Starting phenix.real_space_refine on Fri Dec 8 00:23:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nar_12245/12_2023/7nar_12245_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nar_12245/12_2023/7nar_12245.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nar_12245/12_2023/7nar_12245_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nar_12245/12_2023/7nar_12245_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nar_12245/12_2023/7nar_12245_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nar_12245/12_2023/7nar_12245.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nar_12245/12_2023/7nar_12245.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nar_12245/12_2023/7nar_12245_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nar_12245/12_2023/7nar_12245_neut_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1537 5.49 5 Mg 97 5.21 5 S 79 5.16 5 C 28086 2.51 5 N 10128 2.21 5 O 14523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 86": "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 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 54452 Number of models: 1 Model: "" Number of chains: 25 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': 115, 'rna2p_pyr': 86, 'rna3p': 10, 'rna3p_pur': 754, 'rna3p_pyr': 568} Link IDs: {'rna2p': 201, 'rna3p': 1332} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 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: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1129 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 795 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "S" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "U" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 551 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "W" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2456 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 12, 'TRANS': 301} Chain: "A" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Unusual residues: {' MG': 95} Classifications: {'undetermined': 95} Link IDs: {None: 94} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 2, ' ZN': 1, 'GNP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 53910 SG CYS W 297 114.263 176.581 111.416 1.00138.41 S ATOM 53956 SG CYS W 302 111.612 177.161 109.103 1.00139.90 S ATOM 54015 SG CYS W 310 115.182 176.276 106.993 1.00143.63 S Time building chain proxies: 21.95, per 1000 atoms: 0.40 Number of scatterers: 54452 At special positions: 0 Unit cell: (148.645, 247.38, 195.3, 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 2 29.99 S 79 16.00 P 1537 15.00 Mg 97 11.99 O 14523 8.00 N 10128 7.00 C 28086 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 25.48 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " pdb=" ZN W 401 " pdb="ZN ZN W 401 " - pdb=" ND1 HIS W 304 " pdb="ZN ZN W 401 " - pdb=" SG CYS W 297 " pdb="ZN ZN W 401 " - pdb=" SG CYS W 310 " pdb="ZN ZN W 401 " - pdb=" SG CYS W 302 " Number of angles added : 3 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5030 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 98 helices and 24 sheets defined 38.5% alpha, 15.8% beta 510 base pairs and 828 stacking pairs defined. Time for finding SS restraints: 24.23 Creating SS restraints... Processing helix chain 'B' and resid 6 through 12 removed outlier: 3.706A pdb=" N ALA B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 43 through 63 Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.646A pdb=" N CYS B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 123 removed outlier: 3.616A pdb=" N GLN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 148 Processing helix chain 'B' and resid 170 through 179 Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 207 through 226 Processing helix chain 'C' and resid 7 through 10 No H-bonds generated for 'chain 'C' and resid 7 through 10' Processing helix chain 'C' and resid 29 through 46 Processing helix chain 'C' and resid 73 through 76 No H-bonds generated for 'chain 'C' and resid 73 through 76' Processing helix chain 'C' and resid 82 through 95 Processing helix chain 'C' and resid 109 through 111 No H-bonds generated for 'chain 'C' and resid 109 through 111' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 130 through 144 Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'D' and resid 9 through 15 Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 50 through 65 removed outlier: 3.573A 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 95 removed outlier: 3.650A pdb=" N LEU D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 104 Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 147 through 150 No H-bonds generated for 'chain 'D' and resid 147 through 150' Processing helix chain 'D' and resid 153 through 164 removed outlier: 4.647A pdb=" N GLU D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 205 removed outlier: 3.712A pdb=" N GLU D 202 " --> pdb=" O HIS D 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 68 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 162 through 164 No H-bonds generated