: 0.9139 (tttt) cc_final: 0.8728 (tttt) REVERT: G 11 LYS cc_start: 0.6507 (mmtt) cc_final: 0.6179 (mmtm) REVERT: G 79 ARG cc_start: 0.7307 (ptp90) cc_final: 0.5646 (mmp80) REVERT: G 131 LYS cc_start: 0.6515 (pttp) cc_final: 0.5779 (mmmt) REVERT: H 3 MET cc_start: 0.8754 (tmm) cc_final: 0.8162 (tmm) REVERT: H 27 MET cc_start: 0.8537 (ptp) cc_final: 0.8105 (pmm) REVERT: H 80 ARG cc_start: 0.9460 (mtm110) cc_final: 0.9211 (mtp-110) REVERT: H 88 ARG cc_start: 0.8660 (mtp-110) cc_final: 0.8107 (mtp-110) REVERT: H 96 MET cc_start: 0.8955 (mtp) cc_final: 0.8299 (ttp) REVERT: I 116 VAL cc_start: 0.9588 (p) cc_final: 0.9361 (m) REVERT: J 49 PHE cc_start: 0.8935 (m-80) cc_final: 0.8694 (m-80) REVERT: J 88 MET cc_start: 0.8608 (mmt) cc_final: 0.8126 (mtm) REVERT: K 94 GLU cc_start: 0.9418 (pt0) cc_final: 0.9093 (mp0) REVERT: L 66 TYR cc_start: 0.8508 (t80) cc_final: 0.8172 (t80) REVERT: P 50 THR cc_start: 0.8761 (m) cc_final: 0.8553 (p) REVERT: P 76 LYS cc_start: 0.9719 (ttmm) cc_final: 0.9509 (tptt) REVERT: R 57 ARG cc_start: 0.9369 (mtm-85) cc_final: 0.9145 (mmm160) REVERT: X 143 LYS cc_start: 0.8353 (tptp) cc_final: 0.7931 (mtmm) outliers start: 1 outliers final: 0 residues processed: 602 average time/residue: 0.8443 time to fit residues: 789.0381 Evaluate side-chains 340 residues out of total 2062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 3.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 20.0000 chunk 297 optimal weight: 3.9990 chunk 164 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 200 optimal weight: 5.9990 chunk 158 optimal weight: 30.0000 chunk 307 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 186 optimal weight: 9.9990 chunk 228 optimal weight: 9.9990 chunk 355 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN B 227 GLN C 25 ASN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN C 185 ASN ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 GLN D 140 ASN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 ASN ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 ASN F 14 GLN G 28 ASN G 52 GLN G 68 ASN G 122 ASN ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN ** I 37 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** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 ASN K 40 ASN K 81 ASN K 119 ASN ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 71 HIS O 28 GLN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 GLN O 62 GLN ** P 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 ASN R 19 GLN R 52 GLN ** T 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN T 70 ASN X 47 ASN X 109 ASN ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 56417 Z= 0.361 Angle : 0.764 14.844 83709 Z= 0.400 Chirality : 0.040 0.319 10583 Planarity : 0.007 0.124 4978 Dihedral : 24.551 177.747 26519 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 35.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.61 % Allowed : 20.32 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.16), residues: 2447 helix: -0.95 (0.15), residues: 982 sheet: -1.72 (0.23), residues: 422 loop : -1.34 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 167 HIS 0.010 0.002 HIS X 56 PHE 0.039 0.002 PHE B 184 TYR 0.027 0.002 TYR X 72 ARG 0.013 0.001 ARG I 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 381 time to evaluate : 3.480 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: B 118 GLU cc_start: 0.6788 (pp20) cc_final: 0.6551 (pp20) REVERT: C 193 TYR cc_start: 0.7383 (m-80) cc_final: 0.6900 (m-80) REVERT: D 206 LYS cc_start: 0.9220 (ptmm) cc_final: 0.8671 (ptpp) REVERT: E 12 GLN cc_start: 0.8602 (mp10) cc_final: 0.7924 (pm20) REVERT: E 60 ILE cc_start: 0.9740 (mt) cc_final: 0.9356 (mt) REVERT: E 64 MET cc_start: 0.8879 (mmm) cc_final: 0.8505 (mmm) REVERT: E 96 MET cc_start: 0.8897 (mpp) cc_final: 0.8657 (mpp) REVERT: F 35 LYS cc_start: 0.9567 (mptt) cc_final: 0.9304 (mmtm) REVERT: F 88 MET cc_start: 0.9044 (tpt) cc_final: 0.8235 (tmm) REVERT: F 90 MET cc_start: 0.8856 (mtm) cc_final: 0.8357 (mtp) REVERT: F 93 LYS cc_start: 0.9123 (tttt) cc_final: 0.8778 (tttt) REVERT: G 11 LYS cc_start: 0.6260 (mmtt) cc_final: 0.6013 (mppt) REVERT: G 79 ARG cc_start: 0.7068 (ptp90) cc_final: 0.5167 (mmp80) REVERT: G 113 ASP cc_start: 0.6866 (m-30) cc_final: 0.6636 (p0) REVERT: G 131 LYS cc_start: 0.6794 (pttp) cc_final: 0.6011 (mmmt) REVERT: H 3 MET cc_start: 0.8810 (tmm) cc_final: 0.8168 (tmm) REVERT: H 27 MET cc_start: 0.8588 (ptp) cc_final: 0.7863 (pmm) REVERT: H 80 ARG cc_start: 0.9346 (mtm110) cc_final: 0.8905 (mtp-110) REVERT: H 96 MET cc_start: 0.9074 (mtp) cc_final: 0.8362 (ttp) REVERT: H 121 LEU cc_start: 0.9300 (tp) cc_final: 0.9058 (tp) REVERT: I 88 MET cc_start: 0.6362 (mmt) cc_final: 0.5953 (mmm) REVERT: J 49 PHE cc_start: 0.8829 (m-80) cc_final: 0.8553 (m-80) REVERT: K 56 ARG cc_start: 0.8836 (ttp-110) cc_final: 0.8325 (ptp-170) REVERT: K 110 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8799 (tp) REVERT: L 38 TYR cc_start: 0.9028 (p90) cc_final: 0.8782 (p90) REVERT: L 66 TYR cc_start: 0.8472 (t80) cc_final: 0.7928 (t80) REVERT: L 117 TYR cc_start: 0.8406 (m-80) cc_final: 0.8004 (m-80) REVERT: N 86 GLU cc_start: 0.9622 (mp0) cc_final: 0.9405 (mp0) REVERT: O 59 MET cc_start: 0.9093 (mtm) cc_final: 0.8196 (mtm) REVERT: P 76 LYS cc_start: 0.9632 (ttmm) cc_final: 0.9412 (tptt) REVERT: Q 11 ARG cc_start: 0.8803 (ttp80) cc_final: 0.8602 (ttp80) outliers start: 95 outliers final: 51 residues processed: 439 average time/residue: 0.7507 time to fit residues: 520.5987 Evaluate side-chains 366 residues out of total 2062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 314 time to evaluate : 3.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 124 GLU Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain N residue 77 PHE Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 49 GLU Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 53 CYS Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain S residue 57 HIS Chi-restraints excluded: chain X residue 22 GLU Chi-restraints excluded: chain X residue 91 TYR Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 145 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 296 optimal weight: 8.9990 chunk 242 optimal weight: 9.9990 chunk 98 optimal weight: 30.0000 chunk 356 optimal weight: 4.9990 chunk 385 optimal weight: 5.9990 chunk 317 optimal weight: 10.0000 chunk 353 optimal weight: 10.0000 chunk 121 optimal weight: 20.0000 chunk 286 optimal weight: 2.