Starting phenix.real_space_refine on Sun Feb 25 14:25:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boe_12240/02_2024/7boe_12240_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boe_12240/02_2024/7boe_12240.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boe_12240/02_2024/7boe_12240_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boe_12240/02_2024/7boe_12240_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boe_12240/02_2024/7boe_12240_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boe_12240/02_2024/7boe_12240.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boe_12240/02_2024/7boe_12240.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boe_12240/02_2024/7boe_12240_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boe_12240/02_2024/7boe_12240_neut_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1534 5.49 5 Mg 152 5.21 5 S 69 5.16 5 C 26508 2.51 5 N 9673 2.21 5 O 14032 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 51969 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 32930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 32930 Classifications: {'RNA': 1534} Modifications used: {'rna2p': 1, 'rna2p_pur': 114, 'rna2p_pyr': 86, 'rna3p': 10, 'rna3p_pur': 755, 'rna3p_pyr': 568} Link IDs: {'rna2p': 201, 'rna3p': 1332} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1653 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 7, 'TRANS': 203} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "G" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1021 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 803 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "S" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "U" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 430 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "A" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 152 Unusual residues: {' MG': 152} Classifications: {'undetermined': 152} Link IDs: {None: 151} 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: 27.16, per 1000 atoms: 0.52 Number of scatterers: 51969 At special positions: 0 Unit cell: (205.8, 208.95, 175.35, 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 69 16.00 P 1534 15.00 Mg 152 11.99 O 14032 8.00 N 9673 7.00 C 26508 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 29.66 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4448 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 91 helices and 21 sheets defined 39.8% alpha, 15.6% beta 487 base pairs and 911 stacking pairs defined. Time for finding SS restraints: 34.05 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 62 Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 77 through 86 Processing helix chain 'B' and resid 104 through 123 Processing helix chain 'B' and resid 131 through 148 Processing helix chain 'B' and resid 170 through 179 Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 207 through 226 Processing helix chain 'C' and resid 9 through 11 No H-bonds generated for 'chain 'C' and resid 9 through 11' Processing helix chain 'C' and resid 26 through 50 removed outlier: 4.575A pdb=" N ALA C 30 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ASP C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ALA C 50 " --> pdb=" O GLU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 79 through 94 removed outlier: 6.221A pdb=" N ASP C 83 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL C 84 " --> pdb=" O GLY C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 111 No H-bonds generated for 'chain 'C' and resid 109 through 111' Processing helix chain 'C' and resid 113 through 126 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'D' and resid 9 through 15 Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 50 through 65 removed outlier: 3.764A pdb=" N TYR D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 81 Processing helix chain 'D' and resid 86 through 96 removed outlier: 3.544A pdb=" N LEU D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 105 Processing helix chain 'D' and resid 113 through 119 removed outlier: 4.132A pdb=" N VAL D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 149 No H-bonds generated for 'chain 'D' and resid 147 through 149' Processing helix chain 'D' and resid 153 through 164 removed outlier: 3.780A pdb=" N GLU D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 205 removed outlier: 3.926A pdb=" N SER D 205 " --> pdb=" O VAL D 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 67 Processing helix chain 'E' and resid 109 through 118 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 31 removed outlier: 4.748A pdb=" N GLU F 16 " --> pdb=" O ASP F 13 " (cutoff:3.500A) Proline residue: F 19 - end of helix removed outlier: 3.601A pdb=" N ALA F 28 " --> pdb=" O TYR F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 80 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 52 removed outlier: 3.756A pdb=" N ILE G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER G 45 " --> pdb=" O SER G 41 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 66 removed outlier: 3.584A pdb=" N GLU G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 110 removed outlier: 3.866A pdb=" N LYS G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 128 Processing helix chain 'G' and resid 135 through 147 Processing helix chain 'G' and resid 149 through 151 No H-bonds generated for 'chain 'G' and resid 149 through 151' Processing helix chain 'H' and resid 6 through 19 Processing helix chain 'H' and resid 31 through 42 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 113 through 118 Processing helix chain 'I' and resid 35 through 38 No H-bonds generated for 'chain 'I' and resid 35 through 38' Processing helix chain 'I' and resid 43 through 55 Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 72 through 90 Processing helix chain 