for 'chain 'E' and resid 162 through 164' Processing helix chain 'F' and resid 12 through 14 No H-bonds generated for 'chain 'F' and resid 12 through 14' Processing helix chain 'F' and resid 18 through 32 removed outlier: 4.036A pdb=" N ALA F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 79 Processing helix chain 'G' and resid 21 through 30 Processing helix chain 'G' and resid 36 through 54 Processing helix chain 'G' and resid 58 through 69 removed outlier: 3.688A pdb=" N VAL G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 111 removed outlier: 3.565A pdb=" N ALA G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 128 Processing helix chain 'G' and resid 134 through 143 Processing helix chain 'H' and resid 6 through 19 Processing helix chain 'H' and resid 31 through 42 Processing helix chain 'H' and resid 95 through 98 Processing helix chain 'H' and resid 113 through 119 Processing helix chain 'I' and resid 35 through 38 No H-bonds generated for 'chain 'I' and resid 35 through 38' Processing helix chain 'I' and resid 42 through 47 Processing helix chain 'I' and resid 50 through 54 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 32 Processing helix chain 'J' and resid 84 through 89 Processing helix chain 'K' and resid 54 through 56 No H-bonds generated for 'chain 'K' and resid 54 through 56' Processing helix chain 'K' and resid 60 through 74 removed outlier: 3.766A pdb=" N GLU K 68 " --> pdb=" O GLN K 64 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ALA K 73 " --> pdb=" O ARG K 69 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL K 74 " --> pdb=" O CYS K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 103 removed outlier: 3.942A pdb=" N ILE K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) 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 Processing helix chain 'M' and resid 15 through 21 removed outlier: 3.836A pdb=" N THR M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 37 Processing helix chain 'M' and resid 50 through 62 removed outlier: 4.162A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 83 Processing helix chain 'M' and resid 86 through 93 Processing helix chain 'M' and resid 107 through 110 No H-bonds generated for 'chain 'M' and resid 107 through 110' Processing helix chain 'N' and resid 4 through 32 removed outlier: 3.957A pdb=" N LYS N 19 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ALA N 22 " --> pdb=" O ASP N 18 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS N 23 " --> pdb=" O LYS N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 50 removed outlier: 4.021A pdb=" N GLN N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) removed outlier: 3.745A 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 83 through 89 Processing helix chain 'O' and resid 5 through 15 Processing helix chain 'O' and resid 25 through 45 removed outlier: 4.092A pdb=" N VAL O 29 " --> pdb=" O THR O 25 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU O 45 " --> pdb=" O GLY O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 73 removed outlier: 4.329A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 84 removed outlier: 3.908A pdb=" N ARG O 84 " --> pdb=" O GLN O 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 54 through 63 removed outlier: 3.596A pdb=" N GLN P 63 " --> pdb=" O HIS P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 80 Processing helix chain 'Q' and resid 49 through 51 No H-bonds generated for 'chain 'Q' and resid 49 through 51' Processing helix chain 'R' and resid 12 through 16 Processing helix chain 'R' and resid 29 through 32 Processing helix chain 'R' and resid 42 through 45 No H-bonds generated for 'chain 'R' and resid 42 through 45' Processing helix chain 'R' and resid 49 through 64 Processing helix chain 'S' and resid 13 through 25 Processing helix chain 'S' and resid 42 through 44 No H-bonds generated for 'chain 'S' and resid 42 through 44' Processing helix chain 'S' and resid 64 through 66 No H-bonds generated for 'chain 'S' and resid 64 through 66' Processing helix chain 'S' and resid 71 through 74 Processing helix chain 'T' and resid 5 through 40 Processing helix chain 'T' and resid 45 through 64 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 69 through 86 Processing helix chain 'U' and resid 12 through 25 Processing helix chain 'U' and resid 28 through 34 Processing helix chain 'U' and resid 41 through 64 removed outlier: 3.781A pdb=" N GLU U 63 " --> pdb=" O LYS U 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 138 through 150 removed outlier: 3.506A pdb=" N ASP W 142 " --> pdb=" O LEU W 138 " (cutoff:3.500A) Processing helix chain 'W' and resid 167 through 183 removed outlier: 3.945A pdb=" N GLU W 175 " --> pdb=" O ALA W 171 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLN W 176 " --> pdb=" O PHE W 172 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ILE W 179 " --> pdb=" O GLU W 175 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TYR W 180 " --> pdb=" O GLN W 176 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG W 181 " --> pdb=" O MET W 177 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE W 183 " --> pdb=" O ILE W 179 " (cutoff:3.500A) Processing helix chain 'W' and resid 198 through 205 Processing helix chain 'W' and resid 220 through 228 Processing helix chain 'W' and resid 280 through 286 Processing helix chain 'W' and resid 288 through 293 removed outlier: 3.741A pdb=" N HIS W 291 " --> pdb=" O VAL W 288 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASP W 292 " --> pdb=" O GLU W 289 " (cutoff:3.500A) Processing helix chain 'W' and resid 311 through 317 Processing helix chain 'W' and resid 323 through 340 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: 7.628A pdb=" N VAL B 70 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE B 162 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N PHE B 198 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 7.611A 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: 6.929A 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: 6.124A pdb=" N VAL B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 98 through 101 removed outlier: 3.677A pdb=" N ARG C 54 " --> pdb=" O HIS C 69 " (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: 4.002A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 46 through 53 removed outlier: 6.488A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 92 through 98 Processing sheet with id= H, first strand: chain 'F' and resid 84 through 88 removed outlier: 6.914A pdb=" N MET F 9 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N SER F 87 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL F 7 " --> pdb=" O SER F 87 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLU F 65 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ILE F 36 " --> pdb=" O GLU F 65 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 73 through 78 Processing sheet with id= J, first strand: chain 'H' and resid 24 through 28 removed outlier: 3.981A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 74 through 77 removed outlier: 6.903A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 6 through 12 Processing sheet with id= M, first strand: chain 'J' and resid 97 through 101 removed outlier: 4.543A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'J' and resid 45 through 52 Processing sheet with id= O, first strand: chain 'K' and resid 41 through 46 removed outlier: 6.656A pdb=" N ILE K 34 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TRP K 44 " --> pdb=" O VAL K 32 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL K 32 " --> pdb=" O TRP K 44 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR K 46 " --> pdb=" O THR K 30 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR K 30 " --> pdb=" O THR K 46 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASN K 81 " --> pdb=" O GLY K 19 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ALA K 21 " --> pdb=" O ASN K 81 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLU K 83 " --> pdb=" O ALA K 21 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE K 23 " --> pdb=" O GLU K 83 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N MET K 85 " --> pdb=" O ILE K 23 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ALA K 25 " --> pdb=" O MET K 85 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LYS K 87 " --> pdb=" O ALA K 25 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ARG K 106 " --> pdb=" O LEU K 82 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL K 84 " --> pdb=" O ARG K 106 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N THR K 108 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 12.475A pdb=" N VAL K 86 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 9.805A pdb=" N ILE K 110 " --> pdb=" O VAL K 86 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'L' and resid 95 through 97 removed outlier: 3.761A pdb=" N SER L 78 " --> pdb=" O CYS L 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR L 39 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ARG L 50 " --> pdb=" O THR L 39 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'P' and resid 2 through 9 Processing sheet with id= R, first strand: chain 'P' and resid 37 through 39 Processing sheet with id= S, first strand: chain 'Q' and resid 8 through 11 removed outlier: 9.495A pdb=" N SER Q 72 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N HIS Q 45 " --> pdb=" O SER Q 72 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N THR Q 74 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N HIS Q 47 " --> pdb=" O THR Q 74 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ALA Q 24 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N VAL Q 12 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'Q' and resid 58 through 60 removed outlier: 6.488A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) removed outlier: 5.537A 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 Processing sheet with id= V, first strand: chain 'W' and resid 78 through 81 removed outlier: 6.673A pdb=" N ASP W 53 " --> pdb=" O