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS B 51 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 HIS ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN O 35 GLN ** P 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 109 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 56417 Z= 0.309 Angle : 0.681 13.836 83709 Z= 0.362 Chirality : 0.037 0.368 10583 Planarity : 0.006 0.125 4978 Dihedral : 24.442 178.909 26519 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 32.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.00 % Allowed : 21.68 % Favored : 73.33 % 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: 2447 helix: -0.39 (0.15), residues: 989 sheet: -1.66 (0.23), residues: 429 loop : -1.16 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 167 HIS 0.008 0.001 HIS X 56 PHE 0.019 0.002 PHE C 37 TYR 0.016 0.002 TYR D 51 ARG 0.011 0.001 ARG P 31 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 349 time to evaluate : 3.267 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: C 193 TYR cc_start: 0.7404 (m-80) cc_final: 0.6862 (m-80) REVERT: C 211 MET cc_start: 0.3966 (tpt) cc_final: 0.3427 (tpt) REVERT: D 62 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8212 (ttp-170) REVERT: D 75 TYR cc_start: 0.9059 (m-80) cc_final: 0.8451 (m-80) REVERT: D 105 MET cc_start: 0.9411 (mtp) cc_final: 0.8953 (mtp) REVERT: E 54 ARG cc_start: 0.8525 (tpp80) cc_final: 0.8124 (tpm170) REVERT: E 60 ILE cc_start: 0.9737 (mt) cc_final: 0.9276 (mt) REVERT: E 64 MET cc_start: 0.9069 (mmm) cc_final: 0.8837 (mmm) REVERT: E 66 LYS cc_start: 0.9492 (mtpp) cc_final: 0.9154 (mtmm) REVERT: E 97 GLN cc_start: 0.9068 (tt0) cc_final: 0.8278 (pt0) REVERT: E 148 ASN cc_start: 0.9051 (OUTLIER) cc_final: 0.8690 (t0) REVERT: F 5 GLU cc_start: 0.8389 (tm-30) cc_final: 0.7741 (tm-30) REVERT: F 79 ARG cc_start: 0.8868 (ttp80) cc_final: 0.8425 (ptm-80) REVERT: F 80 PHE cc_start: 0.9342 (t80) cc_final: 0.8984 (m-80) REVERT: F 88 MET cc_start: 0.8977 (tpt) cc_final: 0.8198 (tmm) REVERT: F 90 MET cc_start: 0.8750 (mtm) cc_final: 0.8491 (mtp) REVERT: F 93 LYS cc_start: 0.9108 (tttt) cc_final: 0.8740 (tttt) REVERT: H 3 MET cc_start: 0.8845 (tmm) cc_final: 0.8449 (tmm) REVERT: H 27 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.7996 (pmm) REVERT: H 121 LEU cc_start: 0.9285 (tp) cc_final: 0.8948 (tp) REVERT: I 46 MET cc_start: 0.8686 (mmm) cc_final: 0.8470 (mmm) REVERT: I 88 MET cc_start: 0.6461 (mmt) cc_final: 0.4580 (mmm) REVERT: I 92 GLU cc_start: 0.6662 (mm-30) cc_final: 0.6438 (mm-30) REVERT: I 112 GLU cc_start: 0.7542 (tt0) cc_final: 0.7022 (tp30) REVERT: J 49 PHE cc_start: 0.8725 (m-80) cc_final: 0.8354 (m-80) REVERT: K 56 ARG cc_start: 0.8794 (ttp-110) cc_final: 0.8327 (ptp-170) REVERT: K 101 ASN cc_start: 0.9465 (t0) cc_final: 0.9198 (t0) REVERT: K 126 LYS cc_start: 0.8649 (mmmt) cc_final: 0.8169 (mmtt) REVERT: L 112 GLN cc_start: 0.8651 (mt0) cc_final: 0.8183 (mp-120) REVERT: L 117 TYR cc_start: 0.8444 (m-80) cc_final: 0.8159 (m-80) REVERT: N 86 GLU cc_start: 0.9541 (mp0) cc_final: 0.9333 (mp0) REVERT: P 47 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7144 (mp0) REVERT: P 76 LYS cc_start: 0.9652 (ttmm) cc_final: 0.9319 (ttpp) REVERT: R 67 LEU cc_start: 0.9818 (mm) cc_final: 0.9517 (mp) REVERT: X 21 PHE cc_start: 0.8996 (OUTLIER) cc_final: 0.8790 (m-10) REVERT: X 105 MET cc_start: 0.6776 (OUTLIER) cc_final: 0.6454 (pmm) outliers start: 103 outliers final: 61 residues processed: 419 average time/residue: 0.7198 time to fit residues: 479.4970 Evaluate side-chains 365 residues out of total 2062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 299 time to evaluate : 3.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 27 MET Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 39 GLU Chi-restraints excluded: chain N residue 77 PHE Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 49 GLU Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 53 CYS Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain S residue 57 HIS Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 81 ARG Chi-restraints excluded: chain X residue 21 PHE Chi-restraints excluded: chain X residue 22 GLU Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 91 TYR Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 145 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 1.9990 chunk 268 optimal weight: 8.9990 chunk 185 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 170 optimal weight: 40.0000 chunk 239 optimal weight: 20.0000 chunk 357 optimal weight: 10.0000 chunk 378 optimal weight: 0.0980 chunk 186 optimal weight: 0.9980 chunk 339 optimal weight: 0.7980 chunk 102 optimal weight: 30.0000 overall best weight: 2.5784 ------------------------------------------------------------------------------- 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** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 109 ASN X 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 56417 Z= 0.170 Angle : 0.599 12.997 83709 Z= 0.322 Chirality : 0.033 0.338 10583 Planarity : 0.005 0.117 4978 Dihedral : 24.194 179.881 26519 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 24.