Starting phenix.real_space_refine on Fri Feb 23 09:24:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cai_16526/02_2024/8cai_16526_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cai_16526/02_2024/8cai_16526.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cai_16526/02_2024/8cai_16526_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cai_16526/02_2024/8cai_16526_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cai_16526/02_2024/8cai_16526_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cai_16526/02_2024/8cai_16526.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cai_16526/02_2024/8cai_16526.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cai_16526/02_2024/8cai_16526_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cai_16526/02_2024/8cai_16526_updated.pdb" } resolution = 2.08 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 K 29 8.98 5 P 1114 5.49 5 Mg 55 5.21 5 S 49 5.16 5 C 18401 2.51 5 N 6764 2.21 5 O 11402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 21": "NH1" <-> "NH2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B ASP 159": "OD1" <-> "OD2" Residue "B PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "C GLU 152": "OE1" <-> "OE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 73": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "F GLU 16": "OE1" <-> "OE2" Residue "F GLU 33": "OE1" <-> "OE2" Residue "F GLU 73": "OE1" <-> "OE2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "H GLU 43": "OE1" <-> "OE2" Residue "H GLU 47": "OE1" <-> "OE2" Residue "H GLU 58": "OE1" <-> "OE2" Residue "H ARG 117": "NH1" <-> "NH2" Residue "K GLU 76": "OE1" <-> "OE2" Residue "K TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 25": "OE1" <-> "OE2" Residue "L ARG 56": "NH1" <-> "NH2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "O GLU 83": "OE1" <-> "OE2" Residue "P ARG 28": "NH1" <-> "NH2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "P GLU 47": "OE1" <-> "OE2" Residue "Q GLU 49": "OE1" <-> "OE2" Residue "Q GLU 52": "OE1" <-> "OE2" Residue "Q GLU 60": "OE1" <-> "OE2" Residue "Q GLU 63": "OE1" <-> "OE2" Residue "Q GLU 80": "OE1" <-> "OE2" Residue "R GLU 35": "OE1" <-> "OE2" Residue "T GLU 53": "OE1" <-> "OE2" Residue "U GLU 10": "OE1" <-> "OE2" Residue "U ARG 66": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 37814 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 23941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 23941 Classifications: {'RNA': 1114} Modifications used: {'rna2p': 1, 'rna2p_pur': 86, 'rna2p_pyr': 49, 'rna3p': 8, 'rna3p_pur': 552, 'rna3p_pyr': 418} Link IDs: {'rna2p': 136, 'rna3p': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1616 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain breaks: 1 Chain: "C" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 511 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain breaks: 3 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: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1135 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain: "F" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 839 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} 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: "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 breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'IAS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 910 Classifications: {'peptide': 117} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 109} Chain breaks: 1 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: "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: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "Q" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 641 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 446 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 577 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "A" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 254 Unusual residues: {' K': 27, ' MG': 55, '5I0': 1, 'HY0': 3, 'SCM': 1} Classifications: {'undetermined': 87} Link IDs: {None: 86} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1270, 1270 Classifications: {'water': 1270} Link IDs: {None: 1269} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "K" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "L" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "O" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "P" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "Q" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "R" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "T" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "U" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 22.15, per 1000 atoms: 0.59 Number of scatterers: 37814 At special positions: 0 Unit cell: (201.168, 155.448, 134.874, 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) K 29 19.00 S 49 16.00 P 1114 15.00 Mg 55 11.99 O 11402 8.00 N 6764 7.00 C 18401 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 24.48 Conformation dependent library (CDL) restraints added in 2.7 seconds 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2872 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 14 sheets defined 37.2% alpha, 19.3% beta 380 base pairs and 629 stacking pairs defined. Time for finding SS restraints: 23.20 Creating SS restraints... Processing helix chain 'B' and resid 6 through 9 No H-bonds generated for 'chain 'B' and resid 6 through 9' 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 removed outlier: 3.529A pdb=" N LEU B 54 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 55 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 86 removed outlier: 4.118A pdb=" N LYS B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 121 removed outlier: 4.204A pdb=" N GLN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 151 removed outlier: 3.808A pdb=" N SER B 147 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLY B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ILE B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 207 through 225 removed outlier: 3.699A pdb=" N LEU B 212 " --> pdb=" O ARG B 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 126 No H-bonds generated for 'chain 'C' and resid 124 through 126' Processing helix chain 'C' and resid 130 through 134 Processing helix chain 'D' and resid 8 through 15 removed outlier: 3.699A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 31 No H-bonds generated for 'chain 'D' and resid 28 through 31' Processing helix chain 'D' and resid 50 through 65 Processing helix chain 'D' and resid 69 through 81 Processing helix chain 'D' and resid 86 through 96 Processing helix chain 'D' and resid 98 through 105 Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 153 through 164 Processing helix chain 'D' and resid 197 through 205 removed outlier: 3.620A pdb=" N SER D 205 " --> pdb=" O VAL D 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 70 removed outlier: 3.607A pdb=" N ARG E 69 " --> pdb=" O GLU E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 117 Processing helix chain 'E' and resid 133 through 145 removed outlier: 3.509A pdb=" N ARG E 138 " --> pdb=" O ILE E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 157 Processing helix chain 'F' and resid 12 through 31 removed outlier: 3.507A pdb=" N SER F 15 " --> pdb=" O PRO F 12 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU F 16 " --> pdb=" O ASP F 13 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL F 18 " --> pdb=" O SER F 15 " (cutoff:3.500A) Proline residue: F 19 - end of helix removed outlier: 3.781A pdb=" N ILE F 22 " --> pdb=" O PRO F 19 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR F 26 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA F 27 " --> pdb=" O ARG F 24 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR F 30 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY F 31 " --> pdb=" O ALA F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 80 removed outlier: 3.506A pdb=" N LEU F 74 " --> pdb=" O VAL F 70 " (cutoff:3.500A) 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 119 Processing helix chain 'K' and resid 60 through 71 Processing helix