ILE W 45 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ARG W 47 " --> pdb=" O HIS W 51 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N HIS W 51 " --> pdb=" O ARG W 47 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLY W 95 " --> pdb=" O ASN W 65 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL W 80 " --> pdb=" O GLU W 98 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'W' and resid 254 through 257 removed outlier: 5.661A pdb=" N ARG W 208 " --> pdb=" O ASP W 263 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE W 265 " --> pdb=" O ARG W 208 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N SER W 210 " --> pdb=" O ILE W 265 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLN W 125 " --> pdb=" O ILE W 211 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ALA W 213 " --> pdb=" O GLN W 125 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N VAL W 127 " --> pdb=" O ALA W 213 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLU W 154 " --> pdb=" O ILE W 126 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE W 128 " --> pdb=" O GLU W 154 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE W 156 " --> pdb=" O ILE W 128 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N SER W 130 " --> pdb=" O ILE W 156 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL W 158 " --> pdb=" O SER W 130 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'W' and resid 106 through 111 removed outlier: 3.686A pdb=" N ALA W 120 " --> pdb=" O LEU W 107 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG W 109 " --> pdb=" O PRO W 118 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ASP W 111 " --> pdb=" O VAL W 116 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N VAL W 116 " --> pdb=" O ASP W 111 " (cutoff:3.500A) 851 hydrogen bonds defined for protein. 2466 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1258 hydrogen bonds 1902 hydrogen bond angles 0 basepair planarities 510 basepair parallelities 828 stacking parallelities Total time for adding SS restraints: 45.00 Time building geometry restraints manager: 27.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9341 1.33 - 1.45: 22849 1.45 - 1.58: 23216 1.58 - 1.70: 3072 1.70 - 1.82: 138 Bond restraints: 58616 Sorted by residual: bond pdb=" C1' GNP W 402 " pdb=" C2' GNP W 402 " ideal model delta sigma weight residual 1.273 1.525 -0.252 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C3' GNP W 402 " pdb=" C4' GNP W 402 " ideal model delta sigma weight residual 1.285 1.534 -0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C2 G7M A 527 " pdb=" N3 G7M A 527 " ideal model delta sigma weight residual 1.462 1.307 0.155 2.00e-02 2.50e+03 6.01e+01 bond pdb=" C1' GNP W 402 " pdb=" O4' GNP W 402 " ideal model delta sigma weight residual 1.564 1.410 0.154 2.00e-02 2.50e+03 5.92e+01 bond pdb=" N3 2MG A 966 " pdb=" C4 2MG A 966 " ideal model delta sigma weight residual 1.496 1.344 0.152 2.00e-02 2.50e+03 5.74e+01 ... (remaining 58611 not shown) Histogram of bond angle deviations from ideal: 95.75 - 103.92: 5326 103.92 - 112.09: 34506 112.09 - 120.26: 26470 120.26 - 128.43: 18177 128.43 - 136.59: 2261 Bond angle restraints: 86740 Sorted by residual: angle pdb=" N VAL J 57 " pdb=" CA VAL J 57 " pdb=" C VAL J 57 " ideal model delta sigma weight residual 109.34 122.90 -13.56 2.08e+00 2.31e-01 4.25e+01 angle pdb=" N LEU R 67 " pdb=" CA LEU R 67 " pdb=" C LEU R 67 " ideal model delta sigma weight residual 112.90 104.40 8.50 1.31e+00 5.83e-01 4.21e+01 angle pdb=" N LYS G 114 " pdb=" CA LYS G 114 " pdb=" C LYS G 114 " ideal model delta sigma weight residual 113.51 123.16 -9.65 1.52e+00 4.33e-01 4.03e+01 angle pdb=" C1' 2MG A1207 " pdb=" N9 2MG A1207 " pdb=" C8 2MG A1207 " ideal model delta sigma weight residual 110.07 126.93 -16.86 3.00e+00 1.11e-01 3.16e+01 angle pdb=" N6 MA6 A1518 " pdb=" C6 MA6 A1518 " pdb=" N1 MA6 A1518 " ideal model delta sigma weight residual 103.60 120.42 -16.82 3.00e+00 1.11e-01 3.14e+01 ... (remaining 86735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 32527 35.74 - 71.49: 3203 71.49 - 107.23: 413 107.23 - 142.98: 8 142.98 - 178.72: 8 Dihedral angle restraints: 36159 sinusoidal: 28373 harmonic: 7786 Sorted by residual: dihedral pdb=" O4' U A1008 " pdb=" C1' U A1008 " pdb=" N1 U A1008 " pdb=" C2 U A1008 " ideal model delta sinusoidal sigma weight residual 200.00 23.47 176.53 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 55.23 144.77 1 1.50e+01 4.44e-03 7.75e+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 61.67 138.33 1 1.50e+01 4.44e-03 7.45e+01 ... (remaining 36156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 10364 0.107 - 0.215: 472 0.215 - 0.322: 35 0.322 - 0.430: 7 0.430 - 0.537: 2 Chirality restraints: 10880 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 1.90 0.54 2.00e-01 2.50e+01 7.21e+00 chirality pdb=" CA LYS G 114 " pdb=" N LYS G 114 " pdb=" C LYS G 114 " pdb=" CB LYS G 114 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.51e+00 chirality pdb=" CA GLU F 33 " pdb=" N GLU F 33 " pdb=" C GLU F 