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.93 % Allowed : 22.50 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.16), residues: 2447 helix: 0.08 (0.16), residues: 995 sheet: -1.39 (0.23), residues: 433 loop : -1.00 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 167 HIS 0.008 0.001 HIS X 56 PHE 0.022 0.001 PHE C 37 TYR 0.021 0.001 TYR H 128 ARG 0.007 0.001 ARG L 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 358 time to evaluate : 3.234 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: B 126 PHE cc_start: 0.5370 (m-10) cc_final: 0.4983 (m-10) REVERT: C 193 TYR cc_start: 0.7338 (m-80) cc_final: 0.6759 (m-80) REVERT: D 75 TYR cc_start: 0.9033 (m-80) cc_final: 0.8422 (m-80) REVERT: D 105 MET cc_start: 0.9309 (mtp) cc_final: 0.8800 (mtp) REVERT: D 206 LYS cc_start: 0.9141 (ptmm) cc_final: 0.8512 (ptpp) REVERT: E 54 ARG cc_start: 0.8617 (tpp80) cc_final: 0.8270 (tpm170) REVERT: E 60 ILE cc_start: 0.9743 (mt) cc_final: 0.9368 (mt) REVERT: E 64 MET cc_start: 0.9068 (mmm) cc_final: 0.8807 (mmm) REVERT: E 65 GLU cc_start: 0.8990 (tp30) cc_final: 0.8703 (tp30) REVERT: E 66 LYS cc_start: 0.9549 (mtpp) cc_final: 0.9165 (mtmm) REVERT: E 71 MET cc_start: 0.9172 (tpp) cc_final: 0.8053 (tpp) REVERT: F 5 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7684 (tm-30) REVERT: F 17 GLN cc_start: 0.9480 (tp-100) cc_final: 0.8599 (tp-100) REVERT: F 21 MET cc_start: 0.9644 (OUTLIER) cc_final: 0.8859 (mpp) REVERT: F 35 LYS cc_start: 0.9584 (mptt) cc_final: 0.9223 (mmtm) REVERT: F 80 PHE cc_start: 0.9315 (t80) cc_final: 0.9078 (m-80) REVERT: F 88 MET cc_start: 0.8957 (tpt) cc_final: 0.8209 (tmm) REVERT: F 93 LYS cc_start: 0.9034 (tttt) cc_final: 0.8745 (tttt) REVERT: H 3 MET cc_start: 0.8834 (tmm) cc_final: 0.8402 (tmm) REVERT: H 27 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.7979 (pmm) REVERT: H 80 ARG cc_start: 0.9166 (mtm110) cc_final: 0.8702 (mtp-110) REVERT: H 86 TYR cc_start: 0.8722 (m-80) cc_final: 0.8500 (m-80) REVERT: H 96 MET cc_start: 0.9110 (mtp) cc_final: 0.8494 (ttp) REVERT: H 121 LEU cc_start: 0.9249 (tp) cc_final: 0.8865 (tp) REVERT: I 88 MET cc_start: 0.6430 (mmt) cc_final: 0.4437 (mmt) REVERT: I 112 GLU cc_start: 0.7397 (tt0) cc_final: 0.6940 (tp30) REVERT: J 44 THR cc_start: 0.7160 (p) cc_final: 0.6751 (t) REVERT: J 49 PHE cc_start: 0.8760 (m-80) cc_final: 0.8321 (m-80) REVERT: K 56 ARG cc_start: 0.8838 (ttp-110) cc_final: 0.8292 (ptp-170) REVERT: K 101 ASN cc_start: 0.9492 (t0) cc_final: 0.9246 (t0) REVERT: K 127 ARG cc_start: 0.7659 (mtp-110) cc_final: 0.7415 (mmp80) REVERT: L 49 LEU cc_start: 0.6929 (mt) cc_final: 0.6521 (mt) REVERT: L 117 TYR cc_start: 0.8199 (m-80) cc_final: 0.7943 (m-80) REVERT: M 47 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6531 (pm20) REVERT: N 79 LEU cc_start: 0.8397 (tp) cc_final: 0.7888 (tt) REVERT: N 86 GLU cc_start: 0.9521 (mp0) cc_final: 0.9259 (mp0) REVERT: O 59 MET cc_start: 0.9065 (mtm) cc_final: 0.8552 (mtm) REVERT: P 47 GLU cc_start: 0.7840 (mt-10) cc_final: 0.6967 (mp0) REVERT: P 76 LYS cc_start: 0.9622 (ttmm) cc_final: 0.9148 (ttpp) REVERT: P 80 LYS cc_start: 0.9307 (mmtt) cc_final: 0.9091 (mmtp) REVERT: R 67 LEU cc_start: 0.9789 (mm) cc_final: 0.9531 (mp) REVERT: X 105 MET cc_start: 0.6392 (OUTLIER) cc_final: 0.6134 (pmm) outliers start: 81 outliers final: 51 residues processed: 410 average time/residue: 0.7003 time to fit residues: 460.4163 Evaluate side-chains 366 residues out of total 2062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 311 time to evaluate : 3.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 27 MET Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 124 GLU Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 39 GLU Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain S residue 57 HIS Chi-restraints excluded: chain S residue 81 ARG Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 22 GLU Chi-restraints excluded: chain X residue 44 ASP Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain X residue 146 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 282 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 323 optimal weight: 20.0000 chunk 261 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 193 optimal weight: 7.9990 chunk 340 optimal weight: 9.9990 chunk 95 optimal weight: 20.0000 overall best weight: 5.5188 ------------------------------------------------------------------------------- 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** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 ASN ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN ** M 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 109 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 56417 Z= 0.264 Angle : 0.643 13.255 83709 Z= 0.342 Chirality : 0.035 0.331 10583 Planarity : 0.006 0.121 4978 Dihedral : 24.243 178.430 26519 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 31.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.95 % Allowed : 22.60 % Favored : 72.45 % 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 (0.16), residues: 2447 helix: 0.04 (0.16), residues: 998 sheet: -1.36 (0.24), residues: 428 loop : -0.95 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 167 HIS 0.007 0.001 HIS L 72 PHE 0.035 0.002 PHE F 78 TYR 0.012 0.002 TYR L 38 ARG 0.008 0.001 ARG L 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 327 time to evaluate : 3.347 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: C 193 TYR cc_start: 0.7438 (m-80) cc_final: 0.6800 (m-80) REVERT: D 75 TYR cc_start: 0.9102 (m-80) cc_final: 0.8468 (m-80) REVERT: D 105 MET cc_start: 0.9326 (mtp) cc_final: 0.8825 (mtp) REVERT: D 206 LYS cc_start: 0.9267 (ptmm) cc_final: 0.8654 (ptpp) REVERT: E 54 ARG cc_start: 0.8716 (tpp80) cc_final: 0.8421 (tpm170) REVERT: E 61 GLN cc_start: 0.9470 (OUTLIER) cc_final: 0.8811 (tp-100) REVERT: E 65 GLU cc_start: 0.9050 (tp30) cc_final: 0.8787 (tp30) REVERT: E 66 LYS cc_start: 0.9533 (mtpp) cc_final: 0.9148 (mtmm) REVERT: E 71 MET cc_start: 0.9266 (tpp) cc_final: 0.8549 (tpp) REVERT: E 148 ASN cc_start: 0.9071 (OUTLIER) cc_final: 0.8651 (t0) REVERT: F 5 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8177 (tm-30) REVERT: F 17 GLN cc_start: 0.9577 (tp-100) cc_final: 0.8670 (tp-100) REVERT: F 21 MET cc_start: 0.9656 (OUTLIER) cc_final: 0.9040 (mmm) REVERT: F 35 LYS cc_start: 0.9622 (mptt) cc_final: 0.9245 (mmtm) REVERT: F 80 PHE cc_start: 0.9295 (t80) cc_final: 0.9074 (m-80) REVERT: F 88 MET cc_start: 0.9004 (tpt) cc_final: 0.8215 (tmm) REVERT: F 90 MET cc_start: 0.8626 (mtp) cc_final: 0.8420 (mtp) REVERT: F 93 LYS cc_start: 0.9116 (tttt) cc_final: 0.8820 (tttt) REVERT: H 3 MET cc_start: 0.8809 (tmm) cc_final: 0.8382 (tmm) REVERT: H 27 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.7988 (pmm) REVERT: H 96 MET cc_start: 0.9147 (mtp) cc_final: 0.8559 (ttp) REVERT: H 121 LEU cc_start: 0.9307 (tp) cc_final: 0.8927 (tp) REVERT: I 88 MET cc_start: 0.6203 (mmt) cc_final: 0.5633 (tpp) REVERT: I 115 LYS cc_start: 0.9396 (mmtt) cc_final: 0.8560 (mmtt) REVERT: J 49 PHE cc_start: 0.8734 (m-80) cc_final: 0.8322 (m-80) REVERT: J 82 LYS cc_start: 0.8393 (pttp) cc_final: 0.8087 (pttp) REVERT: K 56 ARG cc_start: 0.8825 (ttp-110) cc_final: 