'I' and resid 95 through 100 Processing helix chain 'J' and resid 15 through 31 removed outlier: 4.260A pdb=" N GLN J 20 " --> pdb=" O ARG J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 88 removed outlier: 4.038A pdb=" N ASP J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET J 88 " --> pdb=" O VAL J 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 77 removed outlier: 4.469A pdb=" N GLU K 76 " --> pdb=" O ASP K 72 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TYR K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 101 Processing helix chain 'L' and resid 4 through 9 Processing helix chain 'L' and resid 22 through 24 No H-bonds generated for 'chain 'L' and resid 22 through 24' Processing helix chain 'L' and resid 114 through 117 No H-bonds generated for 'chain 'L' and resid 114 through 117' 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 62 removed outlier: 4.094A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 83 removed outlier: 3.586A pdb=" N GLU M 72 " --> pdb=" O ASP M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 92 Processing helix chain 'M' and resid 107 through 110 No H-bonds generated for 'chain 'M' and resid 107 through 110' Processing helix chain 'N' and resid 4 through 16 Processing helix chain 'N' and resid 21 through 31 Processing helix chain 'N' and resid 38 through 50 removed outlier: 3.799A pdb=" N GLN N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR N 50 " --> pdb=" O LEU N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 55 No H-bonds generated for 'chain 'N' and resid 53 through 55' Processing helix chain 'N' and resid 57 through 59 No H-bonds generated for 'chain 'N' and resid 57 through 59' Processing helix chain 'N' and resid 81 through 89 Processing helix chain 'O' and resid 5 through 15 Processing helix chain 'O' and resid 25 through 45 removed outlier: 3.735A pdb=" N GLN O 40 " --> pdb=" O ILE O 36 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU O 45 " --> pdb=" O GLY O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 73 removed outlier: 4.057A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 84 Processing helix chain 'P' and resid 54 through 63 removed outlier: 3.593A pdb=" N GLN P 63 " --> pdb=" O HIS P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 81 Processing helix chain 'Q' and resid 49 through 51 No H-bonds generated for 'chain 'Q' and resid 49 through 51' Processing helix chain 'R' and resid 12 through 15 No H-bonds generated for 'chain 'R' and resid 12 through 15' Processing helix chain 'R' and resid 26 through 32 removed outlier: 4.161A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR R 32 " --> pdb=" O THR R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 45 No H-bonds generated for 'chain 'R' and resid 42 through 45' Processing helix chain 'R' and resid 49 through 64 removed outlier: 3.677A pdb=" N GLN R 54 " --> pdb=" O LYS R 50 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.652A pdb=" N SER S 25 " --> pdb=" O LYS S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 44 No H-bonds generated for 'chain 'S' and resid 42 through 44' Processing helix chain 'S' and resid 64 through 66 No H-bonds generated for 'chain 'S' and resid 64 through 66' Processing helix chain 'S' and resid 71 through 73 No H-bonds generated for 'chain 'S' and resid 71 through 73' Processing helix chain 'T' and resid 5 through 38 removed outlier: 3.631A pdb=" N VAL T 35 " --> pdb=" O PHE T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 47 through 63 removed outlier: 3.878A pdb=" N ASN T 52 " --> pdb=" O GLN T 48 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU T 53 " --> pdb=" O LYS T 49 " (cutoff:3.500A) Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 69 through 84 Processing helix chain 'U' and resid 13 through 16 No H-bonds generated for 'chain 'U' and resid 13 through 16' Processing helix chain 'U' and resid 19 through 25 removed outlier: 4.114A pdb=" N GLU U 24 " --> pdb=" O LYS U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 36 removed outlier: 3.510A pdb=" N ARG U 33 " --> pdb=" O LEU U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 57 Processing sheet with id= A, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.696A pdb=" N ALA B 160 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL B 70 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE B 162 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N PHE B 198 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL B 187 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 31 through 35 removed outlier: 6.928A pdb=" N ILE B 40 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 4.432A 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 101 through 105 removed outlier: 6.312A pdb=" N VAL C 66 " --> pdb=" O ASN C 102 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ALA C 104 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE C 68 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 164 through 171 Processing sheet with id= E, first strand: chain 'D' and resid 123 through 125 removed outlier: 4.140A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU D 179 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 46 through 53 removed outlier: 6.648A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 85 through 89 Processing sheet with id= H, first strand: chain 'F' and resid 87 through 92 removed outlier: 3.544A pdb=" N MET F 88 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG F 2 " --> pdb=" O ALA F 66 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 35 through 41 removed outlier: 6.485A pdb=" N ASN F 63 " --> pdb=" O HIS F 37 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU F 39 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU F 61 " --> pdb=" O LEU F 39 " (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 28 removed