33 " pdb=" CB GLU F 33 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.56e+00 ... (remaining 10877 not shown) Planarity restraints: 5330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' G7M A 527 " -0.224 2.00e-02 2.50e+03 7.41e-01 1.24e+04 pdb=" C4' G7M A 527 " -0.530 2.00e-02 2.50e+03 pdb=" O4' G7M A 527 " -0.723 2.00e-02 2.50e+03 pdb=" C3' G7M A 527 " 0.589 2.00e-02 2.50e+03 pdb=" O3' G7M A 527 " 0.980 2.00e-02 2.50e+03 pdb=" C2' G7M A 527 " 0.039 2.00e-02 2.50e+03 pdb=" O2' G7M A 527 " -1.181 2.00e-02 2.50e+03 pdb=" C1' G7M A 527 " -0.122 2.00e-02 2.50e+03 pdb=" N9 G7M A 527 " 1.171 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' MA6 A1519 " -0.077 2.00e-02 2.50e+03 6.31e-01 8.96e+03 pdb=" C4' MA6 A1519 " -0.471 2.00e-02 2.50e+03 pdb=" O4' MA6 A1519 " -0.722 2.00e-02 2.50e+03 pdb=" C3' MA6 A1519 " 0.589 2.00e-02 2.50e+03 pdb=" O3' MA6 A1519 " 0.668 2.00e-02 2.50e+03 pdb=" C2' MA6 A1519 " 0.182 2.00e-02 2.50e+03 pdb=" O2' MA6 A1519 " -0.980 2.00e-02 2.50e+03 pdb=" C1' MA6 A1519 " -0.195 2.00e-02 2.50e+03 pdb=" N9 MA6 A1519 " 1.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GNP W 402 " -0.458 2.00e-02 2.50e+03 6.17e-01 8.57e+03 pdb=" C2' GNP W 402 " 0.627 2.00e-02 2.50e+03 pdb=" C3' GNP W 402 " 0.175 2.00e-02 2.50e+03 pdb=" C4' GNP W 402 " -0.208 2.00e-02 2.50e+03 pdb=" C5' GNP W 402 " 0.920 2.00e-02 2.50e+03 pdb=" N9 GNP W 402 " -0.057 2.00e-02 2.50e+03 pdb=" O2' GNP W 402 " 0.678 2.00e-02 2.50e+03 pdb=" O3' GNP W 402 " -0.968 2.00e-02 2.50e+03 pdb=" O4' GNP W 402 " -0.709 2.00e-02 2.50e+03 ... (remaining 5327 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.10: 82 2.10 - 2.80: 14032 2.80 - 3.50: 80735 3.50 - 4.20: 179211 4.20 - 4.90: 238143 Nonbonded interactions: 512203 Sorted by model distance: nonbonded pdb=" O4' G A1338 " pdb=" OH TYR W 299 " model vdw 1.404 2.440 nonbonded pdb=" OP1 G A1094 " pdb="MG MG A1677 " model vdw 1.456 2.170 nonbonded pdb=" C4 G A1338 " pdb=" CE2 TYR W 299 " model vdw 1.511 3.560 nonbonded pdb=" N9 G A1338 " pdb=" CE2 TYR W 299 " model vdw 1.680 3.420 nonbonded pdb=" OP1 G A1068 " pdb="MG MG A1677 " model vdw 1.822 2.170 ... (remaining 512198 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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 13.460 Check model and map are aligned: 0.650 Set scattering table: 0.430 Process input model: 167.970 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.130 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: 0.000 Load rotamer database and sin/cos tables:9.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 195.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 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 0.252 58616 Z= 0.487 Angle : 0.775 16.859 86740 Z= 0.494 Chirality : 0.049 0.537 10880 Planarity : 0.027 0.741 5330 Dihedral : 21.644 178.720 31129 Min Nonbonded Distance : 1.404 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 12.85 % Favored : 87.15 % Cbeta Deviations : 0.36 % 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: -1.48 (0.15), residues: 2673 helix: -0.53 (0.15), residues: 1080 sheet: -1.11 (0.23), residues: 462 loop : -1.21 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 42 HIS 0.005 0.001 HIS S 14 PHE 0.028 0.002 PHE B 90 TYR 0.012 0.001 TYR L 38 ARG 0.004 0.000 ARG O 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 800 time to evaluate : 2.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 2 residues processed: 800 average time/residue: 1.5684 time to fit residues: 1546.6458 Evaluate side-chains 503 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 501 time to evaluate : 2.809 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 1.2565 time to fit residues: 6.4550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 350 optimal weight: 4.9990 chunk 314 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 212 optimal weight: 0.8980 chunk 168 optimal weight: 10.0000 chunk 325 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 197 optimal weight: 0.0970 chunk 242 optimal weight: 8.9990 chunk 376 optimal weight: 8.9990 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 122 GLN ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 ASN G 52 GLN I 4 ASN ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 HIS J 99 GLN K 38 GLN K 119 ASN ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN S 56 GLN T 52 ASN W 282 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 58616 Z= 0.182 Angle : 0.696 21.119 86740 Z= 0.378 Chirality : 0.034 0.369 10880 Planarity : 0.007 0.130 5330 Dihedral : 22.332 179.603 25744 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.65 % Allowed : 25.75 % Favored : 69.59 % 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: -0.51 (0.16), residues: 2673 helix: 0.25 (0.15), residues: 1083 sheet: -0.70 (0.23), residues: 477 loop : -0.61 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 42 HIS 0.007 0.001 HIS S 57 PHE 0.026 0.001 PHE F 80 TYR 0.030 0.002 TYR B 213 ARG 0.011 0.001 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 588 time to evaluate : 2.