0.8291 (ptp-170) REVERT: K 101 ASN cc_start: 0.9479 (t0) cc_final: 0.9250 (t0) REVERT: K 125 LYS cc_start: 0.8182 (pttt) cc_final: 0.7968 (pttt) REVERT: L 20 ASN cc_start: 0.9435 (p0) cc_final: 0.9193 (p0) REVERT: L 49 LEU cc_start: 0.7080 (mt) cc_final: 0.6748 (mt) REVERT: L 117 TYR cc_start: 0.8416 (m-80) cc_final: 0.8101 (m-80) REVERT: M 47 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.6676 (pm20) REVERT: N 79 LEU cc_start: 0.8621 (tp) cc_final: 0.8399 (tp) REVERT: N 86 GLU cc_start: 0.9520 (mp0) cc_final: 0.9269 (mp0) REVERT: P 47 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7187 (mp0) REVERT: P 76 LYS cc_start: 0.9620 (ttmm) cc_final: 0.9074 (ttpp) REVERT: P 80 LYS cc_start: 0.9380 (mmtt) cc_final: 0.9102 (mmtp) REVERT: R 67 LEU cc_start: 0.9802 (mm) cc_final: 0.9599 (mp) REVERT: X 105 MET cc_start: 0.6441 (OUTLIER) cc_final: 0.6148 (pmm) outliers start: 102 outliers final: 67 residues processed: 395 average time/residue: 0.6985 time to fit residues: 443.6562 Evaluate side-chains 369 residues out of total 2062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 296 time to evaluate : 3.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain H residue 27 MET Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain N residue 39 GLU Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 77 PHE Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 59 HIS Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 53 CYS Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain S residue 57 HIS Chi-restraints excluded: chain S residue 81 ARG Chi-restraints excluded: chain X residue 22 GLU Chi-restraints excluded: chain X residue 44 ASP Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 72 TYR Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 89 GLU Chi-restraints excluded: chain X residue 91 TYR Chi-restraints excluded: chain X residue 100 THR Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 145 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 20.0000 chunk 341 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 222 optimal weight: 8.9990 chunk 93 optimal weight: 30.0000 chunk 379 optimal weight: 8.9990 chunk 314 optimal weight: 30.0000 chunk 175 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 125 optimal weight: 20.0000 chunk 199 optimal weight: 20.0000 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 109 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 56417 Z= 0.400 Angle : 0.749 13.602 83709 Z= 0.392 Chirality : 0.039 0.339 10583 Planarity : 0.006 0.121 4978 Dihedral : 24.469 176.374 26519 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 39.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 5.82 % Allowed : 22.74 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.16), residues: 2447 helix: -0.28 (0.15), residues: 985 sheet: -1.46 (0.23), residues: 433 loop : -1.11 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 167 HIS 0.011 0.002 HIS L 72 PHE 0.023 0.002 PHE B 126 TYR 0.023 0.002 TYR J 65 ARG 0.016 0.001 ARG G 138 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 307 time to evaluate : 2.983 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: C 55 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7218 (pt) REVERT: C 193 TYR cc_start: 0.7502 (m-80) cc_final: 0.7257 (m-80) REVERT: D 75 TYR cc_start: 0.9092 (m-80) cc_final: 0.8477 (m-80) REVERT: D 105 MET cc_start: 0.9397 (mtp) cc_final: 0.8908 (mtp) REVERT: E 54 ARG cc_start: 0.8758 (tpp80) cc_final: 0.8509 (tpp80) REVERT: E 60 ILE cc_start: 0.9698 (mt) cc_final: 0.9346 (pt) REVERT: E 61 GLN cc_start: 0.9210 (OUTLIER) cc_final: 0.8949 (tp-100) REVERT: E 66 LYS cc_start: 0.9450 (mtpp) cc_final: 0.9092 (mtmm) REVERT: E 68 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.9029 (mmt90) REVERT: E 71 MET cc_start: 0.9211 (tpp) cc_final: 0.8786 (tpp) REVERT: E 72 ILE cc_start: 0.9359 (pt) cc_final: 0.8651 (mp) REVERT: E 97 GLN cc_start: 0.9116 (tt0) cc_final: 0.8377 (pt0) REVERT: E 148 ASN cc_start: 0.9073 (OUTLIER) cc_final: 0.8661 (t0) REVERT: F 5 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8255 (tm-30) REVERT: F 35 LYS cc_start: 0.9654 (mptt) cc_final: 0.9420 (mmtm) REVERT: F 88 MET cc_start: 0.9038 (tpt) cc_final: 0.8112 (tmm) REVERT: F 90 MET cc_start: 0.8725 (mtp) cc_final: 0.8518 (mtp) REVERT: F 98 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8375 (tm-30) REVERT: H 27 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.7968 (pmm) REVERT: H 96 MET cc_start: 0.9166 (mtp) cc_final: 0.8640 (ttp) REVERT: H 121 LEU cc_start: 0.9388 (tp) cc_final: 0.9161 (tp) REVERT: I 88 MET cc_start: 0.6531 (mmt) cc_final: 0.5794 (tpt) REVERT: I 115 LYS cc_start: 0.9412 (mmtt) cc_final: 0.8517 (mmtt) REVERT: J 49 PHE cc_start: 0.8656 (m-80) cc_final: 0.8226 (m-80) REVERT: K 110 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8945 (tp) REVERT: L 112 GLN cc_start: 0.8748 (mt0) cc_final: 0.8234 (mp10) REVERT: L 117 TYR cc_start: 0.8551 (m-80) cc_final: 0.8192 (m-80) REVERT: M 47 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.6793 (pm20) REVERT: N 79 LEU cc_start: 0.8734 (tp) cc_final: 0.8469 (tp) REVERT: N 82 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8467 (mm) REVERT: N 86 GLU cc_start: 0.9503 (mp0) cc_final: 0.9301 (mp0) REVERT: O 59 MET cc_start: 0.9192 (mtm) cc_final: 0.8833 (mtm) REVERT: P 47 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7382 (mp0) REVERT: P 76 LYS cc_start: 0.9625 (ttmm) cc_final: 0.9153 (ttpp) REVERT: P 80 LYS cc_start: 0.9475 (mmtt) cc_final: 0.9145 (mmtp) REVERT: Q 52 GLU cc_start: 0.9269 (OUTLIER) cc_final: 0.8978 (pt0) REVERT: S 23 VAL cc_start: 0.7423 (t) cc_final: 0.7033 (p) REVERT: X 42 SER cc_start: 0.8686 (OUTLIER) cc_final: 0.7988 (p) REVERT: X 50 ASP cc_start: 0.9325 (OUTLIER) cc_final: 0.8871 (p0) REVERT: X 56 HIS cc_start: 0.9208 (OUTLIER) cc_final: 0.8592 (p-80) outliers start: 120 outliers final: 81 residues processed: 391 average time/residue: 0.6999 time to fit residues: 440.1598 Evaluate side-chains 383 residues out of total 2062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 290 time to evaluate : 3.