outlier: 3.642A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 74 through 77 removed outlier: 6.717A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 6.845A 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 12 Processing sheet with id= N, first strand: chain 'J' and resid 96 through 101 removed outlier: 4.449A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU J 42 " --> pdb=" O LEU J 71 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'J' and resid 45 through 52 Processing sheet with id= P, first strand: chain 'K' and resid 41 through 46 removed outlier: 6.756A pdb=" N ILE K 34 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TRP K 44 " --> pdb=" O VAL K 32 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL K 32 " --> pdb=" O TRP K 44 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N THR K 46 " --> pdb=" O THR K 30 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR K 30 " --> pdb=" O THR K 46 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'L' and resid 95 through 97 removed outlier: 6.619A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR L 39 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 5.807A 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 9 removed outlier: 6.611A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'Q' and resid 8 through 11 removed outlier: 9.230A pdb=" N SER Q 72 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N HIS Q 45 " --> pdb=" O SER Q 72 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N THR Q 74 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N HIS Q 47 " --> pdb=" O THR Q 74 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER Q 14 " --> pdb=" O VAL Q 22 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ALA Q 24 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL Q 12 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLU Q 26 " --> pdb=" O GLY Q 10 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLY Q 10 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'Q' and resid 58 through 60 removed outlier: 6.491A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL Q 78 " --> pdb=" O GLU Q 60 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'S' and resid 31 through 33 778 hydrogen bonds defined for protein. 2187 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1206 hydrogen bonds 1908 hydrogen bond angles 0 basepair planarities 487 basepair parallelities 911 stacking parallelities Total time for adding SS restraints: 58.73 Time building geometry restraints manager: 30.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5346 1.31 - 1.44: 23944 1.44 - 1.56: 23552 1.56 - 1.69: 3067 1.69 - 1.82: 123 Bond restraints: 56032 Sorted by residual: bond pdb=" C2 4OC A1402 " pdb=" N3 4OC A1402 " ideal model delta sigma weight residual 1.507 1.348 0.159 2.00e-02 2.50e+03 6.33e+01 bond pdb=" N3 2MG A1207 " pdb=" C4 2MG A1207 " ideal model delta sigma weight residual 1.496 1.343 0.153 2.00e-02 2.50e+03 5.81e+01 bond pdb=" N3 2MG A 966 " pdb=" C4 2MG A 966 " ideal model delta sigma weight residual 1.496 1.345 0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N3 2MG A1516 " pdb=" C4 2MG A1516 " ideal model delta sigma weight residual 1.496 1.346 0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" C2 5MC A 967 " pdb=" N3 5MC A 967 " ideal model delta sigma weight residual 1.493 1.345 0.148 2.00e-02 2.50e+03 5.47e+01 ... (remaining 56027 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.75: 9603 106.75 - 114.33: 35236 114.33 - 121.91: 26228 121.91 - 129.49: 11093 129.49 - 137.07: 1075 Bond angle restraints: 83235 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 94.96 131.25 -36.29 3.00e+00 1.11e-01 1.46e+02 angle pdb=" C1' G7M A 527 " pdb=" N9 G7M A 527 " pdb=" C4 G7M A 527 " ideal model delta sigma weight residual 142.80 120.76 22.04 3.00e+00 1.11e-01 5.40e+01 angle pdb=" CA GLY H 109 " pdb=" C GLY H 109 " pdb=" O GLY H 109 " ideal model delta sigma weight residual 122.45 118.21 4.24 7.20e-01 1.93e+00 3.46e+01 angle pdb=" C1' 2MG A1516 " pdb=" N9 2MG A1516 " pdb=" C8 2MG A1516 " ideal model delta sigma weight residual 110.07 126.85 -16.78 3.00e+00 1.11e-01 3.13e+01 angle pdb=" C1' 2MG A 966 " pdb=" N9 2MG A 966 " pdb=" C8 2MG A 966 " ideal model delta sigma weight residual 110.07 126.24 -16.17 3.00e+00 1.11e-01 2.90e+01 ... (remaining 83230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.88: 31471 33.88 - 67.75: 3910 67.75 - 101.63: 419 101.63 - 135.50: 13 135.50 - 169.38: 8 Dihedral angle restraints: 35821 sinusoidal: 28942 harmonic: 6879 Sorted by residual: dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 55.95 144.05 1 1.50e+01 4.44e-03 7.72e+01 dihedral pdb=" O4' C A 754 " pdb=" C1' C A 754 " pdb=" N1 C A 754 " pdb=" C2 C A 754 " ideal model delta sinusoidal sigma weight residual 200.00 61.48 138.52 1 1.50e+01 4.44e-03 7.46e+01 dihedral pdb=" O4' C A 183 " pdb=" C1' C A 183 " pdb=" N1 C A 183 " pdb=" C2 C A 183 " ideal model delta sinusoidal sigma weight residual -128.00 41.38 -169.38 1 1.70e+01 3.46e-03 6.59e+01 ... (remaining 35818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 9685 0.081 - 0.163: 688 0.163 - 0.244: 126 0.244 - 0.326: 11 0.326 - 0.407: 2 Chirality restraints: 10512 Sorted by residual: chirality pdb=" CA VAL J 57 " pdb=" N VAL J 57 " pdb=" C VAL J 57 " pdb=" CB VAL J 57 " both_signs ideal model delta sigma weight residual False 2.44 2.03 0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CB D2T L 89 " pdb=" CA D2T L 89 " pdb=" SB D2T L 89 " pdb=" CG D2T L 89 " both_signs ideal model delta sigma weight residual False -3.02 -3.35 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CB VAL J 57 " pdb=" CA VAL J 57 " pdb=" CG1 VAL J 57 " pdb=" CG2 VAL J 57 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.29 2.00e-01 2.50e+01 2.18e+00 ... (remaining 10509 not shown) Planarity restraints: 