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 35 residues processed: 641 average time/residue: 1.4594 time to fit residues: 1172.5066 Evaluate side-chains 507 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 472 time to evaluate : 2.786 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 21 residues processed: 16 average time/residue: 0.4968 time to fit residues: 16.7261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 209 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 313 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 chunk 103 optimal weight: 30.0000 chunk 377 optimal weight: 3.9990 chunk 407 optimal weight: 9.9990 chunk 336 optimal weight: 10.0000 chunk 374 optimal weight: 5.9990 chunk 128 optimal weight: 20.0000 chunk 302 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 ASN I 31 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 HIS J 99 GLN K 38 GLN ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 62 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 58616 Z= 0.338 Angle : 0.723 16.729 86740 Z= 0.391 Chirality : 0.037 0.333 10880 Planarity : 0.007 0.133 5330 Dihedral : 22.263 178.285 25744 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 6.65 % Allowed : 26.99 % Favored : 66.36 % 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: -0.34 (0.16), residues: 2673 helix: 0.35 (0.15), residues: 1083 sheet: -0.65 (0.23), residues: 464 loop : -0.44 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 42 HIS 0.005 0.001 HIS J 56 PHE 0.028 0.002 PHE B 91 TYR 0.033 0.002 TYR I 90 ARG 0.009 0.001 ARG W 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 508 time to evaluate : 2.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 150 outliers final: 65 residues processed: 597 average time/residue: 1.3759 time to fit residues: 1043.7757 Evaluate side-chains 523 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 458 time to evaluate : 2.790 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 45 residues processed: 21 average time/residue: 0.4946 time to fit residues: 21.0414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 373 optimal weight: 5.9990 chunk 283 optimal weight: 9.9990 chunk 195 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 180 optimal weight: 7.9990 chunk 253 optimal weight: 7.9990 chunk 378 optimal weight: 5.9990 chunk 401 optimal weight: 0.9980 chunk 197 optimal weight: 4.9990 chunk 359 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 GLN I 4 ASN I 81 HIS K 38 GLN L 73 ASN ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 18 GLN ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 9 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 58616 Z= 0.330 Angle : 0.716 16.609 86740 Z= 0.389 Chirality : 0.037 0.339 10880 Planarity : 0.007 0.131 5330 Dihedral : 22.263 177.759 25744 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 7.09 % Allowed : 28.06 % Favored : 64.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.16), residues: 2673 helix: 0.27 (0.15), residues: 1080 sheet: -0.57 (0.24), residues: 456 loop : -0.39 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 42 HIS 0.008 0.001 HIS R 74 PHE 0.026 0.002 PHE B 91 TYR 0.027 0.002 TYR W 299 ARG 0.009 0.001 ARG W 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 502 time to evaluate : 2.796 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 outliers start: 160 outliers final: 85 residues processed: 596 average time/residue: 1.3775 time to fit residues: 1044.3588 Evaluate side-chains 529 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 444 time to evaluate : 2.810 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 62 residues processed: 27 average time/residue: 0.5598 time to fit residues: 27.9452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 334 optimal weight: 0.8980 chunk 227 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 298 optimal weight: 8.9990 chunk 165 optimal weight: 5.9990 chunk 342 optimal weight: 9.9990 chunk 277 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 204 optimal weight: 0.8980 chunk 360 optimal weight: 0.9990 chunk 101 optimal weight: 20.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN C 185 ASN D 196 ASN E 148 ASN I 4 ASN J 99 GLN K 38 GLN ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN W 51 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 58616 Z= 0.231 Angle : 0.689 16.487 86740 Z= 0.376 Chirality : 0.035 0.325 10880 Planarity : 0.007 0.128 5330 Dihedral : 22.232 179.190 25744 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 6.60 % Allowed : 29.70 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.16), residues: 2673 helix: 0.32 (0.16), residues: 1076 sheet: -0.55 (0.24), residues: 461 loop : -0.43 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 42 HIS 0.009 0.001 HIS R 74 PHE 0.021 0.002 PHE F 80 TYR 0.026 0.002 TYR W 299 ARG 0.012 0.001 ARG B 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 497 time to evaluate : 2.