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 27 MET Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 24 HIS Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain N residue 39 GLU Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 59 HIS Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 49 GLU Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 53 CYS Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain S residue 57 HIS Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 81 ARG Chi-restraints excluded: chain T residue 6 SER Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 22 GLU Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 44 ASP Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 56 HIS Chi-restraints excluded: chain X residue 72 TYR Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 89 GLU Chi-restraints excluded: chain X residue 91 TYR Chi-restraints excluded: chain X residue 100 THR Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain X residue 146 LEU Chi-restraints excluded: chain X residue 149 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 8.9990 chunk 42 optimal weight: 20.0000 chunk 216 optimal weight: 5.9990 chunk 276 optimal weight: 7.9990 chunk 214 optimal weight: 6.9990 chunk 319 optimal weight: 10.0000 chunk 211 optimal weight: 8.9990 chunk 377 optimal weight: 5.9990 chunk 236 optimal weight: 5.9990 chunk 230 optimal weight: 9.9990 chunk 174 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 GLN ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN N 35 ASN ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 109 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 56417 Z= 0.279 Angle : 0.669 13.448 83709 Z= 0.354 Chirality : 0.036 0.326 10583 Planarity : 0.006 0.120 4978 Dihedral : 24.389 176.793 26519 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 33.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.09 % Allowed : 24.20 % Favored : 70.71 % 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: -1.29 (0.16), residues: 2447 helix: -0.26 (0.15), residues: 1002 sheet: -1.32 (0.24), residues: 433 loop : -1.09 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 42 HIS 0.009 0.001 HIS L 72 PHE 0.032 0.002 PHE B 126 TYR 0.022 0.002 TYR J 65 ARG 0.007 0.001 ARG S 3 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 318 time to evaluate : 3.031 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: 0.0560 (mmm) cc_final: -0.0454 (mmt) REVERT: C 55 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.6985 (pt) REVERT: C 193 TYR cc_start: 0.7346 (m-80) cc_final: 0.7104 (m-80) REVERT: D 75 TYR cc_start: 0.9079 (m-80) cc_final: 0.8477 (m-80) REVERT: D 105 MET cc_start: 0.9350 (mtp) cc_final: 0.8844 (mtp) REVERT: D 206 LYS cc_start: 0.9298 (ptmm) cc_final: 0.8733 (ptpp) REVERT: E 54 ARG cc_start: 0.8793 (tpp80) cc_final: 0.8544 (tpp80) REVERT: E 61 GLN cc_start: 0.9430 (OUTLIER) cc_final: 0.9161 (tp-100) REVERT: E 66 LYS cc_start: 0.9523 (mtpp) cc_final: 0.9220 (mtmm) REVERT: E 68 ARG cc_start: 0.9395 (OUTLIER) cc_final: 0.9066 (mmt90) REVERT: E 71 MET cc_start: 0.9190 (tpp) cc_final: 0.8533 (tpp) REVERT: E 142 ASP cc_start: 0.8856 (p0) cc_final: 0.8563 (p0) REVERT: E 148 ASN cc_start: 0.9123 (OUTLIER) cc_final: 0.8748 (t0) REVERT: F 1 MET cc_start: 0.9160 (tpt) cc_final: 0.8956 (tpp) REVERT: F 5 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8203 (tm-30) REVERT: F 35 LYS cc_start: 0.9653 (mptt) cc_final: 0.9425 (mmtm) REVERT: F 79 ARG cc_start: 0.8834 (ttp80) cc_final: 0.8316 (ptm-80) REVERT: F 80 PHE cc_start: 0.9287 (t80) cc_final: 0.8997 (m-80) REVERT: F 88 MET cc_start: 0.9044 (tpt) cc_final: 0.8128 (tmm) REVERT: F 93 LYS cc_start: 0.9135 (tttt) cc_final: 0.8866 (tttt) REVERT: F 98 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8810 (mp0) REVERT: G 15 ASP cc_start: 0.2139 (OUTLIER) cc_final: 0.1857 (t0) REVERT: H 3 MET cc_start: 0.8691 (tmm) cc_final: 0.8444 (tmm) REVERT: H 27 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.7920 (pmm) REVERT: H 96 MET cc_start: 0.9163 (mtp) cc_final: 0.8605 (ttp) REVERT: H 121 LEU cc_start: 0.9369 (tp) cc_final: 0.9132 (tp) REVERT: I 88 MET cc_start: 0.6600 (mmt) cc_final: 0.5911 (tpt) REVERT: I 115 LYS cc_start: 0.9404 (mmtt) cc_final: 0.8518 (mmtt) REVERT: J 49 PHE cc_start: 0.8649 (m-80) cc_final: 0.8196 (m-80) REVERT: K 126 LYS cc_start: 0.8600 (mmmt) cc_final: 0.7997 (mmtm) REVERT: L 112 GLN cc_start: 0.8772 (mt0) cc_final: 0.8245 (mp10) REVERT: L 117 TYR cc_start: 0.8363 (m-80) cc_final: 0.8078 (m-80) REVERT: M 47 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.6581 (pm20) REVERT: N 79 LEU cc_start: 0.8685 (tp) cc_final: 0.8407 (tp) REVERT: N 86 GLU cc_start: 0.9452 (mp0) cc_final: 0.9234 (mp0) REVERT: O 59 MET cc_start: 0.9155 (mtm) cc_final: 0.8843 (mtm) REVERT: P 47 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7302 (mp0) REVERT: P 76 LYS cc_start: 0.9633 (ttmm) cc_final: 0.9160 (ttpp) REVERT: P 80 LYS cc_start: 0.9459 (mmtt) cc_final: 0.9136 (mmtp) REVERT: Q 17 MET cc_start: 0.8103 (pmm) cc_final: 0.7738 (pmm) REVERT: S 23 VAL cc_start: 0.7441 (t) cc_final: 0.7052 (p) REVERT: X 42 SER cc_start: 0.8778 (OUTLIER) cc_final: 0.8152 (p) REVERT: X 56 HIS cc_start: 0.9209 (OUTLIER) cc_final: 0.8561 (p90) REVERT: X 105 MET cc_start: 0.6737 (OUTLIER) cc_final: 0.6480 (pmm) REVERT: X 124 MET cc_start: 0.9211 (tmm) cc_final: 0.8561 (tmm) outliers start: 105 outliers final: 76 residues processed: 395 average time/residue: 0.7375 time to fit residues: 475.3880 Evaluate side-chains 378 residues out of total 2062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 292 time to evaluate : 3.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 27 MET Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 24 HIS Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain N residue 39 GLU Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 59 HIS Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 53 CYS Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain S residue 57 HIS Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 81 ARG Chi-restraints excluded: chain T residue 6 SER Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 22 GLU Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 44 ASP Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 56 HIS Chi-restraints excluded: chain X residue 72 TYR Chi-restraints excluded: chain X residue 86 PHE Chi-restraints excluded: chain X residue 89 GLU Chi-restraints excluded: chain X residue 91 TYR Chi-restraints excluded: chain X residue 100 THR Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain X residue 146 LEU Chi-restraints excluded: chain X residue 149 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 225 optimal weight: 0.7980 chunk 113 optimal weight: 30.0000 chunk 74 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 chunk 257 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 296 optimal weight: 30.0000 overall best weight: 5.