4867 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1207 " -0.055 2.00e-02 2.50e+03 5.80e-01 7.57e+03 pdb=" C4' 2MG A1207 " -0.431 2.00e-02 2.50e+03 pdb=" O4' 2MG A1207 " -0.596 2.00e-02 2.50e+03 pdb=" C3' 2MG A1207 " 0.597 2.00e-02 2.50e+03 pdb=" O3' 2MG A1207 " 0.605 2.00e-02 2.50e+03 pdb=" C2' 2MG A1207 " 0.188 2.00e-02 2.50e+03 pdb=" O2' 2MG A1207 " -0.952 2.00e-02 2.50e+03 pdb=" C1' 2MG A1207 " -0.233 2.00e-02 2.50e+03 pdb=" N9 2MG A1207 " 0.875 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A 966 " 0.020 2.00e-02 2.50e+03 5.60e-01 7.06e+03 pdb=" C4' 2MG A 966 " 0.436 2.00e-02 2.50e+03 pdb=" O4' 2MG A 966 " 0.629 2.00e-02 2.50e+03 pdb=" C3' 2MG A 966 " -0.585 2.00e-02 2.50e+03 pdb=" O3' 2MG A 966 " -0.538 2.00e-02 2.50e+03 pdb=" C2' 2MG A 966 " -0.225 2.00e-02 2.50e+03 pdb=" O2' 2MG A 966 " 0.882 2.00e-02 2.50e+03 pdb=" C1' 2MG A 966 " 0.232 2.00e-02 2.50e+03 pdb=" N9 2MG A 966 " -0.850 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A1407 " 0.035 2.00e-02 2.50e+03 5.47e-01 6.72e+03 pdb=" C4' 5MC A1407 " 0.429 2.00e-02 2.50e+03 pdb=" O4' 5MC A1407 " 0.560 2.00e-02 2.50e+03 pdb=" C3' 5MC A1407 " -0.583 2.00e-02 2.50e+03 pdb=" O3' 5MC A1407 " -0.543 2.00e-02 2.50e+03 pdb=" C2' 5MC A1407 " -0.217 2.00e-02 2.50e+03 pdb=" O2' 5MC A1407 " 0.892 2.00e-02 2.50e+03 pdb=" C1' 5MC A1407 " 0.239 2.00e-02 2.50e+03 pdb=" N1 5MC A1407 " -0.810 2.00e-02 2.50e+03 ... (remaining 4864 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 281 2.49 - 3.09: 34094 3.09 - 3.69: 95977 3.69 - 4.30: 150566 4.30 - 4.90: 200626 Nonbonded interactions: 481544 Sorted by model distance: nonbonded pdb=" OP2 C A1054 " pdb="MG MG A1717 " model vdw 1.885 2.170 nonbonded pdb=" OP1 C A 770 " pdb="MG MG A1689 " model vdw 1.913 2.170 nonbonded pdb=" O6 G A1178 " pdb="MG MG A1712 " model vdw 1.918 2.170 nonbonded pdb=" OP1 G A 945 " pdb="MG MG A1744 " model vdw 1.936 2.170 nonbonded pdb=" O6 G A1108 " pdb="MG MG A1736 " model vdw 1.936 2.170 ... (remaining 481539 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 17.060 Check model and map are aligned: 0.730 Set scattering table: 0.500 Process input model: 205.770 Find NCS groups from input model: 1.160 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:11.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 240.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.159 56032 Z= 0.498 Angle : 0.785 36.292 83235 Z= 0.507 Chirality : 0.047 0.407 10512 Planarity : 0.018 0.580 4867 Dihedral : 22.579 169.376 31373 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.66 % Allowed : 4.54 % Favored : 94.80 % Cbeta Deviations : 0.13 % 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: -1.12 (0.16), residues: 2357 helix: -0.52 (0.16), residues: 985 sheet: -0.73 (0.25), residues: 390 loop : -0.78 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 201 HIS 0.010 0.001 HIS R 74 PHE 0.013 0.002 PHE O 43 TYR 0.015 0.002 TYR Q 34 ARG 0.009 0.001 ARG T 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 575 time to evaluate : 3.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 100 MET cc_start: 0.6579 (ttm) cc_final: 0.6220 (ttm) REVERT: G 5 ARG cc_start: 0.4295 (tmt170) cc_final: 0.3643 (ttt-90) REVERT: G 31 MET cc_start: 0.3401 (ttp) cc_final: 0.3081 (tmm) REVERT: J 37 ARG cc_start: -0.0899 (mmm160) cc_final: -0.1150 (mmm160) outliers start: 13 outliers final: 4 residues processed: 587 average time/residue: 2.0247 time to fit residues: 1436.0028 Evaluate side-chains 351 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 347 time to evaluate : 3.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain Q residue 15 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 325 optimal weight: 3.9990 chunk 291 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 99 optimal weight: 40.0000 chunk 196 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 301 optimal weight: 0.6980 chunk 116 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 349 optimal weight: 0.7980 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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 51 ASN B 122 GLN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN D 126 ASN E 12 GLN E 83 HIS E 89 HIS E 135 ASN E 148 ASN I 4 ASN J 3 ASN K 15 GLN K 81 ASN L 6 GLN L 73 ASN L 77 HIS L 96 HIS N 35 ASN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 HIS P 26 ASN S 57 HIS T 52 ASN T 61 GLN T 78 ASN T 82 GLN T 84 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 56032 Z= 0.192 Angle : 0.632 14.243 83235 Z= 0.345 Chirality : 0.036 0.344 10512 Planarity : 0.006 0.117 4867 Dihedral : 23.171 171.494 26605 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.84 % Allowed : 18.78 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.17), residues: 2357 helix: 0.22 (0.16), residues: 984 sheet: -0.21 (0.26), residues: 390 loop : -0.31 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 167 HIS 0.008 0.001 HIS L 77 PHE 0.021 0.002 PHE U 12 TYR 0.014 0.002 TYR F 59 ARG 0.011 0.001 ARG O 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 375 time to evaluate : 3.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 MET cc_start: -0.1959 (ttm) cc_final: -0.2671 (mtm) REVERT: B 73 LYS cc_start: 0.0659 (OUTLIER) cc_final: 0.0388 (ttmt) REVERT: B 137 ARG cc_start: 0.6898 (tpp80) cc_final: 0.6598 (tmm160) REVERT: D 105 MET cc_start: 0.6784 (mtt) cc_final: 0.6545 (mtt) REVERT: E 61 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.7046 (tp40) REVERT: G 5 ARG cc_start: 0.4490 (tmt170) cc_final: 0.3742 (ttt-90) REVERT: G 23 LEU cc_start: 0.6211 (tp) cc_final: 0.5570 (pp) REVERT: G 31 MET cc_start: 0.3611 (ttp) cc_final: 0.3290 (tmm) REVERT: G 58 GLU cc_start: 0.1767 (pp20) cc_final: 0.0421 (pt0) REVERT: G 110 LYS cc_start: 0.2650 (pptt) cc_final: 0.1593 (ptpt) REVERT: H 5 ASP cc_start: 0.7048 (t0) cc_final: 0.6768 (t70) REVERT: K 85 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6413 (mmt) REVERT: U 12 PHE cc_start: 0.6890 (t80) cc_final: 0.6487 (t80) outliers start: 76 outliers final: 26 residues processed: 413 average time/residue: 1.9713 time to fit residues: 993.3730 Evaluate side-chains 356 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 327 time to evaluate : 3.