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 149 outliers final: 83 residues processed: 595 average time/residue: 1.3761 time to fit residues: 1040.6200 Evaluate side-chains 540 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 457 time to evaluate : 2.809 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 67 residues processed: 17 average time/residue: 0.6016 time to fit residues: 19.4503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 134 optimal weight: 10.0000 chunk 361 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 235 optimal weight: 5.9990 chunk 99 optimal weight: 30.0000 chunk 401 optimal weight: 1.9990 chunk 333 optimal weight: 1.9990 chunk 185 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 210 optimal weight: 0.4980 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 ASN C 185 ASN ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 118 GLN I 4 ASN J 99 GLN K 38 GLN ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 58616 Z= 0.221 Angle : 0.690 16.386 86740 Z= 0.376 Chirality : 0.034 0.313 10880 Planarity : 0.007 0.128 5330 Dihedral : 22.193 179.533 25744 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.63 % Allowed : 31.83 % Favored : 62.54 % 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: -0.25 (0.16), residues: 2673 helix: 0.40 (0.16), residues: 1066 sheet: -0.49 (0.24), residues: 459 loop : -0.41 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 103 HIS 0.007 0.001 HIS R 74 PHE 0.016 0.002 PHE B 184 TYR 0.027 0.002 TYR D 51 ARG 0.010 0.001 ARG B 113 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 493 time to evaluate : 2.833 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 outliers start: 127 outliers final: 85 residues processed: 578 average time/residue: 1.3669 time to fit residues: 1006.0059 Evaluate side-chains 532 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 447 time to evaluate : 2.834 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 66 residues processed: 20 average time/residue: 0.5946 time to fit residues: 22.3294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 387 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 228 optimal weight: 6.9990 chunk 293 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 338 optimal weight: 4.9990 chunk 224 optimal weight: 2.9990 chunk 399 optimal weight: 0.9990 chunk 250 optimal weight: 7.9990 chunk 243 optimal weight: 0.0040 chunk 184 optimal weight: 3.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN D 196 ASN F 37 HIS H 67 GLN I 4 ASN ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN K 38 GLN ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN R 54 GLN T 52 ASN W 51 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 58616 Z= 0.180 Angle : 0.689 16.293 86740 Z= 0.376 Chirality : 0.033 0.301 10880 Planarity : 0.007 0.125 5330 Dihedral : 22.150 179.966 25744 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 6.03 % Allowed : 32.31 % Favored : 61.66 % 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 (0.16), residues: 2673 helix: 0.42 (0.16), residues: 1052 sheet: -0.40 (0.24), residues: 459 loop : -0.32 (0.19), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP G 103 HIS 0.011 0.001 HIS C 6 PHE 0.043 0.002 PHE W 172 TYR 0.028 0.002 TYR D 51 ARG 0.009 0.000 ARG W 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 498 time to evaluate : 3.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 136 outliers final: 82 residues processed: 586 average time/residue: 1.3580 time to fit residues: 1012.7936 Evaluate side-chains 529 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 447 time to evaluate : 2.812 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 63 residues processed: 21 average time/residue: 0.5670 time to fit residues: 22.5760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 247 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 238 optimal weight: 0.1980 chunk 120 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 254 optimal weight: 7.9990 chunk 272 optimal weight: 5.9990 chunk 197 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 314 optimal weight: 9.9990 overall best weight: 5.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS C 185 ASN ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 ASN J 99 GLN K 38 GLN ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 74 HIS W 51 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 58616 Z= 0.329 Angle : 0.745 16.427 86740 Z= 0.402 Chirality : 0.037 0.306 10880 Planarity : 0.007 0.130 5330 Dihedral : 22.192 178.455 25744 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.41 % Allowed : 33.87 % Favored : 60.73 % 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: -0.40 (0.16), residues: 2673 helix: 0.21 (0.16), residues: 1064 sheet: -0.50 (0.24), residues: 459 loop : -0.45 (0.19), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 103 HIS 0.012 0.001 HIS F 3 PHE 0.029 0.002 PHE B 91 TYR 0.031 0.002 TYR D 51 ARG 0.015 0.001 ARG I 119 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 456 time to evaluate : 2.