chain 'K' and resid 95 through 103 Processing helix chain 'L' and resid 4 through 9 Processing helix chain 'L' and resid 22 through 24 No H-bonds generated for 'chain 'L' and resid 22 through 24' Processing helix chain 'L' and resid 114 through 116 No H-bonds generated for 'chain 'L' and resid 114 through 116' Processing helix chain 'O' and resid 5 through 15 Processing helix chain 'O' and resid 25 through 45 removed outlier: 4.249A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU O 45 " --> pdb=" O GLY O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 73 removed outlier: 3.777A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 85 Processing helix chain 'P' and resid 54 through 62 Processing helix chain 'P' and resid 69 through 78 Processing helix chain 'R' and resid 26 through 32 removed outlier: 3.828A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 3.927A 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 Processing helix chain 'T' and resid 5 through 41 removed outlier: 3.714A pdb=" N VAL T 35 " --> pdb=" O PHE T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 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 26 Processing helix chain 'U' and resid 28 through 34 Processing helix chain 'U' and resid 41 through 62 removed outlier: 3.559A pdb=" N LYS U 59 " --> pdb=" O ARG U 55 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA U 61 " --> pdb=" O ALA U 57 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.717A pdb=" N ALA B 160 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL B 70 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE B 162 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N VAL B 163 " --> pdb=" O PRO B 182 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE B 184 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N PHE B 198 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL B 187 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 164 through 171 Processing sheet with id= C, first strand: chain 'D' and resid 123 through 125 removed outlier: 3.724A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 46 through 53 removed outlier: 6.872A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 85 through 89 Processing sheet with id= F, first strand: chain 'F' and resid 43 through 46 removed outlier: 3.673A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N HIS F 11 " --> pdb=" O VAL F 84 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL F 84 " --> pdb=" O HIS F 11 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 35 through 41 removed outlier: 3.567A pdb=" N GLU F 65 " --> pdb=" O LYS F 35 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASN F 63 " --> pdb=" O HIS F 37 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU F 39 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU F 61 " --> pdb=" O LEU F 39 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 24 through 28 removed outlier: 3.845A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 74 through 77 removed outlier: 6.740A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'K' and resid 41 through 46 removed outlier: 7.043A pdb=" N ILE K 34 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TRP K 44 " --> pdb=" O VAL K 32 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL K 32 " --> pdb=" O TRP K 44 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR K 46 " --> pdb=" O THR K 30 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR K 30 " --> pdb=" O THR K 46 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASN K 81 " --> pdb=" O GLY K 19 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ALA K 21 " --> pdb=" O ASN K 81 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU K 83 " --> pdb=" O ALA K 21 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE K 23 " --> pdb=" O GLU K 83 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N MET K 85 " --> pdb=" O ILE K 23 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA K 25 " --> pdb=" O MET K 85 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LYS K 87 " --> pdb=" O ALA K 25 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ARG K 106 " --> pdb=" O LEU K 82 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N VAL K 84 " --> pdb=" O ARG K 106 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N THR K 108 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 12.340A pdb=" N VAL K 86 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 9.715A pdb=" N ILE K 110 " --> pdb=" O VAL K 86 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'L' and resid 29 through 33 removed outlier: 9.465A pdb=" N ARG L 94 " --> pdb=" O GLU L 62 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N THR L 64 " --> pdb=" O ARG L 94 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N HIS L 96 " --> pdb=" O THR L 64 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N TYR L 66 " --> pdb=" O HIS L 96 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ARG L 56 " --> pdb=" O CYS L 34 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N CYS L 34 " --> pdb=" O ARG L 56 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'P' and resid 2 through 11 removed outlier: 3.509A pdb=" N PHE P 16 " --> pdb=" O HIS P 9 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'Q' and resid 8 through 11 removed outlier: 9.303A pdb=" N SER Q 72 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N HIS Q 45 " --> pdb=" O SER Q 72 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N THR Q 74 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N HIS Q 47 " --> pdb=" O THR Q 74 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA Q 24 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N VAL Q 12 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'Q' and resid 58 through 60 removed outlier: 6.412A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL Q 78 " --> pdb=" O GLU Q 60 " (cutoff:3.500A) 498 hydrogen bonds defined for protein. 1425 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 953 hydrogen bonds 1494 hydrogen bond angles 0 basepair planarities 380 basepair parallelities 629 stacking parallelities Total time for adding SS restraints: 61.90 Time building geometry restraints manager: 25.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5531 1.34 - 1.46: 18127 1.46 - 1.58: 13400 1.58 - 1.70: 2220 1.70 - 1.83: 86 Bond restraints: 39364 Sorted by residual: bond pdb=" C23 HY0 A1605 " pdb=" O22 HY0 A1605 " ideal model delta sigma weight residual 0.786 1.413 -0.627 2.00e-02 2.50e+03 9.83e+02 bond pdb=" C23 HY0 A1604 " pdb=" O22 HY0 A1604 " ideal model delta sigma weight residual 0.786 1.407 -0.621 2.00e-02 2.50e+03 9.63e+02 bond pdb=" C23 HY0 A1603 " pdb=" O22 HY0 A1603 " ideal model delta sigma weight residual 0.786 1.406 -0.620 2.00e-02 2.50e+03 9.60e+02 bond pdb=" C6 SCM A1607 " pdb=" O1 SCM A1607 " ideal model delta sigma weight residual 0.917 1.419 -0.502 2.00e-02 2.50e+03 6.30e+02 bond pdb=" C3 SCM A1607 " pdb=" C4 SCM A1607 " ideal model delta sigma weight residual 1.054 1.507 -0.453 2.00e-02 2.50e+03 5.13e+02 ... (remaining 39359 not shown) Histogram of bond angle deviations from ideal: 92.00 - 100.51: 1289 100.51 - 109.02: 10694 109.02 - 117.53: 24235 117.53 - 126.04: 18621 126.04 - 134.55: 3850 Bond angle restraints: 58689 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 94.96 125.93 -30.97 3.00e+00 1.11e-01 1.07e+02 angle pdb=" O3' A A 780 " pdb=" P A A 781 " pdb=" O5' A A 781 " ideal model delta sigma weight residual 104.00 92.00 12.00 1.50e+00 4.44e-01 6.40e+01 angle pdb=" O3' G A 836 " pdb=" P U A 837 " pdb=" O5' U A 837 " ideal model delta sigma weight residual 104.00 92.82 11.18 1.50e+00 4.44e-01 5.55e+01 angle pdb=" O3' U A 561 " pdb=" P U A 562 " pdb=" O5' U A 562 " ideal model delta sigma weight residual 104.00 93.36 10.64 1.50e+00 4.44e-01 5.03e+01 angle pdb=" O3' U A 921 " pdb=" P G A 922 " pdb=" O5' G A 922 " ideal model delta sigma weight residual 104.00 93.37 10.63 1.50e+00 4.44e-01 5.02e+01 ... (remaining 58684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.20: 22002 29.20 - 58.39: 1955 58.39 - 87.59: 1224 87.59 - 116.79: 19 116.79 - 145.98: 3 Dihedral angle restraints: 25203 sinusoidal: 20761 harmonic: 4442 