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 80 LYS Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 29 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 194 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 290 optimal weight: 3.9990 chunk 238 optimal weight: 0.0040 chunk 96 optimal weight: 30.0000 chunk 350 optimal weight: 5.9990 chunk 378 optimal weight: 4.9990 chunk 311 optimal weight: 7.9990 chunk 347 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 280 optimal weight: 9.9990 overall best weight: 4.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN B 227 GLN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN E 82 GLN H 18 GLN ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 15 HIS K 38 GLN K 64 GLN ** M 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 HIS T 20 HIS ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 56032 Z= 0.346 Angle : 0.680 13.827 83235 Z= 0.364 Chirality : 0.039 0.373 10512 Planarity : 0.007 0.126 4867 Dihedral : 23.141 172.709 26600 Min Nonbonded Distance : 1.127 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 5.91 % Allowed : 19.69 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.17), residues: 2357 helix: 0.28 (0.16), residues: 966 sheet: -0.16 (0.26), residues: 399 loop : -0.32 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 167 HIS 0.008 0.001 HIS R 74 PHE 0.048 0.002 PHE F 8 TYR 0.020 0.002 TYR U 38 ARG 0.011 0.001 ARG C 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 342 time to evaluate : 3.237 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: B 66 LYS cc_start: 0.4633 (OUTLIER) cc_final: 0.3452 (ptmm) REVERT: B 154 MET cc_start: 0.3670 (tpt) cc_final: 0.2961 (tpt) REVERT: C 62 LYS cc_start: 0.4935 (OUTLIER) cc_final: 0.3062 (pmtt) REVERT: C 65 ARG cc_start: 0.2541 (OUTLIER) cc_final: 0.1652 (tpt90) REVERT: C 109 PRO cc_start: 0.4024 (Cg_endo) cc_final: 0.3788 (Cg_exo) REVERT: C 142 MET cc_start: 0.5664 (mmm) cc_final: 0.5406 (mmm) REVERT: E 14 LYS cc_start: 0.8145 (mmtt) cc_final: 0.7631 (mmtt) REVERT: E 29 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.6983 (mtm180) REVERT: E 61 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.7215 (tp40) REVERT: G 31 MET cc_start: 0.3912 (ttp) cc_final: 0.3651 (tmm) REVERT: G 110 LYS cc_start: 0.2761 (pptt) cc_final: 0.1681 (ptpt) REVERT: H 41 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8094 (tptp) REVERT: J 15 HIS cc_start: 0.2439 (OUTLIER) cc_final: 0.0983 (p90) REVERT: K 85 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6473 (mmt) REVERT: P 31 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.7934 (ttp-170) REVERT: S 44 MET cc_start: 0.0144 (tmt) cc_final: -0.1309 (ppp) outliers start: 117 outliers final: 44 residues processed: 404 average time/residue: 1.9815 time to fit residues: 974.2404 Evaluate side-chains 360 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 307 time to evaluate : 3.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 65 ARG Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 80 LYS Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 15 ASP Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 60 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 346 optimal weight: 0.9990 chunk 263 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 167 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 chunk 351 optimal weight: 1.9990 chunk 372 optimal weight: 0.0020 chunk 183 optimal weight: 0.9990 chunk 333 optimal weight: 6.9990 chunk 100 optimal weight: 40.0000 overall best weight: 0.9996 ------------------------------------------------------------------------------- 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 170 HIS B 227 GLN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN E 97 GLN E 146 ASN F 37 HIS I 110 GLN K 38 GLN L 5 ASN M 105 ASN N 4 GLN O 35 GLN T 13 GLN ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 56032 Z= 0.138 Angle : 0.575 13.677 83235 Z= 0.316 Chirality : 0.033 0.344 10512 Planarity : 0.005 0.120 4867 Dihedral : 23.007 173.752 26600 Min Nonbonded Distance : 1.168 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 4.04 % Allowed : 22.92 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.17), residues: 2357 helix: 0.70 (0.17), residues: 977 sheet: 0.11 (0.26), residues: 391 loop : -0.09 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 201 HIS 0.020 0.001 HIS J 15 PHE 0.024 0.001 PHE U 12 TYR 0.010 0.001 TYR L 95 ARG 0.009 0.000 ARG Q 6 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 352 time to evaluate : 3.777 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: B 154 MET cc_start: 0.3461 (tpt) cc_final: 0.3090 (tpt) REVERT: C 65 ARG cc_start: 0.2235 (OUTLIER) cc_final: 0.1281 (tpt90) REVERT: C 109 PRO cc_start: 0.4105 (Cg_endo) cc_final: 0.3904 (Cg_exo) REVERT: C 177 THR cc_start: 0.5471 (m) cc_final: 0.5226 (t) REVERT: E 14 LYS cc_start: 0.7897 (mmtt) cc_final: 0.7408 (mttt) REVERT: E 29 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.6652 (mtm180) REVERT: I 79 ILE cc_start: 0.4194 (mp) cc_final: 0.3891 (mt) REVERT: K 85 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6347 (mmt) REVERT: S 44 MET cc_start: -0.0109 (tmt) cc_final: -0.1407 (ppp) REVERT: U 12 PHE cc_start: 0.6636 (t80) cc_final: 0.6292 (t80) REVERT: U 39 GLU cc_start: 0.7760 (tt0) cc_final: 0.7319 (tt0) outliers start: 80 outliers final: 29 residues processed: 393 average time/residue: 1.9469 time to fit residues: 938.4457 Evaluate side-chains 348 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 316 time to evaluate : 3.