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 GLN ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 56417 Z= 0.259 Angle : 0.657 13.508 83709 Z= 0.349 Chirality : 0.035 0.316 10583 Planarity : 0.006 0.120 4978 Dihedral : 24.307 176.250 26519 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 31.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.95 % Allowed : 24.78 % Favored : 70.27 % 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: -1.23 (0.16), residues: 2447 helix: -0.19 (0.16), residues: 1008 sheet: -1.24 (0.24), residues: 431 loop : -1.12 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 42 HIS 0.008 0.001 HIS L 72 PHE 0.033 0.002 PHE B 126 TYR 0.021 0.002 TYR J 65 ARG 0.007 0.001 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 319 time to evaluate : 3.056 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: B 27 MET cc_start: 0.0305 (mmm) cc_final: -0.0891 (mmt) REVERT: C 55 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.6924 (pt) REVERT: C 193 TYR cc_start: 0.7242 (m-80) cc_final: 0.6997 (m-80) REVERT: D 75 TYR cc_start: 0.9063 (m-80) cc_final: 0.8512 (m-80) REVERT: D 105 MET cc_start: 0.9329 (mtp) cc_final: 0.8813 (mtp) REVERT: D 206 LYS cc_start: 0.9267 (ptmm) cc_final: 0.8683 (ptpp) REVERT: E 61 GLN cc_start: 0.9459 (OUTLIER) cc_final: 0.9195 (tp-100) REVERT: E 66 LYS cc_start: 0.9558 (mtpp) cc_final: 0.9226 (mtmm) REVERT: E 71 MET cc_start: 0.9199 (tpp) cc_final: 0.8702 (tpp) REVERT: E 148 ASN cc_start: 0.9136 (OUTLIER) cc_final: 0.8730 (t0) REVERT: F 1 MET cc_start: 0.9201 (tpt) cc_final: 0.8916 (tpp) REVERT: F 5 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8036 (tm-30) REVERT: F 17 GLN cc_start: 0.9570 (OUTLIER) cc_final: 0.9202 (tp-100) REVERT: F 35 LYS cc_start: 0.9614 (mptt) cc_final: 0.9412 (mmtm) REVERT: F 79 ARG cc_start: 0.8853 (ttp80) cc_final: 0.8359 (ptm-80) REVERT: F 80 PHE cc_start: 0.9275 (t80) cc_final: 0.8972 (m-80) REVERT: F 88 MET cc_start: 0.8994 (tpt) cc_final: 0.8159 (tmm) REVERT: F 93 LYS cc_start: 0.9125 (tttt) cc_final: 0.8834 (tttt) REVERT: G 79 ARG cc_start: 0.6218 (ptp90) cc_final: 0.5267 (ptm160) REVERT: H 3 MET cc_start: 0.8686 (tmm) cc_final: 0.8191 (tmm) REVERT: H 27 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7939 (pmm) REVERT: H 96 MET cc_start: 0.9153 (mtp) cc_final: 0.8595 (ttp) REVERT: H 121 LEU cc_start: 0.9335 (tp) cc_final: 0.9071 (tp) REVERT: I 88 MET cc_start: 0.6685 (mmt) cc_final: 0.5975 (tpt) REVERT: I 115 LYS cc_start: 0.9390 (mmtt) cc_final: 0.8543 (mmtt) REVERT: J 49 PHE cc_start: 0.8641 (m-80) cc_final: 0.8152 (m-80) REVERT: K 125 LYS cc_start: 0.8101 (pttt) cc_final: 0.7800 (pttt) REVERT: K 126 LYS cc_start: 0.8640 (mmmt) cc_final: 0.8088 (mmtm) REVERT: L 49 LEU cc_start: 0.7808 (mt) cc_final: 0.7569 (mp) REVERT: L 102 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8919 (pp) REVERT: L 112 GLN cc_start: 0.8764 (mt0) cc_final: 0.8232 (mp10) REVERT: M 47 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6553 (pm20) REVERT: N 79 LEU cc_start: 0.8616 (tp) cc_final: 0.8330 (tp) REVERT: N 82 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8444 (mm) REVERT: O 59 MET cc_start: 0.9139 (mtm) cc_final: 0.8843 (mtm) REVERT: P 1 MET cc_start: 0.7998 (tpp) cc_final: 0.7022 (tpp) REVERT: P 76 LYS cc_start: 0.9626 (ttmm) cc_final: 0.9144 (ttpp) REVERT: P 80 LYS cc_start: 0.9450 (mmtt) cc_final: 0.9124 (mmtp) REVERT: S 23 VAL cc_start: 0.7453 (t) cc_final: 0.7071 (p) REVERT: X 50 ASP cc_start: 0.9341 (OUTLIER) cc_final: 0.8798 (p0) REVERT: X 56 HIS cc_start: 0.9227 (OUTLIER) cc_final: 0.8602 (p90) REVERT: X 124 MET cc_start: 0.9255 (tmm) cc_final: 0.8630 (tmm) outliers start: 102 outliers final: 83 residues processed: 388 average time/residue: 0.6865 time to fit residues: 428.6469 Evaluate side-chains 394 residues out of total 2062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 301 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 27 MET Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 24 HIS Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain N residue 39 GLU Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 77 PHE Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 59 HIS Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 49 GLU Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 53 CYS Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain S residue 57 HIS Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 81 ARG Chi-restraints excluded: chain T residue 6 SER Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 22 GLU Chi-restraints excluded: chain X residue 44 ASP Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 56 HIS Chi-restraints excluded: chain X residue 72 TYR Chi-restraints excluded: chain X residue 86 PHE Chi-restraints excluded: chain X residue 89 GLU Chi-restraints excluded: chain X residue 91 TYR Chi-restraints excluded: chain X residue 100 THR Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain X residue 146 LEU Chi-restraints excluded: chain X residue 149 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 9.9990 chunk 361 optimal weight: 5.9990 chunk 330 optimal weight: 10.0000 chunk 352 optimal weight: 4.9990 chunk 211 optimal weight: 9.9990 chunk 153 optimal weight: 40.0000 chunk 276 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 318 optimal weight: 4.9990 chunk 332 optimal weight: 0.9990 chunk 350 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 GLN ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 HIS ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 53 ASN ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 109 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 56417 Z= 0.231 Angle : 0.644 13.518 83709 Z= 0.343 Chirality : 0.035 0.306 10583 Planarity : 0.006 0.120 4978 Dihedral : 24.228 176.373 26519 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 29.