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 54.02 145.98 1 1.50e+01 4.44e-03 7.80e+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 61.00 139.00 1 1.50e+01 4.44e-03 7.49e+01 dihedral pdb=" O4' C A 422 " pdb=" C1' C A 422 " pdb=" N1 C A 422 " pdb=" C2 C A 422 " ideal model delta sinusoidal sigma weight residual -128.00 14.63 -142.63 1 1.70e+01 3.46e-03 5.96e+01 ... (remaining 25200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.979: 7465 0.979 - 1.957: 6 1.957 - 2.936: 0 2.936 - 3.914: 1 3.914 - 4.893: 1 Chirality restraints: 7473 Sorted by residual: chirality pdb=" C5 SCM A1607 " pdb=" C4 SCM A1607 " pdb=" C6 SCM A1607 " pdb=" O1B SCM A1607 " both_signs ideal model delta sigma weight residual False 2.40 -2.50 4.89 2.00e-01 2.50e+01 5.99e+02 chirality pdb=" C6 SCM A1607 " pdb=" C5 SCM A1607 " pdb=" O1 SCM A1607 " pdb=" O2B SCM A1607 " both_signs ideal model delta sigma weight residual False 1.09 -2.33 3.42 2.00e-01 2.50e+01 2.93e+02 chirality pdb=" C23 HY0 A1604 " pdb=" C24 HY0 A1604 " pdb=" O22 HY0 A1604 " pdb=" O28 HY0 A1604 " both_signs ideal model delta sigma weight residual False 0.80 2.35 -1.55 2.00e-01 2.50e+01 6.04e+01 ... (remaining 7470 not shown) Planarity restraints: 3267 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A1407 " -0.083 2.00e-02 2.50e+03 6.16e-01 8.54e+03 pdb=" C4' 5MC A1407 " -0.430 2.00e-02 2.50e+03 pdb=" O4' 5MC A1407 " -0.645 2.00e-02 2.50e+03 pdb=" C3' 5MC A1407 " 0.638 2.00e-02 2.50e+03 pdb=" O3' 5MC A1407 " 0.675 2.00e-02 2.50e+03 pdb=" C2' 5MC A1407 " 0.136 2.00e-02 2.50e+03 pdb=" O2' 5MC A1407 " -1.002 2.00e-02 2.50e+03 pdb=" C1' 5MC A1407 " -0.226 2.00e-02 2.50e+03 pdb=" N1 5MC A1407 " 0.935 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " -0.102 2.00e-02 2.50e+03 6.08e-01 8.31e+03 pdb=" C4' 2MG A1516 " -0.420 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " -0.586 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " 0.638 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " 0.676 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " 0.115 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " -1.017 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " -0.218 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " 0.913 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1207 " 0.043 2.00e-02 2.50e+03 5.63e-01 7.13e+03 pdb=" C4' 2MG A1207 " 0.417 2.00e-02 2.50e+03 pdb=" O4' 2MG A1207 " 0.634 2.00e-02 2.50e+03 pdb=" C3' 2MG A1207 " -0.619 2.00e-02 2.50e+03 pdb=" O3' 2MG A1207 " -0.545 2.00e-02 2.50e+03 pdb=" C2' 2MG A1207 " -0.186 2.00e-02 2.50e+03 pdb=" O2' 2MG A1207 " 0.886 2.00e-02 2.50e+03 pdb=" C1' 2MG A1207 " 0.224 2.00e-02 2.50e+03 pdb=" N9 2MG A1207 " -0.853 2.00e-02 2.50e+03 ... (remaining 3264 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.50: 209 2.50 - 3.16: 30979 3.16 - 3.82: 93690 3.82 - 4.48: 135337 4.48 - 5.14: 176649 Nonbonded interactions: 436864 Sorted by model distance: nonbonded pdb=" OP1 G A 21 " pdb="MG MG A1645 " model vdw 1.839 2.170 nonbonded pdb=" OP2 C A 352 " pdb="MG MG A1614 " model vdw 1.891 2.170 nonbonded pdb=" O6 G A1108 " pdb="MG MG A1612 " model vdw 1.893 2.170 nonbonded pdb="MG MG A1629 " pdb=" O HOH A2065 " model vdw 1.904 2.170 nonbonded pdb=" OP2 A A 116 " pdb="MG MG A1636 " model vdw 1.912 2.170 ... (remaining 436859 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: 6.900 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: 0.020 Extract box with map and model: 28.720 Check model and map are aligned: 0.640 Set scattering table: 0.380 Process input model: 171.000 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.120 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:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 222.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 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 : 0.014 0.627 39364 Z= 0.896 Angle : 1.517 30.972 58689 Z= 0.940 Chirality : 0.129 4.893 7473 Planarity : 0.025 0.616 3267 Dihedral : 22.057 145.982 22331 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.71 % Favored : 96.22 % Rotamer: Outliers : 0.86 % Allowed : 5.72 % Favored : 93.42 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 1.92 % 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: -1.66 (0.19), residues: 1509 helix: -1.10 (0.18), residues: 611 sheet: -0.85 (0.29), residues: 238 loop : -1.00 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP P 60 HIS 0.014 0.003 HIS E 89 PHE 0.028 0.003 PHE Q 37 TYR 0.035 0.005 TYR D 76 ARG 0.039 0.004 ARG U 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 347 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 MET cc_start: 0.6802 (mmm) cc_final: 0.6441 (mmm) REVERT: B 35 ARG cc_start: 0.4467 (mtt90) cc_final: 0.4032 (tpm170) REVERT: B 42 ASN cc_start: 0.4239 (t0) cc_final: 0.3901 (t0) REVERT: B 59 LYS cc_start: 0.4998 (ttmm) cc_final: 0.4746 (ttpm) REVERT: B 66 LYS cc_start: 0.3587 (mtmt) cc_final: 0.3274 (mtpt) REVERT: B 106 THR cc_start: 0.5346 (m) cc_final: 0.4961 (t) REVERT: B 108 ARG cc_start: 0.5347 (ptm160) cc_final: 0.4929 (ptm-80) REVERT: B 169 GLU cc_start: 0.5715 (mm-30) cc_final: 0.5515 (mm-30) REVERT: B 178 ASN cc_start: 0.5658 (t0) cc_final: 0.5435 (t0) REVERT: C 129 MET cc_start: 0.3527 (mmt) cc_final: 0.3095 (mtt) REVERT: C 164 ARG cc_start: 0.5103 (OUTLIER) cc_final: 0.4839 (ttt-90) REVERT: C 166 GLU cc_start: 0.6463 (mt-10) cc_final: 0.6139 (tp30) REVERT: C 169 ARG cc_start: 0.7175 (ttp-170) cc_final: 0.6200 (ttp80) REVERT: D 35 GLU cc_start: 0.5585 (mt-10) cc_final: 0.5232 (pm20) REVERT: D 36 GLN cc_start: 0.6338 (tt0) cc_final: 0.5978 (tt0) REVERT: D 50 ASP cc_start: 0.6770 (p0) cc_final: 0.6528 (m-30) REVERT: D 57 GLU cc_start: 0.7888 (tp30) cc_final: 0.7659 (tp30) REVERT: D 73 ARG cc_start: 0.7415 (ttp-170) cc_final: 0.6503 (tpp80) REVERT: D 76 TYR cc_start: 0.7927 (t80) cc_final: 0.7525 (t80) REVERT: D 115 ARG cc_start: 0.6751 (ttt180) cc_final: 0.6234 (ttt180) REVERT: D 146 ARG cc_start: 0.6334 (mtp180) cc_final: 0.5841 (mtp180) REVERT: D 147 GLU cc_start: 0.5877 (mp0) cc_final: 0.5668 (tp30) REVERT: E 12 GLN cc_start: 0.6836 (mp10) cc_final: 0.6430 (tt0) REVERT: E 13 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7038 (mt-10) REVERT: E 20 ARG cc_start: 0.7852 (ttp-170) cc_final: 0.7484 (ttp-110) REVERT: E 45 ARG cc_start: 0.6461 (ttt90) cc_final: 0.5873 (ttp80) REVERT: E 55 GLU cc_start: 0.6955 (mp0) cc_final: 0.6622 (mt-10) REVERT: E 61 GLN cc_start: 0.6592 (tt0) cc_final: 0.6004 (tm-30) REVERT: E 68 ARG cc_start: 0.6571 (mtt180) cc_final: 0.6321 (mtt180) REVERT: E 69 ARG cc_start: 0.6592 (ptp90) cc_final: 0.5880 (ptm160) REVERT: E 70 ASN cc_start: 0.6115 (m-40) cc_final: 0.5842 (p0) REVERT: E 86 LYS cc_start: 0.7998 (mtmt) cc_final: 0.7779 (mtmp) REVERT: E 142 ASP cc_start: 0.6758 (t70) cc_final: 0.6399 (t70) REVERT: F 5 GLU cc_start: 0.7695 (tt0) cc_final: 0.7467 (tt0) REVERT: F 21 MET cc_start: 0.5527 (mtt) cc_final: 0.5259 (mtm) REVERT: F 38 ARG cc_start: 0.7257 (ttp-170) cc_final: 0.6465 (ttp-170) REVERT: F 44 ARG cc_start: 0.7007 (mtm-85) cc_final: 0.6683 (mtm-85) REVERT: F 45 ARG cc_start: 0.7351 (mtp85) cc_final: 0.7127 (mtp-110) REVERT: F 55 HIS cc_start: 0.7650 (m90) cc_final: 0.7252 (m170) REVERT: F 88 MET cc_start: 0.8233 (ttm) cc_final: 0.7947 (ttm) REVERT: F 90 MET cc_start: 0.8026 (mtm) cc_final: 0.7360 (mtm) REVERT: H 43 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7341 (mm-30) REVERT: H 50 LYS cc_start: 0.7284 (pttt) cc_final: 0.6994 (pttp) REVERT: H 58 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6550 (mp0) REVERT: H 60 GLU cc_start: 0.7457 (tt0) cc_final: 0.6933 (tp30) REVERT: H 114 ARG cc_start: 0.7071 (ttm110) cc_final: 0.6308 (ttm-80) REVERT: K 37 ARG cc_start: 0.5885 (mtp-110) cc_final: 0.5517 (mmm160) REVERT: K 53 ARG cc_start: 0.5504 (mmm160) cc_final: 0.5133 (mmp80) REVERT: K 87 LYS cc_start: 0.7523 (ttmt) cc_final: 0.7308 (ttmp) REVERT: K 108 THR cc_start: 0.6321 (p) cc_final: 0.5754 (t) REVERT: L 10 LYS cc_start: 0.7654 (tttt) cc_final: 0.7365 (ttpm) REVERT: L 25 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6849 (mt-10) REVERT: L 64 THR cc_start: 0.8012 (m) cc_final: 0.7652 (p) REVERT: L 75 GLN cc_start: 0.5692 (mt0) cc_final: 0.5430 (pt0) REVERT: L 86 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7614 (ptt180) REVERT: L 108 LYS cc_start: 0.7194 (mmtt) cc_final: 0.6463 (mmtm) REVERT: L 121 ARG cc_start: 0.7164 (ttt-90) cc_final: 0.6604 (ttp80) REVERT: O 2 SER cc_start: 0.6543 (p) cc_final: 0.6308 (m) REVERT: O 6 GLU cc_start: 0.6715 (mp0) cc_final: 0.6509 (mp0) REVERT: O 58 ARG cc_start: 0.7954 (ttp-170) cc_final: 0.6886 (ttp-110) REVERT: O 62 GLN cc_start: 0.7937 (tt0) cc_final: 0.7548 (tt0) REVERT: O 68 ASP cc_start: 0.8130 (m-30) cc_final: 0.7844 (m-30) REVERT: P 53 ASP cc_start: 0.7274 (t0) cc_final: 0.6947 (t0) REVERT: P 76 LYS cc_start: 0.6575 (mtpp) cc_final: 0.6152 (mttp) REVERT: Q 6 ARG cc_start: 0.5898 (mtp180) cc_final: 0.5548 (ttp80) REVERT: Q 9 GLN cc_start: 0.7995 (tt0) cc_final: 0.7734 (tt0) REVERT: Q 11 ARG cc_start: 0.6513 (ttt90) cc_final: 0.6221 (mtp-110) REVERT: Q 16 LYS cc_start: 0.6995 (mttm) cc_final: 0.6750 (mttm) REVERT: Q 17 MET cc_start: 0.6915 (mtm) cc_final: 0.6391 (mtm) REVERT: Q 29 VAL cc_start: 0.7560 (t) cc_final: 0.7200 (p) REVERT: Q 40 ARG cc_start: 0.7360 (mmp-170) cc_final: 0.7130 (mmm160) REVERT: Q 60 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6768 (tt0) REVERT: Q 75 LEU cc_start: 0.7465 (mt) cc_final: 0.7227 (tp) REVERT: R 22 ASP cc_start: 0.6798 (t0) cc_final: 0.6472 (t0) REVERT: R 44 ILE cc_start: 0.7684 (mm) cc_final: 0.7451 (mt) REVERT: R 48 ARG cc_start: 0.6346 (mpt180) cc_final: 0.5489 (mtm110) REVERT: R 57 ARG cc_start: 0.7704 (mtt90) cc_final: 0.7502 (mtm-85) REVERT: T 27 MET cc_start: 0.8207 (tmm) cc_final: 0.7824 (tmm) REVERT: T 49 LYS cc_start: 0.6925 (ttpt) cc_final: 0.6661 (ptmm) REVERT: U 21 ARG cc_start: 0.5283 (ttt90) cc_final: 0.4954 (mpp-170) REVERT: U 31 GLU cc_start: 0.5913 (OUTLIER) cc_final: 0.5521 (tp30) REVERT: U 44 GLU cc_start: 0.7110 (tt0) cc_final: 0.6558 (tm-30) outliers start: 11 outliers final: 2 residues processed: 356 average time/residue: 2.1216 time to fit residues: 872.5904 Evaluate side-chains 289 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 284 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain U residue 31 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 217 optimal weight: 0.0020 chunk 195 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 chunk 202 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 234 optimal weight: 0.9980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN B 89 GLN B 103 ASN B 177 ASN B 190 ASN D 40 GLN D 71 GLN D 100 ASN D 152 GLN E 19 ASN E 148 ASN F 11 HIS F 46 GLN F 68 GLN H 38 ASN K 15 GLN L 20 ASN L 112 GLN O 35 GLN O 40 GLN P 26 ASN P 63 GLN T 3 ASN T 13 GLN T 52 ASN T 68 HIS T 84 ASN U 64 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 39364 Z= 0.146 Angle : 0.631 23.550 58689 Z= 0.338 Chirality : 0.042 1.948 7473 Planarity : 0.006 0.128 3267 Dihedral : 22.743 143.718 19288 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.99 % Favored : 97.95 % Rotamer: Outliers : 1.80 % Allowed : 9.24 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.21), residues: 1509 helix: 1.00 (0.20), residues: 609 sheet: -0.35 (0.29), residues: 280 loop : -0.38 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 201 HIS 0.008 0.001 HIS F 11 PHE 0.017 0.002 PHE Q 28 TYR 0.016 0.002 TYR L 117 ARG 0.005 0.000 ARG K 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 309 time to evaluate : 2.375 Fit side-chains revert: symmetry clash REVERT: B 27 MET cc_start: 0.6642 (mmm) cc_final: 0.6374 (mmm) REVERT: B 35 ARG cc_start: 0.4408 (mtt90) cc_final: 0.3921 (tpp-160) REVERT: B 66 LYS cc_start: 0.3967 (mtmt) cc_final: 0.3503 (mttt) REVERT: B 105 LYS cc_start: 0.5187 (pttt) cc_final: 0.4845 (pptt) REVERT: B 108 ARG cc_start: 0.5422 (ptm160) cc_final: 0.4631 (ptm-80) REVERT: B 112 LYS cc_start: 0.4492 (OUTLIER) cc_final: 0.3950 (mtpt) REVERT: B 169 GLU cc_start: 0.5583 (mm-30) cc_final: 0.5364 (mm-30) REVERT: B 208 ARG cc_start: 0.4554 (ttt90) cc_final: 0.4305 (ptm160) REVERT: C 129 MET cc_start: 0.3536 (mmt) cc_final: 0.3261 (mtt) REVERT: C 166 GLU cc_start: 0.6475 (mt-10) cc_final: 0.6073 (tp30) REVERT: C 169 ARG cc_start: 0.7125 (ttp-170) cc_final: 0.6173 (ttp80) REVERT: C 170 GLU cc_start: 0.7174 (mp0) cc_final: 0.6894 (mp0) REVERT: D 35 GLU cc_start: 0.5614 (mt-10) cc_final: 0.5279 (pm20) REVERT: D 36 GLN cc_start: 0.6321 (tt0) cc_final: 0.5928 (tt0) REVERT: D 47 ARG cc_start: 0.5966 (ttm110) cc_final: 0.5463 (ttp-110) REVERT: D 50 ASP cc_start: 0.6857 (p0) cc_final: 0.6393 (m-30) REVERT: D 57 GLU cc_start: 0.7824 (tp30) cc_final: 0.7586 (tp30) REVERT: D 73 ARG cc_start: 0.7267 (ttp-170) cc_final: 0.6452 (ttm170) REVERT: D 115 ARG cc_start: 0.6622 (ttt180) cc_final: 0.6391 (ttt180) REVERT: D 159 LEU cc_start: 0.4586 (mt) cc_final: 0.4382 (mp) REVERT: D 166 GLU cc_start: 0.6027 (tt0) cc_final: 0.5692 (pm20) REVERT: E 12 GLN cc_start: 0.6853 (mp10) cc_final: 0.6339 (tt0) REVERT: E 20 ARG cc_start: 0.7819 (ttp-170) cc_final: 0.7479 (ttp-110) REVERT: E 41 ASP cc_start: 0.7138 (p0) cc_final: 0.6607 (p0) REVERT: E 45 ARG cc_start: 0.6451 (ttt90) cc_final: 0.5792 (ttp80) REVERT: E 55 GLU cc_start: 0.6776 (mp0) cc_final: 0.6467 (mt-10) REVERT: E 61 GLN cc_start: 0.6441 (tt0) cc_final: 0.6150 (tp40) REVERT: E 64 MET cc_start: 0.6885 (mmt) cc_final: 0.6559 (mmt) REVERT: E 69 ARG cc_start: 0.6165 (ptp90) cc_final: 0.5363 (ptm160) REVERT: E 142 ASP cc_start: 0.6669 (t70) cc_final: 0.6370 (t70) REVERT: F 2 ARG cc_start: 0.7050 (mtt-85) cc_final: 0.6714 (mtp85) REVERT: F 44 ARG cc_start: 0.7071 (mtm-85) cc_final: 0.6584 (mtm-85) REVERT: F 55 HIS cc_start: 0.7498 (m90) cc_final: 0.7140 (m170) REVERT: F 90 MET cc_start: 0.7764 (mtm) cc_final: 0.7378 (mtm) REVERT: H 43 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7723 (mm-30) REVERT: H 47 GLU cc_start: 0.7225 (tp30) cc_final: 0.6899 (tp30) REVERT: H 50 LYS cc_start: 0.7148 (pttt) cc_final: 0.6851 (pttp) REVERT: H 58 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6595 (mp0) REVERT: H 60 GLU cc_start: 0.7358 (tt0) cc_final: 0.6798 (tp30) REVERT: H 88 ARG cc_start: 0.7743 (mtm180) cc_final: 0.7106 (mtp-110) REVERT: H 114 ARG cc_start: 0.6942 (ttm110) cc_final: 0.6138 (ttm-80) REVERT: K 37 ARG cc_start: 0.5922 (mtp-110) cc_final: 0.5613 (mmm160) REVERT: K 87 LYS cc_start: 0.7541 (ttmt) cc_final: 0.7193 (ttmm) REVERT: K 98 ARG cc_start: 0.6374 (mtp180) cc_final: 0.6170 (mtt90) REVERT: K 108 THR cc_start: 0.6396 (p) cc_final: 0.5829 (t) REVERT: L 10 LYS cc_start: 0.7407 (tttt) cc_final: 0.7116 (ttpm) REVERT: L 25 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6782 (mm-30) REVERT: L 64 THR cc_start: 0.7989 (m) cc_final: 0.7578 (p) REVERT: L 75 GLN cc_start: 0.5788 (mt0) cc_final: 0.5408 (pt0) REVERT: L 81 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7527 (tp) REVERT: L 108 LYS cc_start: 0.7021 (mmtt) cc_final: 0.6227 (mmtm) REVERT: L 121 ARG cc_start: 0.7068 (ttt-90) cc_final: 0.6432 (ttp80) REVERT: O 2 SER cc_start: 0.6566 (p) cc_final: 0.6324 (m) REVERT: O 10 LYS cc_start: 0.6462 (mptt) cc_final: 0.6106 (tttt) REVERT: O 57 LEU cc_start: 0.8241 (mt) cc_final: 0.7951 (mm) REVERT: O 58 ARG cc_start: 0.7821 (ttp-170) cc_final: 0.6795 (ttp-110) REVERT: O 62 GLN cc_start: 0.7903 (tt0) cc_final: 0.7524 (tt0) REVERT: O 68 ASP cc_start: 0.8077 (m-30) cc_final: 0.7762 (m-30) REVERT: O 84 ARG cc_start: 0.6601 (mtp180) cc_final: 0.6229 (mmm160) REVERT: P 76 LYS cc_start: 0.6340 (mtpp) cc_final: 0.6041 (mttp) REVERT: Q 6 ARG cc_start: 0.5935 (mtp180) cc_final: 0.5067 (ttt180) REVERT: Q 9 GLN cc_start: 0.7994 (tt0) cc_final: 0.7652 (tt0) REVERT: Q 11 ARG cc_start: 0.6471 (ttt90) cc_final: 0.6186 (mtp-110) REVERT: Q 17 MET cc_start: 0.6830 (mtm) cc_final: 0.6411 (mtm) REVERT: R 44 ILE cc_start: 0.7609 (mm) cc_final: 0.7407 (mm) REVERT: R 48 ARG cc_start: 0.6241 (mpt180) cc_final: 0.5967 (mmt90) REVERT: T 27 MET cc_start: 0.8074 (tmm) cc_final: 0.7671 (tmm) REVERT: U 21 ARG cc_start: 0.5154 (ttt90) cc_final: 0.4790 (ttt-90) REVERT: U 31 GLU cc_start: 0.5857 (OUTLIER) cc_final: 0.5516 (tp30) REVERT: U 44 GLU cc_start: 0.6937 (tt0) cc_final: 0.6449 (tm-30) outliers start: 23 outliers final: 6 residues processed: 321 average time/residue: 2.2369 time to fit residues: 832.1929 Evaluate side-chains 296 