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 122 outliers final: 77 residues processed: 538 average time/residue: 1.3614 time to fit residues: 932.8353 Evaluate side-chains 507 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 430 time to evaluate : 2.869 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 64 residues processed: 14 average time/residue: 0.6513 time to fit residues: 17.8785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 363 optimal weight: 6.9990 chunk 383 optimal weight: 10.0000 chunk 349 optimal weight: 10.0000 chunk 372 optimal weight: 5.9990 chunk 224 optimal weight: 1.9990 chunk 162 optimal weight: 10.0000 chunk 292 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 336 optimal weight: 5.9990 chunk 352 optimal weight: 5.9990 chunk 371 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS C 185 ASN ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 ASN ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 58616 Z= 0.316 Angle : 0.753 16.500 86740 Z= 0.405 Chirality : 0.037 0.312 10880 Planarity : 0.007 0.129 5330 Dihedral : 22.228 178.120 25744 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.83 % Allowed : 34.57 % Favored : 60.59 % 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: -0.51 (0.16), residues: 2673 helix: 0.10 (0.16), residues: 1058 sheet: -0.58 (0.24), residues: 448 loop : -0.49 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 103 HIS 0.007 0.001 HIS R 74 PHE 0.048 0.002 PHE W 172 TYR 0.037 0.002 TYR D 51 ARG 0.016 0.001 ARG J 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 450 time to evaluate : 3.249 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 outliers start: 109 outliers final: 83 residues processed: 531 average time/residue: 1.3308 time to fit residues: 904.8743 Evaluate side-chains 517 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 434 time to evaluate : 2.810 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 69 residues processed: 18 average time/residue: 0.5460 time to fit residues: 19.3955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 244 optimal weight: 20.0000 chunk 394 optimal weight: 0.7980 chunk 240 optimal weight: 10.0000 chunk 186 optimal weight: 0.3980 chunk 274 optimal weight: 10.0000 chunk 413 optimal weight: 0.6980 chunk 380 optimal weight: 7.9990 chunk 329 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 254 optimal weight: 6.9990 chunk 201 optimal weight: 4.9990 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN C 185 ASN ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 ASN ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 58616 Z= 0.227 Angle : 0.747 17.195 86740 Z= 0.402 Chirality : 0.035 0.305 10880 Planarity : 0.007 0.126 5330 Dihedral : 22.216 178.887 25744 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.17 % Allowed : 35.51 % Favored : 60.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.16), residues: 2673 helix: 0.13 (0.16), residues: 1054 sheet: -0.50 (0.24), residues: 448 loop : -0.48 (0.19), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 103 HIS 0.008 0.001 HIS R 74 PHE 0.020 0.002 PHE I 103 TYR 0.037 0.002 TYR D 51 ARG 0.015 0.001 ARG J 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 458 time to evaluate : 2.786 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 outliers start: 94 outliers final: 74 residues processed: 529 average time/residue: 1.3826 time to fit residues: 931.2436 Evaluate side-chains 504 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 430 time to evaluate : 2.852 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 65 residues processed: 12 average time/residue: 0.6107 time to fit residues: 14.7817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 261 optimal weight: 3.9990 chunk 350 optimal weight: 5.9990 chunk 100 optimal weight: 30.0000 chunk 303 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 329 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 338 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 overall best weight: 5.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 GLN I 4 ASN K 38 GLN L 73 ASN ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.042965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.030992 restraints weight = 363690.385| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 2.46 r_work: 0.2639 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9031 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 58616 Z= 0.343 Angle : 0.780 18.255 86740 Z= 0.418 Chirality : 0.038 0.308 10880 Planarity : 0.007 0.130 5330 Dihedral : 22.244 178.166 25744 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.86 % Allowed : 35.99 % Favored : 60.15 % 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: -0.70 (0.16), residues: 2673 helix: -0.08 (0.16), residues: 1059 sheet: -0.68 (0.23), residues: 458 loop : -0.56 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 103 HIS 0.011 0.001 HIS R 74 PHE 0.047 0.002 PHE W 172 TYR 0.039 0.002 TYR D 51 ARG 0.015 0.001 ARG J 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16386.54 seconds wall clock time: 286 minutes 54.00 seconds (17214.00 seconds total)