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.70 % Allowed : 25.65 % Favored : 69.64 % 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: -1.10 (0.17), residues: 2447 helix: -0.11 (0.16), residues: 1001 sheet: -1.16 (0.24), residues: 430 loop : -1.00 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 42 HIS 0.008 0.001 HIS L 72 PHE 0.028 0.002 PHE B 126 TYR 0.019 0.002 TYR J 65 ARG 0.008 0.001 ARG K 56 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 319 time to evaluate : 3.106 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: C 55 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.6916 (pt) REVERT: C 193 TYR cc_start: 0.7175 (m-80) cc_final: 0.6927 (m-80) REVERT: D 75 TYR cc_start: 0.9041 (m-80) cc_final: 0.8521 (m-80) REVERT: D 105 MET cc_start: 0.9294 (mtp) cc_final: 0.8790 (mtp) REVERT: D 121 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8448 (mmtt) REVERT: D 206 LYS cc_start: 0.9275 (ptmm) cc_final: 0.8706 (ptpp) REVERT: E 61 GLN cc_start: 0.9478 (OUTLIER) cc_final: 0.9202 (tp-100) REVERT: E 66 LYS cc_start: 0.9538 (mtpp) cc_final: 0.9219 (mtmm) REVERT: E 71 MET cc_start: 0.9275 (tpp) cc_final: 0.8717 (tpp) REVERT: E 96 MET cc_start: 0.8516 (mpp) cc_final: 0.8114 (mpp) REVERT: E 148 ASN cc_start: 0.9148 (OUTLIER) cc_final: 0.8726 (t0) REVERT: F 1 MET cc_start: 0.9154 (tpt) cc_final: 0.8566 (tpp) REVERT: F 5 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8129 (tm-30) REVERT: F 17 GLN cc_start: 0.9508 (OUTLIER) cc_final: 0.8619 (tp-100) REVERT: F 21 MET cc_start: 0.9638 (tpp) cc_final: 0.8775 (mpp) REVERT: F 35 LYS cc_start: 0.9612 (mptt) cc_final: 0.9411 (mmtm) REVERT: F 79 ARG cc_start: 0.8860 (ttp80) cc_final: 0.8390 (ptm-80) REVERT: F 80 PHE cc_start: 0.9234 (t80) cc_final: 0.8978 (m-80) REVERT: F 88 MET cc_start: 0.8973 (tpt) cc_final: 0.8161 (tmm) REVERT: F 93 LYS cc_start: 0.9107 (tttt) cc_final: 0.8852 (tttt) REVERT: G 79 ARG cc_start: 0.6050 (ptp90) cc_final: 0.4974 (ptm160) REVERT: H 3 MET cc_start: 0.8739 (tmm) cc_final: 0.8235 (tmm) REVERT: H 27 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8012 (pmm) REVERT: H 96 MET cc_start: 0.9154 (mtp) cc_final: 0.8572 (ttp) REVERT: H 121 LEU cc_start: 0.9324 (tp) cc_final: 0.9063 (tp) REVERT: I 88 MET cc_start: 0.6718 (mmt) cc_final: 0.5997 (tpt) REVERT: I 115 LYS cc_start: 0.9379 (mmtt) cc_final: 0.8541 (mmtt) REVERT: I 124 ARG cc_start: 0.8002 (ttp-170) cc_final: 0.7480 (ttp-110) REVERT: J 49 PHE cc_start: 0.8643 (m-80) cc_final: 0.8115 (m-80) REVERT: K 125 LYS cc_start: 0.8048 (pttt) cc_final: 0.7802 (pttt) REVERT: K 126 LYS cc_start: 0.8613 (mmmt) cc_final: 0.8067 (mmtm) REVERT: L 49 LEU cc_start: 0.7781 (mt) cc_final: 0.7486 (mt) REVERT: L 102 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8936 (pp) REVERT: L 112 GLN cc_start: 0.8775 (mt0) cc_final: 0.8249 (mp10) REVERT: M 47 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6726 (pm20) REVERT: M 75 MET cc_start: 0.8945 (ppp) cc_final: 0.8404 (pmm) REVERT: N 79 LEU cc_start: 0.8566 (tp) cc_final: 0.7911 (tt) REVERT: O 59 MET cc_start: 0.9130 (mtm) cc_final: 0.8832 (mtm) REVERT: P 1 MET cc_start: 0.8061 (tpp) cc_final: 0.7173 (tpp) REVERT: P 76 LYS cc_start: 0.9623 (ttmm) cc_final: 0.9146 (ttpp) REVERT: P 80 LYS cc_start: 0.9436 (mmtt) cc_final: 0.9124 (mmtp) REVERT: Q 17 MET cc_start: 0.8253 (pmm) cc_final: 0.7786 (pmm) REVERT: S 23 VAL cc_start: 0.7428 (t) cc_final: 0.7056 (p) REVERT: T 15 GLU cc_start: 0.8411 (tp30) cc_final: 0.8146 (tm-30) REVERT: T 18 ARG cc_start: 0.9439 (ttp80) cc_final: 0.9143 (tmm-80) REVERT: X 42 SER cc_start: 0.8719 (OUTLIER) cc_final: 0.8044 (p) REVERT: X 50 ASP cc_start: 0.9344 (OUTLIER) cc_final: 0.8798 (p0) REVERT: X 56 HIS cc_start: 0.9243 (OUTLIER) cc_final: 0.8634 (p90) REVERT: X 124 MET cc_start: 0.9243 (tmm) cc_final: 0.8609 (tmm) outliers start: 97 outliers final: 77 residues processed: 386 average time/residue: 0.6954 time to fit residues: 428.9733 Evaluate side-chains 391 residues out of total 2062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 302 time to evaluate : 2.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain F residue 5 GLU Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 27 MET Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 24 HIS Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain N residue 39 GLU Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 59 HIS Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 49 GLU Chi-restraints excluded: chain Q residue 53 CYS Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain S residue 53 ASN Chi-restraints excluded: chain S residue 57 HIS Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 81 ARG Chi-restraints excluded: chain T residue 6 SER Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 22 GLU Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 44 ASP Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 56 HIS Chi-restraints excluded: chain X residue 72 TYR Chi-restraints excluded: chain X residue 86 PHE Chi-restraints excluded: chain X residue 89 GLU Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain X residue 146 LEU Chi-restraints excluded: chain X residue 149 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 0.7980 chunk 372 optimal weight: 6.9990 chunk 227 optimal weight: 6.9990 chunk 176 optimal weight: 6.9990 chunk 258 optimal weight: 7.9990 chunk 390 optimal weight: 4.9990 chunk 359 optimal weight: 7.9990 chunk 310 optimal weight: 0.1980 chunk 32 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 GLN ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.287 56417 Z= 0.301 Angle : 0.750 59.200 83709 Z= 0.420 Chirality : 0.037 1.129 10583 Planarity : 0.006 0.160 4978 Dihedral : 24.230 176.371 26519 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 31.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.96 % Favored : 96.00 % Rotamer: Outliers : 4.66 % Allowed : 25.95 % Favored : 69.40 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.17), residues: 2447 helix: -0.11 (0.16), residues: 1001 sheet: -1.17 (0.24), residues: 431 loop : -1.02 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 167 HIS 0.008 0.001 HIS K 22 PHE 0.095 0.002 PHE K 52 TYR 0.023 0.002 TYR I 90 ARG 0.051 0.001 ARG B 222 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 304 time to evaluate : 3.