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 287 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain O residue 4 SER Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 31 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 130 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 234 optimal weight: 6.9990 chunk 253 optimal weight: 1.9990 chunk 209 optimal weight: 0.0670 chunk 232 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 188 optimal weight: 0.0170 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 19 ASN E 73 ASN E 148 ASN K 22 HIS L 20 ASN O 40 GLN P 63 GLN Q 51 ASN T 52 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 39364 Z= 0.203 Angle : 0.679 23.451 58689 Z= 0.358 Chirality : 0.044 1.966 7473 Planarity : 0.006 0.131 3267 Dihedral : 22.809 143.699 19277 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.43 % Allowed : 11.35 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.49 (0.21), residues: 1509 helix: 1.16 (0.21), residues: 610 sheet: -0.14 (0.30), residues: 277 loop : -0.16 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP P 60 HIS 0.006 0.001 HIS D 198 PHE 0.021 0.002 PHE O 43 TYR 0.018 0.002 TYR L 117 ARG 0.005 0.001 ARG T 60 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 288 time to evaluate : 3.531 Fit side-chains REVERT: B 35 ARG cc_start: 0.4508 (mtt90) cc_final: 0.3924 (tpp-160) REVERT: B 63 ARG cc_start: 0.4054 (ttp-110) cc_final: 0.3683 (ptt90) REVERT: B 66 LYS cc_start: 0.4062 (mtmt) cc_final: 0.3577 (mttt) REVERT: B 78 GLU cc_start: 0.4370 (OUTLIER) cc_final: 0.3727 (tm-30) REVERT: B 105 LYS cc_start: 0.5233 (pttt) cc_final: 0.4868 (pptt) REVERT: B 108 ARG cc_start: 0.5587 (ptm160) cc_final: 0.5128 (ptm160) REVERT: B 169 GLU cc_start: 0.5620 (mm-30) cc_final: 0.5401 (mm-30) REVERT: C 129 MET cc_start: 0.3381 (mmt) cc_final: 0.3160 (mtt) REVERT: C 164 ARG cc_start: 0.5110 (OUTLIER) cc_final: 0.4306 (ttt-90) REVERT: C 166 GLU cc_start: 0.6498 (mt-10) cc_final: 0.6238 (tp30) REVERT: C 169 ARG cc_start: 0.7094 (ttp-170) cc_final: 0.6136 (ttp80) REVERT: C 170 GLU cc_start: 0.7148 (mp0) cc_final: 0.6919 (mp0) REVERT: D 35 GLU cc_start: 0.5580 (mt-10) cc_final: 0.5305 (pm20) REVERT: D 36 GLN cc_start: 0.6282 (tt0) cc_final: 0.5847 (tt0) REVERT: D 47 ARG cc_start: 0.6018 (ttm110) cc_final: 0.5609 (ttp-170) REVERT: D 50 ASP cc_start: 0.6892 (p0) cc_final: 0.6475 (m-30) REVERT: D 57 GLU cc_start: 0.7865 (tp30) cc_final: 0.7648 (tp30) REVERT: D 73 ARG cc_start: 0.7281 (ttp-170) cc_final: 0.6424 (ttm170) REVERT: D 115 ARG cc_start: 0.6669 (ttt180) cc_final: 0.6455 (ttt180) REVERT: D 166 GLU cc_start: 0.6206 (tt0) cc_final: 0.5811 (pm20) REVERT: E 12 GLN cc_start: 0.6715 (mp10) cc_final: 0.6256 (tt0) REVERT: E 20 ARG cc_start: 0.7818 (ttp-170) cc_final: 0.7541 (ttp-110) REVERT: E 41 ASP cc_start: 0.7203 (p0) cc_final: 0.6705 (p0) REVERT: E 45 ARG cc_start: 0.6430 (ttt90) cc_final: 0.5791 (ttp80) REVERT: E 55 GLU cc_start: 0.6708 (mp0) cc_final: 0.6427 (mt-10) REVERT: E 61 GLN cc_start: 0.6461 (tt0) cc_final: 0.6144 (tp40) REVERT: E 69 ARG cc_start: 0.6267 (ptp90) cc_final: 0.5484 (ptm160) REVERT: F 2 ARG cc_start: 0.7103 (mtt-85) cc_final: 0.6859 (mtp85) REVERT: F 44 ARG cc_start: 0.6980 (mtm-85) cc_final: 0.6524 (mtm-85) REVERT: F 90 MET cc_start: 0.7784 (mtm) cc_final: 0.7364 (mtm) REVERT: H 43 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7769 (mm-30) REVERT: H 50 LYS cc_start: 0.7128 (pttt) cc_final: 0.6800 (pttp) REVERT: H 58 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6484 (mp0) REVERT: H 60 GLU cc_start: 0.7373 (tt0) cc_final: 0.6796 (tp30) REVERT: H 88 ARG cc_start: 0.7748 (mtm180) cc_final: 0.7065 (mtp-110) REVERT: H 114 ARG cc_start: 0.6999 (ttm110) cc_final: 0.6179 (ttm-80) REVERT: K 37 ARG cc_start: 0.5863 (mtp-110) cc_final: 0.5582 (mmm160) REVERT: K 98 ARG cc_start: 0.6363 (mtp180) cc_final: 0.6161 (mtt90) REVERT: K 108 THR cc_start: 0.6396 (p) cc_final: 0.5827 (t) REVERT: L 10 LYS cc_start: 0.7399 (tttt) cc_final: 0.7104 (ttpm) REVERT: L 75 GLN cc_start: 0.5697 (mt0) cc_final: 0.5338 (pt0) REVERT: L 81 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7555 (tp) REVERT: L 108 LYS cc_start: 0.7012 (mmtt) cc_final: 0.6249 (mmtm) REVERT: L 121 ARG cc_start: 0.7051 (ttt-90) cc_final: 0.6785 (ttt180) REVERT: O 2 SER cc_start: 0.6535 (p) cc_final: 0.6249 (t) REVERT: O 57 LEU cc_start: 0.8212 (mt) cc_final: 0.7936 (mm) REVERT: O 58 ARG cc_start: 0.7846 (ttp-170) cc_final: 0.6813 (ttp-110) REVERT: O 62 GLN cc_start: 0.7867 (tt0) cc_final: 0.7489 (tt0) REVERT: O 68 ASP cc_start: 0.8020 (m-30) cc_final: 0.7777 (m-30) REVERT: O 84 ARG cc_start: 0.6598 (mtp180) cc_final: 0.6209 (mmm160) REVERT: P 76 LYS cc_start: 0.6449 (mtpp) cc_final: 0.6135 (mttp) REVERT: Q 6 ARG cc_start: 0.5852 (mtp180) cc_final: 0.5152 (ttt180) REVERT: Q 9 GLN cc_start: 0.7987 (tt0) cc_final: 0.7688 (tt0) REVERT: Q 11 ARG cc_start: 0.6593 (ttt90) cc_final: 0.6165 (tmt90) REVERT: Q 17 MET cc_start: 0.6746 (mtm) cc_final: 0.6401 (mtm) REVERT: Q 26 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6812 (mm-30) REVERT: R 48 ARG cc_start: 0.6401 (mpt180) cc_final: 0.6148 (mmt90) REVERT: T 27 MET cc_start: 0.8138 (tmm) cc_final: 0.7734 (tmm) REVERT: U 21 ARG cc_start: 0.5151 (ttt90) cc_final: 0.4775 (ttt-90) REVERT: U 31 GLU cc_start: 0.6028 (OUTLIER) cc_final: 0.5661 (tp30) REVERT: U 44 GLU cc_start: 0.6882 (tt0) cc_final: 0.6565 (tm-30) outliers start: 31 outliers final: 14 residues processed: 308 average time/residue: 2.2368 time to fit residues: 792.6814 Evaluate side-chains 294 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 275 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain K residue 126 LYS Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain O residue 4 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain Q residue 26 GLU Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 31 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 231 optimal weight: 0.9980 chunk 176 optimal weight: 0.0170 chunk 121 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 157 optimal weight: 0.3980 chunk 235 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 223 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN E 78 ASN L 20 ASN O 40 GLN P 63 GLN T 52 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 39364 Z= 0.130 Angle : 0.593 23.234 58689 Z= 0.320 Chirality : 0.040 1.936 7473 Planarity : 0.005 0.125 3267 Dihedral : 22.719 143.925 19277 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.96 % Allowed : 12.22 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.86 (0.22), residues: 1509 helix: 1.55 (0.21), residues: 606 sheet: 0.01 (0.31), residues: 264 loop : -0.03 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 201 HIS 0.003 0.001 HIS D 198 PHE 0.014 0.001 PHE F 8 TYR 0.012 0.001 TYR L 117 ARG 0.009 0.000 ARG B 7 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 284 time to evaluate : 2.354 Fit side-chains REVERT: B 35 ARG cc_start: 0.4547 (mtt90) cc_final: 0.3965 (tpp-160) REVERT: B 63 ARG cc_start: 0.4055 (ttp-110) cc_final: 0.3491 (ttp80) REVERT: B 66 LYS cc_start: 0.4047 (mtmt) cc_final: 0.3531 (mttt) REVERT: B 74 ARG cc_start: 0.3161 (OUTLIER) cc_final: 0.2856 (mtt90) REVERT: B 78 GLU cc_start: 0.4295 (OUTLIER) cc_final: 0.3541 (tm-30) REVERT: B 82 ASP cc_start: 0.5429 (m-30) cc_final: 0.5045 (m-30) REVERT: B 105 LYS cc_start: 0.5274 (pttt) cc_final: 0.4821 (pptt) REVERT: B 106 THR cc_start: 0.5891 (OUTLIER) cc_final: 0.5489 (p) REVERT: B 108 ARG cc_start: 0.5560 (ptm160) cc_final: 0.4437 (ptt90) REVERT: B 154 MET cc_start: 0.3711 (mtt) cc_final: 0.3445 (mtp) REVERT: B 169 GLU cc_start: 0.5607 (mm-30) cc_final: 0.5407 (mm-30) REVERT: C 129 MET cc_start: 0.3415 (mmt) cc_final: 0.2960 (mtt) REVERT: C 166 GLU cc_start: 0.6451 (mt-10) cc_final: 0.6042 (tp30) REVERT: C 169 ARG cc_start: 0.7084 (ttp-170) cc_final: 0.6131 (ttp80) REVERT: C 170 GLU cc_start: 0.7140 (mp0) cc_final: 0.6923 (mp0) REVERT: D 35 GLU cc_start: 0.5635 (mt-10) cc_final: 0.5329 (pm20) REVERT: D 36 GLN cc_start: 0.6293 (tt0) cc_final: 0.5872 (tt0) REVERT: D 47 ARG cc_start: 0.6056 (ttm110) cc_final: 0.5642 (ttp-170) REVERT: D 50 ASP cc_start: 0.6919 (p0) cc_final: 0.6458 (m-30) REVERT: D 73 