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain C residue 65 ARG Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain J residue 9 ARG Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 80 LYS Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain U residue 29 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 309 optimal weight: 6.9990 chunk 211 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 277 optimal weight: 0.4980 chunk 153 optimal weight: 7.9990 chunk 317 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 334 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 overall best weight: 4.4988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 HIS ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN E 89 HIS E 146 ASN H 18 GLN I 110 GLN K 38 GLN L 20 ASN M 105 ASN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 13 GLN ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 56032 Z= 0.337 Angle : 0.662 13.653 83235 Z= 0.355 Chirality : 0.037 0.357 10512 Planarity : 0.006 0.122 4867 Dihedral : 23.062 175.836 26600 Min Nonbonded Distance : 1.100 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.50 % Favored : 97.45 % Rotamer: Outliers : 5.20 % Allowed : 23.07 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.17), residues: 2357 helix: 0.47 (0.17), residues: 979 sheet: 0.03 (0.26), residues: 393 loop : -0.16 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 18 HIS 0.007 0.001 HIS J 15 PHE 0.040 0.002 PHE F 8 TYR 0.022 0.002 TYR U 38 ARG 0.008 0.001 ARG Q 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 330 time to evaluate : 3.231 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: E 14 LYS cc_start: 0.8042 (mmtt) cc_final: 0.7600 (mtpt) REVERT: E 29 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.6903 (mtm180) REVERT: G 79 ARG cc_start: 0.4239 (mtp180) cc_final: 0.4008 (ptt-90) REVERT: K 85 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6461 (mmt) REVERT: P 31 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.7934 (ttp-170) REVERT: R 38 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8300 (mtpp) REVERT: U 12 PHE cc_start: 0.6778 (t80) cc_final: 0.6300 (t80) REVERT: U 56 HIS cc_start: 0.6468 (OUTLIER) cc_final: 0.6013 (t70) outliers start: 103 outliers final: 51 residues processed: 388 average time/residue: 1.8752 time to fit residues: 893.6106 Evaluate side-chains 359 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 303 time to evaluate : 3.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 65 ARG Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain J residue 9 ARG Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 80 LYS Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 15 ASP Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain R residue 38 LYS Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 56 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 125 optimal weight: 30.0000 chunk 335 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 218 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 372 optimal weight: 0.9980 chunk 309 optimal weight: 2.9990 chunk 172 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 123 optimal weight: 40.0000 chunk 195 optimal weight: 20.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN E 43 ASN E 146 ASN F 63 ASN I 110 GLN ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN L 20 ASN M 105 ASN N 4 GLN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 56032 Z= 0.273 Angle : 0.626 13.527 83235 Z= 0.338 Chirality : 0.036 0.362 10512 Planarity : 0.006 0.121 4867 Dihedral : 23.040 175.919 26600 Min Nonbonded Distance : 1.107 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.33 % Favored : 97.62 % Rotamer: Outliers : 4.44 % Allowed : 24.58 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.17), residues: 2357 helix: 0.54 (0.17), residues: 973 sheet: -0.00 (0.26), residues: 388 loop : -0.19 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 201 HIS 0.005 0.001 HIS J 15 PHE 0.019 0.002 PHE K 52 TYR 0.021 0.002 TYR U 38 ARG 0.011 0.001 ARG Q 6 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 326 time to evaluate : 3.327 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: C 177 THR cc_start: 0.5665 (m) cc_final: 0.5452 (t) REVERT: G 17 LYS cc_start: -0.0091 (mmpt) cc_final: -0.1937 (mmtt) REVERT: G 110 LYS cc_start: 0.2681 (pptt) cc_final: 0.1417 (ptpt) REVERT: H 41 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8096 (tptp) REVERT: I 21 ILE cc_start: 0.5201 (pp) cc_final: 0.4809 (pt) REVERT: K 85 MET cc_start: 0.7226 (OUTLIER) cc_final: 0.6463 (mmt) REVERT: P 31 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.7915 (ttp-170) REVERT: R 38 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8273 (mtpp) REVERT: U 12 PHE cc_start: 0.6805 (t80) cc_final: 0.6406 (t80) outliers start: 88 outliers final: 47 residues processed: 378 average time/residue: 1.8945 time to fit residues: 878.9283 Evaluate side-chains 358 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 307 time to evaluate : 2.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 80 LYS Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 15 ASP Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain R residue 38 LYS Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 53 ASN Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 60 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 359 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 212 optimal weight: 0.9990 chunk 272 optimal weight: 0.9980 chunk 210 optimal weight: 0.9980 chunk 313 optimal weight: 40.0000 chunk 208 optimal weight: 5.9990 chunk 371 optimal weight: 20.0000 chunk 232 optimal weight: 0.9980 chunk 226 optimal weight: 5.9990 chunk 171 optimal weight: 7.