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 55 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.6956 (pt) REVERT: C 193 TYR cc_start: 0.7174 (m-80) cc_final: 0.6920 (m-80) REVERT: D 75 TYR cc_start: 0.9041 (m-80) cc_final: 0.8517 (m-80) REVERT: D 105 MET cc_start: 0.9292 (mtp) cc_final: 0.8768 (mtp) REVERT: D 121 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8447 (mmtt) REVERT: D 206 LYS cc_start: 0.9275 (ptmm) cc_final: 0.8702 (ptpp) REVERT: E 61 GLN cc_start: 0.9478 (OUTLIER) cc_final: 0.9208 (tp-100) REVERT: E 66 LYS cc_start: 0.9536 (mtpp) cc_final: 0.9218 (mtmm) REVERT: E 71 MET cc_start: 0.9270 (tpp) cc_final: 0.8721 (tpp) REVERT: E 96 MET cc_start: 0.8571 (mpp) cc_final: 0.8150 (mpp) REVERT: E 148 ASN cc_start: 0.9150 (OUTLIER) cc_final: 0.8727 (t0) REVERT: F 1 MET cc_start: 0.9153 (tpt) cc_final: 0.8560 (tpp) REVERT: F 5 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8128 (tm-30) REVERT: F 17 GLN cc_start: 0.9363 (OUTLIER) cc_final: 0.8941 (tp40) REVERT: F 21 MET cc_start: 0.9587 (tpp) cc_final: 0.8804 (mpp) REVERT: F 35 LYS cc_start: 0.9611 (mptt) cc_final: 0.9411 (mmtm) REVERT: F 79 ARG cc_start: 0.8859 (ttp80) cc_final: 0.8387 (ptm-80) REVERT: F 80 PHE cc_start: 0.9234 (t80) cc_final: 0.8976 (m-80) REVERT: F 88 MET cc_start: 0.8966 (tpt) cc_final: 0.8160 (tmm) REVERT: F 93 LYS cc_start: 0.9106 (tttt) cc_final: 0.8852 (tttt) REVERT: G 79 ARG cc_start: 0.6052 (ptp90) cc_final: 0.4973 (ptm160) REVERT: H 3 MET cc_start: 0.8736 (tmm) cc_final: 0.8230 (tmm) REVERT: H 27 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8011 (pmm) REVERT: H 96 MET cc_start: 0.9137 (mtp) cc_final: 0.8570 (ttp) REVERT: H 121 LEU cc_start: 0.9322 (tp) cc_final: 0.9058 (tp) REVERT: I 88 MET cc_start: 0.6715 (mmt) cc_final: 0.5996 (tpt) REVERT: I 115 LYS cc_start: 0.9379 (mmtt) cc_final: 0.8528 (mmtt) REVERT: I 124 ARG cc_start: 0.8000 (ttp-170) cc_final: 0.7482 (ttp-110) REVERT: J 49 PHE cc_start: 0.8650 (m-80) cc_final: 0.8114 (m-80) REVERT: K 125 LYS cc_start: 0.8048 (pttt) cc_final: 0.7797 (pttt) REVERT: K 126 LYS cc_start: 0.8634 (mmmt) cc_final: 0.8123 (mmtm) REVERT: L 49 LEU cc_start: 0.7781 (mt) cc_final: 0.7484 (mt) REVERT: L 102 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8935 (pp) REVERT: L 112 GLN cc_start: 0.8775 (mt0) cc_final: 0.8247 (mp10) REVERT: M 47 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6724 (pm20) REVERT: N 79 LEU cc_start: 0.8549 (tp) cc_final: 0.7896 (tt) REVERT: O 59 MET cc_start: 0.9129 (mtm) cc_final: 0.8829 (mtm) REVERT: P 1 MET cc_start: 0.8063 (tpp) cc_final: 0.7184 (tpp) REVERT: P 76 LYS cc_start: 0.9623 (ttmm) cc_final: 0.9143 (ttpp) REVERT: P 80 LYS cc_start: 0.9435 (mmtt) cc_final: 0.9123 (mmtp) REVERT: Q 17 MET cc_start: 0.8252 (pmm) cc_final: 0.7801 (pmm) REVERT: S 23 VAL cc_start: 0.7432 (t) cc_final: 0.7057 (p) REVERT: X 42 SER cc_start: 0.8717 (OUTLIER) cc_final: 0.8043 (p) REVERT: X 50 ASP cc_start: 0.9343 (OUTLIER) cc_final: 0.8798 (p0) REVERT: X 56 HIS cc_start: 0.9243 (OUTLIER) cc_final: 0.8633 (p90) REVERT: X 124 MET cc_start: 0.9243 (tmm) cc_final: 0.8610 (tmm) outliers start: 96 outliers final: 77 residues processed: 369 average time/residue: 0.6745 time to fit residues: 400.6013 Evaluate side-chains 392 residues out of total 2062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 303 time to evaluate : 3.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain F residue 5 GLU Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 27 MET Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 24 HIS Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain N residue 39 GLU Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 59 HIS Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 49 GLU Chi-restraints excluded: chain Q residue 53 CYS Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain S residue 57 HIS Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 81 ARG Chi-restraints excluded: chain T residue 6 SER Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 22 GLU Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 44 ASP Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 56 HIS Chi-restraints excluded: chain X residue 72 TYR Chi-restraints excluded: chain X residue 86 PHE Chi-restraints excluded: chain X residue 89 GLU Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain X residue 146 LEU Chi-restraints excluded: chain X residue 149 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 6.9990 chunk 331 optimal weight: 0.0170 chunk 95 optimal weight: 5.9990 chunk 286 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 311 optimal weight: 7.9990 chunk 130 optimal weight: 30.0000 chunk 319 optimal weight: 0.0980 chunk 39 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 overall best weight: 4.2224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 GLN ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 14 HIS ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.035880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.023733 restraints weight = 628223.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.024474 restraints weight = 269764.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.024886 restraints weight = 172059.511| |-----------------------------------------------------------------------------| r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 56417 Z= 0.219 Angle : 0.640 13.529 83709 Z= 0.341 Chirality : 0.034 0.301 10583 Planarity : 0.006 0.120 4978 Dihedral : 24.186 176.729 26519 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 29.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.51 % Allowed : 26.29 % Favored : 69.20 % 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: -1.07 (0.17), residues: 2447 helix: -0.10 (0.16), residues: 997 sheet: -1.16 (0.24), residues: 421 loop : -0.97 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 167 HIS 0.017 0.001 HIS S 52 PHE 0.030 0.002 PHE B 126 TYR 0.034 0.002 TYR I 90 ARG 0.010 0.001 ARG B 222 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9998.68 seconds wall clock time: 184 minutes 31.84 seconds (11071.84 seconds total)