ARG cc_start: 0.7234 (ttp-170) cc_final: 0.6391 (ttm170) REVERT: D 115 ARG cc_start: 0.6599 (ttt180) cc_final: 0.6368 (ttt180) REVERT: D 156 LYS cc_start: 0.5965 (mtmm) cc_final: 0.5511 (tptm) REVERT: D 166 GLU cc_start: 0.6345 (tt0) cc_final: 0.5867 (pm20) REVERT: E 12 GLN cc_start: 0.6712 (mp10) cc_final: 0.6203 (tt0) REVERT: E 20 ARG cc_start: 0.7743 (ttp-170) cc_final: 0.7477 (ttp-110) REVERT: E 41 ASP cc_start: 0.7157 (p0) cc_final: 0.6675 (p0) REVERT: E 45 ARG cc_start: 0.6465 (ttt90) cc_final: 0.5851 (ttp80) REVERT: E 55 GLU cc_start: 0.6660 (mp0) cc_final: 0.6437 (mp0) REVERT: E 61 GLN cc_start: 0.6444 (tt0) cc_final: 0.6171 (tp40) REVERT: E 69 ARG cc_start: 0.6326 (ptp90) cc_final: 0.5545 (ptm160) REVERT: F 2 ARG cc_start: 0.7109 (mtt-85) cc_final: 0.6791 (mtp85) REVERT: F 44 ARG cc_start: 0.6978 (mtm-85) cc_final: 0.6498 (mtm-85) REVERT: F 55 HIS cc_start: 0.7524 (m90) cc_final: 0.7192 (m170) REVERT: F 90 MET cc_start: 0.7732 (mtm) cc_final: 0.7179 (mtm) REVERT: H 43 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7800 (mm-30) REVERT: H 50 LYS cc_start: 0.7086 (pttt) cc_final: 0.6762 (pttp) REVERT: H 58 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6486 (mp0) REVERT: H 60 GLU cc_start: 0.7367 (tt0) cc_final: 0.6801 (tp30) REVERT: H 88 ARG cc_start: 0.7720 (mtm180) cc_final: 0.7049 (mtp-110) REVERT: K 37 ARG cc_start: 0.5807 (mtp-110) cc_final: 0.5571 (mmm160) REVERT: K 98 ARG cc_start: 0.6349 (mtp180) cc_final: 0.6142 (mtt90) REVERT: K 108 THR cc_start: 0.6504 (p) cc_final: 0.5958 (t) REVERT: L 10 LYS cc_start: 0.7338 (tttt) cc_final: 0.7064 (ttpm) REVERT: L 75 GLN cc_start: 0.5725 (mt0) cc_final: 0.5384 (pt0) REVERT: L 81 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7489 (tp) REVERT: L 108 LYS cc_start: 0.7008 (mmtt) cc_final: 0.6260 (mmtm) REVERT: L 121 ARG cc_start: 0.6994 (ttt-90) cc_final: 0.6742 (ttt180) REVERT: O 2 SER cc_start: 0.6546 (p) cc_final: 0.6251 (t) REVERT: O 57 LEU cc_start: 0.8188 (mt) cc_final: 0.7943 (mm) REVERT: O 62 GLN cc_start: 0.7864 (tt0) cc_final: 0.7362 (tt0) REVERT: P 76 LYS cc_start: 0.6436 (mtpp) cc_final: 0.6111 (mttp) REVERT: Q 6 ARG cc_start: 0.5926 (mtp180) cc_final: 0.5103 (ttt180) REVERT: Q 9 GLN cc_start: 0.7941 (tt0) cc_final: 0.7640 (tt0) REVERT: Q 11 ARG cc_start: 0.6552 (ttt90) cc_final: 0.6139 (tmt90) REVERT: Q 17 MET cc_start: 0.6679 (mtm) cc_final: 0.6315 (mtm) REVERT: Q 26 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6834 (mm-30) REVERT: R 48 ARG cc_start: 0.6329 (mpt180) cc_final: 0.6118 (mmt90) REVERT: T 27 MET cc_start: 0.8110 (tmm) cc_final: 0.7667 (tmm) REVERT: U 21 ARG cc_start: 0.5193 (ttt90) cc_final: 0.4807 (ttt-90) REVERT: U 31 GLU cc_start: 0.5905 (OUTLIER) cc_final: 0.5557 (tp30) REVERT: U 44 GLU cc_start: 0.6904 (tt0) cc_final: 0.6507 (tm-30) outliers start: 25 outliers final: 11 residues processed: 298 average time/residue: 2.1755 time to fit residues: 750.3537 Evaluate side-chains 286 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 269 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain K residue 126 LYS Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain O residue 4 SER Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain Q residue 26 GLU Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 31 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 207 optimal weight: 6.9990 chunk 141 optimal weight: 0.0030 chunk 3 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 212 optimal weight: 3.9990 chunk 172 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 223 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 overall best weight: 3.3998 ------------------------------------------------------------------------------- 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** E 78 ASN K 38 GLN L 20 ASN O 40 GLN T 3 ASN T 52 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 39364 Z= 0.405 Angle : 0.925 22.881 58689 Z= 0.460 Chirality : 0.053 2.029 7473 Planarity : 0.008 0.143 3267 Dihedral : 22.954 142.560 19277 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.90 % Allowed : 12.61 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.12 (0.21), residues: 1509 helix: 0.64 (0.20), residues: 617 sheet: -0.08 (0.31), residues: 275 loop : -0.26 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP P 60 HIS 0.010 0.002 HIS D 198 PHE 0.032 0.003 PHE O 43 TYR 0.021 0.003 TYR L 117 ARG 0.009 0.001 ARG C 127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 271 time to evaluate : 2.579 Fit side-chains revert: symmetry clash REVERT: B 35 ARG cc_start: 0.4476 (mtt90) cc_final: 0.3965 (tpp-160) REVERT: B 49 MET cc_start: 0.3908 (OUTLIER) cc_final: 0.3597 (mtt) REVERT: B 59 LYS cc_start: 0.5583 (tttm) cc_final: 0.5263 (ttpm) REVERT: B 66 LYS cc_start: 0.4051 (mtmt) cc_final: 0.3555 (mttt) REVERT: B 78 GLU cc_start: 0.4453 (OUTLIER) cc_final: 0.3822 (tm-30) REVERT: B 105 LYS cc_start: 0.5364 (pttt) cc_final: 0.5026 (pptt) REVERT: B 108 ARG cc_start: 0.5602 (ptm160) cc_final: 0.4995 (ptm-80) REVERT: B 154 MET cc_start: 0.3943 (mtt) cc_final: 0.3603 (mtp) REVERT: B 169 GLU cc_start: 0.5685 (mm-30) cc_final: 0.5480 (mm-30) REVERT: C 129 MET cc_start: 0.3468 (mmt) cc_final: 0.3245 (mtt) REVERT: C 166 GLU cc_start: 0.6497 (mt-10) cc_final: 0.6138 (tp30) REVERT: C 169 ARG cc_start: 0.7075 (ttp-170) cc_final: 0.6028 (ttp80) REVERT: C 170 GLU cc_start: 0.7144 (mp0) cc_final: 0.6942 (mp0) REVERT: D 35 GLU cc_start: 0.5586 (mt-10) cc_final: 0.5327 (pm20) REVERT: D 36 GLN cc_start: 0.6202 (tt0) cc_final: 0.5733 (tt0) REVERT: D 47 ARG cc_start: 0.5994 (ttm110) cc_final: 0.5593 (ttp-170) REVERT: D 50 ASP cc_start: 0.6791 (p0) cc_final: 0.6429 (m-30) REVERT: D 166 GLU cc_start: 0.6360 (tt0) cc_final: 0.5879 (pm20) REVERT: E 12 GLN cc_start: 0.6604 (mp10) cc_final: 0.6056 (tt0) REVERT: E 20 ARG cc_start: 0.7768 (ttp-170) cc_final: 0.7473 (ttp-110) REVERT: E 45 ARG cc_start: 0.6352 (ttt90) cc_final: 0.5934 (ttp80) REVERT: E 55 GLU cc_start: 0.6770 (mp0) cc_final: 0.6500 (mt-10) REVERT: E 61 GLN cc_start: 0.6544 (tt0) cc_final: 0.6230 (tp40) REVERT: E 69 ARG cc_start: 0.6394 (ptp90) cc_final: 0.5606 (ptm160) REVERT: F 2 ARG cc_start: 0.7191 (mtt-85) cc_final: 0.6871 (mtp85) REVERT: F 44 ARG cc_start: 0.6951 (mtm-85) cc_final: 0.6484 (mtm-85) REVERT: F 90 MET cc_start: 0.7589 (mtm) cc_final: 0.7191 (mtm) REVERT: H 50 LYS cc_start: 0.7164 (pttt) cc_final: 0.6846 (pttp) REVERT: H 58 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6508 (mp0) REVERT: H 60 GLU cc_start: 0.7367 (tt0) cc_final: 0.7035 (tp30) REVERT: H 88 ARG cc_start: 0.7815 (mtm180) cc_final: 0.7118 (mtp-110) REVERT: K 37 ARG cc_start: 0.5951 (mtp180) cc_final: 0.5751 (mtm180) REVERT: K 98 ARG cc_start: 0.6328 (mtp180) cc_final: 0.6043 (mtt90) REVERT: L 10 LYS cc_start: 0.7549 (tttt) cc_final: 0.7342 (ttpp) REVERT: L 75 GLN cc_start: 0.5462 (mt0) cc_final: 0.5147 (pt0) REVERT: L 81 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7664 (tp) REVERT: L 108 LYS cc_start: 0.7054 (mmtt) cc_final: 0.6308 (mmtm) REVERT: L 121 ARG cc_start: 0.6988 (ttt-90) cc_final: 0.6741 (ttt180) REVERT: O 2 SER cc_start: 0.6670 (p) cc_final: 0.6305 (t) REVERT: O 58 ARG cc_start: 0.7900 (ttp-170) cc_final: 0.6810 (ttp-110) REVERT: O 62 GLN cc_start: 0.7911 (tt0) cc_final: 0.7592 (tt0) REVERT: P 76 LYS cc_start: 0.6458 (mtpp) cc_final: 0.6153 (mttp) REVERT: Q 6 ARG cc_start: 0.5805 (mtp180) cc_final: 0.5106 (ttt180) REVERT: Q 9 GLN cc_start: 0.8004 (tt0) cc_final: 0.7709 (mt0) REVERT: Q 11 ARG cc_start: 0.6640 (ttt90) cc_final: 0.6374 (ttp80) REVERT: Q 26 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6910 (mm-30) REVERT: Q 60 GLU cc_start: 0.7158 (tt0) cc_final: 0.6776 (tt0) REVERT: Q 62 ARG cc_start: 0.7827 (ptt-90) cc_final: 0.7588 (ptm-80) REVERT: R 48 ARG cc_start: 0.6429 (mpt180) cc_final: 0.6209 (mmt90) REVERT: T 27 MET cc_start: 0.8152 (tmm) cc_final: 0.7800 (tmm) REVERT: T 39 ILE cc_start: 0.7082 (mm) cc_final: 0.6816 (mt) REVERT: U 21 ARG cc_start: 0.5141 (ttt90) cc_final: 0.4797 (tmt170) REVERT: U 31 GLU cc_start: 0.5864 (OUTLIER) cc_final: 0.5596 (tp30) REVERT: U 44 GLU cc_start: 0.6920 (tt0) cc_final: 0.6620 (tm-30) outliers start: 37 outliers final: 26 residues processed: 296 average time/residue: 2.2558 time to fit residues: 769.4250 Evaluate side-chains 299 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 268 time to evaluate : 2.