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN E 43 ASN E 146 ASN I 110 GLN J 64 GLN ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN L 5 ASN L 20 ASN ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 ASN ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 56032 Z= 0.172 Angle : 0.586 13.295 83235 Z= 0.318 Chirality : 0.033 0.334 10512 Planarity : 0.005 0.120 4867 Dihedral : 22.971 176.703 26600 Min Nonbonded Distance : 1.150 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.33 % Favored : 97.62 % Rotamer: Outliers : 4.09 % Allowed : 25.24 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.17), residues: 2357 helix: 0.71 (0.17), residues: 976 sheet: 0.11 (0.26), residues: 388 loop : -0.12 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 201 HIS 0.004 0.001 HIS J 15 PHE 0.037 0.002 PHE F 8 TYR 0.018 0.001 TYR U 38 ARG 0.011 0.000 ARG Q 6 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 334 time to evaluate : 3.357 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: B 115 LYS cc_start: 0.7237 (mmmm) cc_final: 0.6570 (mttp) REVERT: C 177 THR cc_start: 0.5540 (m) cc_final: 0.5333 (t) REVERT: E 14 LYS cc_start: 0.7537 (mmmt) cc_final: 0.6857 (mtpt) REVERT: G 17 LYS cc_start: -0.0301 (mmpt) cc_final: -0.2497 (pttt) REVERT: G 23 LEU cc_start: 0.5430 (tp) cc_final: 0.4737 (pp) REVERT: G 67 GLU cc_start: 0.2089 (pm20) cc_final: 0.1666 (tm-30) REVERT: H 41 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8081 (tptp) REVERT: I 21 ILE cc_start: 0.5088 (pp) cc_final: 0.4712 (pt) REVERT: I 88 MET cc_start: 0.2410 (mpp) cc_final: 0.1584 (tpp) REVERT: K 85 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6345 (mmt) REVERT: O 26 GLU cc_start: 0.7207 (mp0) cc_final: 0.6873 (mp0) REVERT: P 31 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.7855 (ttp-170) REVERT: Q 60 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6436 (mt-10) REVERT: S 49 ILE cc_start: 0.3016 (OUTLIER) cc_final: 0.2723 (pt) REVERT: U 12 PHE cc_start: 0.6791 (t80) cc_final: 0.6421 (t80) outliers start: 81 outliers final: 42 residues processed: 380 average time/residue: 1.8275 time to fit residues: 855.5670 Evaluate side-chains 357 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 311 time to evaluate : 3.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain K residue 80 LYS Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 15 ASP Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain U residue 60 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 229 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 221 optimal weight: 3.9990 chunk 111 optimal weight: 30.0000 chunk 72 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 235 optimal weight: 8.9990 chunk 252 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 291 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN B 203 ASN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN E 146 ASN I 110 GLN ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN K 15 GLN K 38 GLN L 20 ASN M 105 ASN ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 56032 Z= 0.404 Angle : 0.707 14.255 83235 Z= 0.374 Chirality : 0.040 0.370 10512 Planarity : 0.007 0.124 4867 Dihedral : 23.128 179.729 26600 Min Nonbonded Distance : 1.081 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.35 % Favored : 96.61 % Rotamer: Outliers : 4.90 % Allowed : 25.09 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.17), residues: 2357 helix: 0.39 (0.17), residues: 967 sheet: -0.08 (0.27), residues: 389 loop : -0.29 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 42 HIS 0.008 0.001 HIS I 81 PHE 0.026 0.003 PHE U 19 TYR 0.029 0.002 TYR U 38 ARG 0.014 0.001 ARG Q 6 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 320 time to evaluate : 3.379 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: E 64 MET cc_start: 0.7576 (mmp) cc_final: 0.7363 (mmp) REVERT: H 41 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8122 (tptp) REVERT: H 118 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.6952 (tp40) REVERT: I 21 ILE cc_start: 0.5198 (pp) cc_final: 0.4928 (pt) REVERT: I 88 MET cc_start: 0.2443 (mpp) cc_final: 0.2145 (mpp) REVERT: K 85 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.6504 (mmm) REVERT: L 62 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6180 (mp0) REVERT: P 31 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.7960 (ttp-170) REVERT: R 38 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8349 (mtpp) REVERT: S 49 ILE cc_start: 0.3720 (OUTLIER) cc_final: 0.3401 (pt) REVERT: T 85 LYS cc_start: 0.6502 (OUTLIER) cc_final: 0.6177 (ptmm) REVERT: U 12 PHE cc_start: 0.6912 (t80) cc_final: 0.6526 (t80) REVERT: U 56 HIS cc_start: 0.6557 (t70) cc_final: 0.5947 (t70) outliers start: 97 outliers final: 55 residues processed: 375 average time/residue: 1.8469 time to fit residues: 857.3288 Evaluate side-chains 365 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 302 time to evaluate : 2.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 80 LYS Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain O residue 59 MET Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 15 ASP Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain R residue 38 LYS Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 60 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 337 optimal weight: 2.9990 chunk 355 optimal weight: 1.9990 chunk 324 optimal weight: 30.0000 chunk 345 optimal weight: 0.9990 chunk 208 optimal weight: 7.9990 chunk 150 optimal weight: 7.9990 chunk 271 optimal weight: 20.0000 chunk 106 optimal weight: 20.0000 chunk 312 optimal weight: 3.9990 chunk 327 optimal weight: 8.9990 chunk 344 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN E 146 ASN I 110 GLN J 64 GLN K 38 GLN L 5 ASN M 105 ASN N 4 GLN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 56032 Z= 0.215 Angle : 0.614 13.867 83235 Z= 0.332 Chirality : 0.034 0.353 10512 Planarity : 0.006 0.120 4867 Dihedral : 23.057 179.646 26600 Min Nonbonded Distance : 1.123 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.46 % Favored : 97.50 % Rotamer: Outliers : 3.69 % Allowed : 26.55 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.17), residues: 2357 helix: 0.58 (0.17), residues: 960 sheet: -0.09 (0.26), residues: 395 loop : -0.25 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 104 HIS 0.004 0.001 HIS F 11 PHE 0.046 0.002 PHE F 8 TYR 0.029 0.002 TYR B 213 ARG 0.013 0.001 ARG Q 6 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 320 time to evaluate : 3.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 LYS cc_start: 0.7359 (mmmm) cc_final: 0.6813 (mtmm) REVERT: B 137 ARG cc_start: 0.6836 (tpp80) cc_final: 0.6394 (mmm-85) REVERT: C 177 THR cc_start: 0.5579 (m) cc_final: 0.5348 (t) REVERT: E 116 GLU cc_start: 0.6722 (pt0) cc_final: 0.6426 (pt0) REVERT: G 67 GLU cc_start: 0.2194 (pm20) cc_final: 0.1782 (tm-30) REVERT: H 41 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8112 (tptp) REVERT: I 21 ILE cc_start: 0.5296 (pp) cc_final: 0.4981 (pt) REVERT: I 88 MET cc_start: 0.2317 (mpp) cc_final: 0.2053 (mpp) REVERT: K 85 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.6427 (mmm) REVERT: P 31 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.7877 (ttp-170) REVERT: R 38 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8265 (mtpp) REVERT: S 49 ILE cc_start: 0.3031 (OUTLIER) cc_final: 0.2667 (pt) REVERT: U 12 PHE cc_start: 0.6909 (t80) cc_final: 0.6532 (t80) REVERT: U 56 HIS cc_start: 0.6485 (t70) cc_final: 0.5887 (t70) outliers start: 73 outliers final: 46 residues processed: 368 average time/residue: 1.7179 time to fit residues: 786.3429 Evaluate side-chains 353 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 302 time to evaluate : 3.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 15 ASP Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain R residue 38 LYS Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 43 THR Chi-restraints excluded: chain U residue 60 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 227 optimal weight: 10.0000 chunk 365 optimal weight: 9.9990 chunk 223 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 254 optimal weight: 0.7980 chunk 383 optimal weight: 4.9990 chunk 353 optimal weight: 7.9990 chunk 305 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 235 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN E 146 ASN G 122 ASN I 110 GLN ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN K 38 GLN M 105 ASN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 56032 Z= 0.375 Angle : 0.703 14.111 83235 Z= 0.373 Chirality : 0.039 0.365 10512 Planarity : 0.007 0.123 4867 Dihedral : 23.146 176.802 26600 Min Nonbonded Distance : 1.081 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.44 % Favored : 96.52 % Rotamer: Outliers : 3.74 % Allowed : 27.31 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.17), residues: 2357 helix: 0.38 (0.17), residues: 957 sheet: -0.09 (0.27), residues: 387 loop : -0.38 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 42 HIS 0.007 0.001 HIS C 190 PHE 0.033 0.003 PHE R 13 TYR 0.037 0.002 TYR B 213 ARG 0.015 0.001 ARG Q 6 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 314 time to evaluate : 2.958 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: G 17 LYS cc_start: -0.0738 (mmpt) cc_final: -0.2512 (mmtt) REVERT: G 67 GLU cc_start: 0.2264 (pm20) cc_final: 0.1869 (tm-30) REVERT: H 41 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8073 (tptp) REVERT: I 21 ILE cc_start: 0.5485 (pp) cc_final: 0.5225 (pt) REVERT: I 88 MET cc_start: 0.2341 (mpp) cc_final: 0.2102 (mpp) REVERT: P 31 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.7947 (ttp-170) REVERT: R 38 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8356 (mtpp) REVERT: S 44 MET cc_start: -0.0212 (tmt) cc_final: -0.0464 (tmt) REVERT: S 49 ILE cc_start: 0.3393 (OUTLIER) cc_final: 0.3030 (pt) REVERT: U 12 PHE cc_start: 0.6955 (t80) cc_final: 0.6580 (t80) outliers start: 74 outliers final: 49 residues processed: 360 average time/residue: 1.6877 time to fit residues: 751.0871 Evaluate side-chains 359 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 306 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 15 ASP Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain R residue 38 LYS Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 60 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 242 optimal weight: 0.9990 chunk 325 optimal weight: 0.9990 chunk 93 optimal weight: 20.0000 chunk 281 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 84 optimal weight: 20.0000 chunk 305 optimal weight: 0.1980 chunk 128 optimal weight: 50.0000 chunk 314 optimal weight: 30.0000 chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN K 38 GLN L 5 ASN M 105 ASN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.111078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.067960 restraints weight = 145946.551| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.75 r_work: 0.2899 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 56032 Z= 0.229 Angle : 0.631 13.633 83235 Z= 0.340 Chirality : 0.035 0.356 10512 Planarity : 0.006 0.119 4867 Dihedral : 23.082 177.655 26600 Min Nonbonded Distance : 1.118 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.72 % Favored : 97.24 % Rotamer: Outliers : 3.03 % Allowed : 28.17 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.17), residues: 2357 helix: 0.51 (0.17), residues: 955 sheet: 0.04 (0.27), residues: 381 loop : -0.38 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 42 HIS 0.004 0.001 HIS J 15 PHE 0.064 0.002 PHE I 127 TYR 0.031 0.002 TYR B 213 ARG 0.015 0.001 ARG Q 6 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16690.54 seconds wall clock time: 296 minutes 31.53 seconds (17791.53 seconds total)