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain K residue 126 LYS Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain O residue 4 SER Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain Q residue 26 GLU Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 31 GLU Chi-restraints excluded: chain U residue 68 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 83 optimal weight: 4.9990 chunk 224 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 249 optimal weight: 0.6980 chunk 207 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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** E 78 ASN L 20 ASN O 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 39364 Z= 0.256 Angle : 0.736 23.171 58689 Z= 0.381 Chirality : 0.046 1.978 7473 Planarity : 0.007 0.136 3267 Dihedral : 22.863 143.601 19277 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.19 % Allowed : 14.02 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.21), residues: 1509 helix: 0.92 (0.21), residues: 608 sheet: 0.06 (0.31), residues: 257 loop : -0.16 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 201 HIS 0.007 0.002 HIS E 89 PHE 0.021 0.002 PHE O 43 TYR 0.018 0.002 TYR L 117 ARG 0.006 0.001 ARG C 127 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 280 time to evaluate : 2.636 Fit side-chains REVERT: B 7 ARG cc_start: 0.3103 (mpp-170) cc_final: 0.2813 (tpp-160) REVERT: B 35 ARG cc_start: 0.4414 (mtt90) cc_final: 0.3916 (tpp-160) REVERT: B 59 LYS cc_start: 0.5627 (tttm) cc_final: 0.5307 (ttpp) REVERT: B 63 ARG cc_start: 0.4080 (ttp-110) cc_final: 0.3438 (ttp80) REVERT: B 66 LYS cc_start: 0.4054 (mtmt) cc_final: 0.3560 (mttt) REVERT: B 74 ARG cc_start: 0.3522 (mpp80) cc_final: 0.3246 (mtt90) REVERT: B 78 GLU cc_start: 0.4468 (OUTLIER) cc_final: 0.3841 (tm-30) REVERT: B 105 LYS cc_start: 0.5426 (pttt) cc_final: 0.4994 (pptt) REVERT: B 108 ARG cc_start: 0.5549 (ptm160) cc_final: 0.5253 (ptm160) REVERT: B 169 GLU cc_start: 0.5704 (mm-30) cc_final: 0.5486 (mm-30) REVERT: C 129 MET cc_start: 0.3390 (mmt) cc_final: 0.3176 (mtt) REVERT: C 166 GLU cc_start: 0.6577 (mt-10) cc_final: 0.6175 (tp30) REVERT: C 169 ARG cc_start: 0.7082 (ttp-170) cc_final: 0.6050 (ttp80) REVERT: D 35 GLU cc_start: 0.5650 (mt-10) cc_final: 0.5314 (pm20) REVERT: D 36 GLN cc_start: 0.6309 (tt0) cc_final: 0.5842 (tt0) REVERT: D 47 ARG cc_start: 0.5968 (ttm110) cc_final: 0.5557 (ttp-170) REVERT: D 50 ASP cc_start: 0.6947 (p0) cc_final: 0.6514 (m-30) REVERT: D 166 GLU cc_start: 0.6349 (tt0) cc_final: 0.5842 (pm20) REVERT: E 12 GLN cc_start: 0.6637 (mp10) cc_final: 0.6092 (tt0) REVERT: E 20 ARG cc_start: 0.7759 (ttp-170) cc_final: 0.7467 (ttp-110) REVERT: E 45 ARG cc_start: 0.6418 (ttt90) cc_final: 0.5990 (ttp80) REVERT: E 55 GLU cc_start: 0.6751 (mp0) cc_final: 0.6505 (mt-10) REVERT: E 61 GLN cc_start: 0.6502 (tt0) cc_final: 0.6193 (tp40) REVERT: E 69 ARG cc_start: 0.6360 (ptp90) cc_final: 0.5615 (ptm160) REVERT: F 2 ARG cc_start: 0.7188 (mtt-85) cc_final: 0.6806 (mtp85) REVERT: F 44 ARG cc_start: 0.6942 (mtm-85) cc_final: 0.6481 (mtm-85) REVERT: F 90 MET cc_start: 0.7606 (mtm) cc_final: 0.7287 (mtm) REVERT: H 50 LYS cc_start: 0.7174 (pttt) cc_final: 0.6843 (pttp) REVERT: H 58 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6488 (mp0) REVERT: H 60 GLU cc_start: 0.7335 (tt0) cc_final: 0.6867 (tp30) REVERT: H 88 ARG cc_start: 0.7779 (mtm180) cc_final: 0.7084 (mtp-110) REVERT: L 10 LYS cc_start: 0.7528 (tttt) cc_final: 0.7205 (ttpm) REVERT: L 75 GLN cc_start: 0.5472 (mt0) cc_final: 0.5152 (pt0) REVERT: L 81 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7600 (tp) REVERT: L 108 LYS cc_start: 0.7054 (mmtt) cc_final: 0.6301 (mmtm) REVERT: L 121 ARG cc_start: 0.6966 (ttt-90) cc_final: 0.6671 (ttt180) REVERT: O 2 SER cc_start: 0.6678 (p) cc_final: 0.6280 (t) REVERT: O 58 ARG cc_start: 0.7894 (ttp-170) cc_final: 0.6806 (ttp-110) REVERT: O 62 GLN cc_start: 0.7898 (tt0) cc_final: 0.7559 (tt0) REVERT: P 76 LYS cc_start: 0.6472 (mtpp) cc_final: 0.6101 (mttp) REVERT: Q 9 GLN cc_start: 0.7973 (tt0) cc_final: 0.7684 (mt0) REVERT: Q 11 ARG cc_start: 0.6616 (ttt90) cc_final: 0.6357 (ttp80) REVERT: Q 26 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6876 (mm-30) REVERT: Q 60 GLU cc_start: 0.7157 (tt0) cc_final: 0.6756 (tt0) REVERT: T 27 MET cc_start: 0.8134 (tmm) cc_final: 0.7787 (tmm) REVERT: T 39 ILE cc_start: 0.7012 (mm) cc_final: 0.6768 (mt) REVERT: U 21 ARG cc_start: 0.5151 (ttt90) cc_final: 0.4885 (mpp-170) REVERT: U 31 GLU cc_start: 0.5850 (OUTLIER) cc_final: 0.5610 (tp30) REVERT: U 44 GLU cc_start: 0.6967 (tt0) cc_final: 0.6639 (tm-30) outliers start: 28 outliers final: 18 residues processed: 297 average time/residue: 2.2136 time to fit residues: 755.8573 Evaluate side-chains 297 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 275 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain K residue 126 LYS Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain O residue 4 SER Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain Q residue 26 GLU Chi-restraints excluded: chain U residue 31 GLU Chi-restraints excluded: chain U residue 68 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 240 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 182 optimal weight: 0.0070 chunk 141 optimal weight: 0.0020 chunk 210 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.3610 ------------------------------------------------------------------------------- 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** E 78 ASN L 20 ASN O 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39364 Z= 0.202 Angle : 0.684 23.414 58689 Z= 0.360 Chirality : 0.044 1.952 7473 Planarity : 0.006 0.133 3267 Dihedral : 22.870 143.651 19277 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.11 % Allowed : 14.64 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.21), residues: 1509 helix: 1.03 (0.21), residues: 607 sheet: 0.10 (0.31), residues: 255 loop : -0.12 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 201 HIS 0.005 0.001 HIS E 89 PHE 0.017 0.002 PHE O 43 TYR 0.016 0.002 TYR D 51 ARG 0.006 0.001 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 279 time to evaluate : 2.582 Fit side-chains REVERT: B 7 ARG cc_start: 0.3167 (mpp-170) cc_final: 0.2886 (tpp-160) REVERT: B 35 ARG cc_start: 0.4418 (mtt90) cc_final: 0.3904 (tpp-160) REVERT: B 59 LYS cc_start: 0.5634 (tttm) cc_final: 0.5316 (ttpm) REVERT: B 63 ARG cc_start: 0.4081 (ttp-110) cc_final: 0.3439 (ttp80) REVERT: B 66 LYS cc_start: 0.4062 (mtmt) cc_final: 0.3571 (mttt) REVERT: B 74 ARG cc_start: 0.3559 (mpp80) cc_final: 0.3265 (mtt90) REVERT: B 78 GLU cc_start: 0.4471 (OUTLIER) cc_final: 0.3840 (tm-30) REVERT: B 105 LYS cc_start: 0.5456 (pttt) cc_final: 0.5082 (pptt) REVERT: B 108 ARG cc_start: 0.5575 (ptm160) cc_final: 0.4965 (ptm-80) REVERT: B 154 MET cc_start: 0.3853 (mtt) cc_final: 0.3635 (mtp) REVERT: B 169 GLU cc_start: 0.5666 (mm-30) cc_final: 0.5450 (mm-30) REVERT: C 129 MET cc_start: 0.3377 (mmt) cc_final: 0.3145 (mtt) REVERT: C 166 GLU cc_start: 0.6583 (mt-10) cc_final: 0.6172 (tp30) REVERT: C 169 ARG cc_start: 0.7063 (ttp-170) cc_final: 0.6094 (ttp80) REVERT: D 35 GLU cc_start: 0.5610 (mt-10) cc_final: 0.5318 (pm20) REVERT: D 36 GLN cc_start: 0.6298 (tt0) cc_final: 0.5837 (tt0) REVERT: D 47 ARG cc_start: 0.5969 (ttm110) cc_final: 0.5556 (ttp-170) REVERT: D 50 ASP cc_start: 0.6942 (p0) cc_final: 0.6512 (m-30) REVERT: D 156 LYS cc_start: 0.5981 (mtmm) cc_final: 0.5499 (tptm) REVERT: D 166 GLU cc_start: 0.6346 (tt0) cc_final: 0.5840 (pm20) REVERT: E 12 GLN cc_start: 0.6616 (mp10) cc_final: 0.6073 (tt0) REVERT: E 20 ARG cc_start: 0.7753 (ttp-170) cc_final: 0.7464 (ttp-110) REVERT: E 45 ARG cc_start: 0.6456 (ttt90) cc_final: 0.6000 (ttp80) REVERT: E 55 GLU cc_start: 0.6706 (mp0) cc_final: 0.6467 (mt-10) REVERT: E 61 GLN cc_start: 0.6510 (tt0) cc_final: 0.6178 (tp40) REVERT: E 69 ARG cc_start: 0.6361 (ptp90) cc_final: 0.5608 (ptm160) REVERT: F 2 ARG cc_start: 0.7176 (mtt-85) cc_final: 0.6785 (mtp85) REVERT: F 44 ARG cc_start: 0.6945 (mtm-85) cc_final: 0.6481 (mtm-85) REVERT: F 90 MET cc_start: 0.7620 (mtm) cc_final: 0.7251 (mtm) REVERT: H 50 LYS cc_start: 0.7175 (pttt) cc_final: 0.6838 (pttp) REVERT: H 58 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6435 (mp0) REVERT: H 60 GLU cc_start: 0.7328 (tt0) cc_final: 0.6868 (tp30) REVERT: H 88 ARG cc_start: 0.7776 (mtm180) cc_final: 0.7083 (mtp-110) REVERT: L 10 LYS cc_start: 0.7515 (tttt) cc_final: 0.7197 (ttpm) REVERT: L 75 GLN cc_start: 0.5539 (mt0) cc_final: 0.5185 (pt0) REVERT: L 81 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7585 (tp) REVERT: L 108 LYS cc_start: 0.7053 (mmtt) cc_final: 0.6300 (mmtm) REVERT: L 121 ARG cc_start: 0.6953 (ttt-90) cc_final: 0.6738 (ttt180) REVERT: O 2 SER cc_start: 0.6682 (p) cc_final: 0.6281 (t) REVERT: O 58 ARG cc_start: 0.7884 (ttp-170) cc_final: 0.6800 (ttp-110) REVERT: O 62 GLN cc_start: 0.7896 (tt0) cc_final: 0.7554 (tt0) REVERT: P 76 LYS cc_start: 0.6467 (mtpp) cc_final: 0.6092 (mttp) REVERT: Q 9 GLN cc_start: 0.7980 (tt0) cc_final: 0.7733 (tt0) REVERT: Q 11 ARG cc_start: 0.6617 (ttt90) cc_final: 0.6353 (ttp80) REVERT: Q 26 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6882 (mm-30) REVERT: Q 60 GLU cc_start: 0.7163 (tt0) cc_final: 0.6754 (tt0) REVERT: T 27 MET cc_start: 0.8128 (tmm) cc_final: 0.7783 (tmm) REVERT: U 21 ARG cc_start: 0.5171 (ttt90) cc_final: 0.4889 (mpp-170) REVERT: U 31 GLU cc_start: 0.5860 (OUTLIER) cc_final: 0.5603 (tp30) REVERT: U 44 GLU cc_start: 0.6937 (tt0) cc_final: 0.6592 (tm-30) outliers start: 27 outliers final: 18 residues processed: 294 average time/residue: 2.2031 time to fit residues: 745.8090 Evaluate side-chains 300 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 278 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain K residue 126 LYS Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain O residue 4 SER Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain Q residue 26 GLU Chi-restraints excluded: chain U residue 31 GLU Chi-restraints excluded: chain U residue 68 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 153 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 158 optimal weight: 7.9990 chunk 169 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 226 optimal weight: 0.1980 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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** L 20 ASN O 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 39364 Z= 0.307 Angle : 0.795 23.066 58689 Z= 0.406 Chirality : 0.048 1.995 7473 Planarity : 0.007 0.138 3267 Dihedral : 22.892 143.318 19277 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.19 % Allowed : 14.88 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 (0.21), residues: 1509 helix: 0.84 (0.20), residues: 607 sheet: 0.06 (0.31), residues: 257 loop : -0.16 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 201 HIS 0.008 0.002 HIS E 89 PHE 0.025 0.002 PHE O 43 TYR 0.019 0.003 TYR L 117 ARG 0.006 0.001 ARG C 127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 274 time to evaluate : 2.541 Fit side-chains REVERT: B 7 ARG cc_start: 0.3171 (mpp-170) cc_final: 0.2890 (tpp-160) REVERT: B 35 ARG cc_start: 0.4424 (mtt90) cc_final: 0.3905 (tpp-160) REVERT: B 59 LYS cc_start: 0.5620 (tttm) cc_final: 0.5294 (ttpm) REVERT: B 63 ARG cc_start: 0.4138 (ttp-110) cc_final: 0.3881 (ptp90) REVERT: B 74 ARG cc_start: 0.3570 (mpp80) cc_final: 0.3218 (mtt90) REVERT: B 78 GLU cc_start: 0.4490 (OUTLIER) cc_final: 0.4046 (pm20) REVERT: B 105 LYS cc_start: 0.5369 (pttt) cc_final: 0.5018 (pttt) REVERT: B 108 ARG cc_start: 0.5560 (ptm160) cc_final: 0.5237 (ptm160) REVERT: B 154 MET cc_start: 0.3870 (mtt) cc_final: 0.3528 (mtp) REVERT: B 169 GLU cc_start: 0.5677 (mm-30) cc_final: 0.5434 (mm-30) REVERT: C 129 MET cc_start: 0.3394 (mmt) cc_final: 0.3173 (mtt) REVERT: C 166 GLU cc_start: 0.6563 (mt-10) cc_final: 0.6185 (tp30) REVERT: C 169 ARG cc_start: 0.7086 (ttp-170) cc_final: 0.6045 (ttp80) REVERT: D 35 GLU cc_start: 0.5683 (mt-10) cc_final: 0.5361 (pm20) REVERT: D 36 GLN cc_start: 0.6281 (tt0) cc_final: 0.5813 (tt0) REVERT: D 47 ARG cc_start: 0.5942 (ttm110) cc_final: 0.5542 (ttp-170) REVERT: D 50 ASP cc_start: 0.6945 (p0) cc_final: 0.6527 (m-30) REVERT: D 166 GLU cc_start: 0.6343 (tt0) cc_final: 0.5863 (pm20) REVERT: E 12 GLN cc_start: 0.6588 (mp10) cc_final: 0.6058 (tt0) REVERT: E 20 ARG cc_start: 0.7759 (ttp-170) cc_final: 0.7470 (ttp-110) REVERT: E 45 ARG cc_start: 0.6429 (ttt90) cc_final: 0.5980 (ttp80) REVERT: E 55 GLU cc_start: 0.6696 (mp0) cc_final: 0.6462 (mt-10) REVERT: E 61 GLN cc_start: 0.6511 (tt0) cc_final: 0.6179 (tp40) REVERT: E 69 ARG cc_start: 0.6376 (ptp90) cc_final: 0.5597 (ptm160) REVERT: F 2 ARG cc_start: 0.7171 (mtt-85) cc_final: 0.6784 (mtp85) REVERT: F 44 ARG cc_start: 0.6925 (mtm-85) cc_final: 0.6595 (mtm-85) REVERT: F 90 MET cc_start: 0.7598 (mtm) cc_final: 0.7178 (mtm) REVERT: H 50 LYS cc_start: 0.7168 (pttt) cc_final: 0.6829 (pttp) REVERT: H 58 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6476 (mp0) REVERT: H 60 GLU cc_start: 0.7351 (tt0) cc_final: 0.7022 (tp30) REVERT: H 88 ARG cc_start: 0.7806 (mtm180) cc_final: 0.7105 (mtp-110) REVERT: L 75 GLN cc_start: 0.5444 (mt0) cc_final: 0.5090 (pt0) REVERT: L 81 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7630 (tp) REVERT: L 108 LYS cc_start: 0.7025 (mmtt) cc_final: 0.6291 (mmtm) REVERT: L 121 ARG cc_start: 0.6946 (ttt-90) cc_final: 0.6709 (ttt180) REVERT: O 2 SER cc_start: 0.6609 (p) cc_final: 0.6211 (t) REVERT: O 58 ARG cc_start: 0.7899 (ttp-170) cc_final: 0.6806 (ttp-110) REVERT: O 62 GLN cc_start: 0.7910 (tt0) cc_final: 0.7574 (tt0) REVERT: P 76 LYS cc_start: 0.6463 (mtpp) cc_final: 0.6085 (mttp) REVERT: Q 9 GLN cc_start: 0.7984 (tt0) cc_final: 0.7759 (tt0) REVERT: Q 11 ARG cc_start: 0.6612 (ttt90) cc_final: 0.6351 (ttp80) REVERT: Q 26 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6875 (mm-30) REVERT: Q 60 GLU cc_start: 0.7137 (tt0) cc_final: 0.6732 (tt0) REVERT: Q 62 ARG cc_start: 0.7833 (ptt-90) cc_final: 0.7588 (ptm-80) REVERT: T 27 MET cc_start: 0.8142 (tmm) cc_final: 0.7756 (tmm) REVERT: T 39 ILE cc_start: 0.7013 (mm) cc_final: 0.6780 (mt) REVERT: U 21 ARG cc_start: 0.5148 (ttt90) cc_final: 0.4870 (mtp180) REVERT: U 31 GLU cc_start: 0.5878 (OUTLIER) cc_final: 0.5638 (tp30) REVERT: U 44 GLU cc_start: 0.6937 (tt0) cc_final: 0.6631 (tm-30) outliers start: 28 outliers final: 21 residues processed: 290 average time/residue: 2.2266 time to fit residues: 743.4510 Evaluate side-chains 298 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 273 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain K residue 126 LYS Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain O residue 4 SER Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain Q residue 26 GLU Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain U residue 31 GLU Chi-restraints excluded: chain U residue 68 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 238 optimal weight: 1.9990 chunk 217 optimal weight: 0.0170 chunk 231 optimal weight: 3.9990 chunk 139 optimal weight: 0.5980 chunk 100 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 209 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 overall best weight: 1.3224 ------------------------------------------------------------------------------- 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** L 20 ASN O 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 39364 Z= 0.196 Angle : 0.664 23.241 58689 Z= 0.350 Chirality : 0.043 1.961 7473 Planarity : 0.006 0.130 3267 Dihedral : 22.818 143.675 19277 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.96 % Allowed : 15.51 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.59 (0.21), residues: 1509 helix: 1.11 (0.21), residues: 608 sheet: 0.13 (0.31), residues: 255 loop : -0.07 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 201 HIS 0.005 0.001 HIS E 89 PHE 0.018 0.002 PHE O 43 TYR 0.015 0.002 TYR L 117 ARG 0.005 0.000 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 284 time to evaluate : 2.510 Fit side-chains REVERT: B 35 ARG cc_start: 0.4284 (mtt90) cc_final: 0.3776 (tpp-160) REVERT: B 59 LYS cc_start: 0.5616 (tttm) cc_final: 0.5300 (ttpm) REVERT: B 63 ARG cc_start: 0.4017 (ttp-110) cc_final: 0.3388 (ttp80) REVERT: B 78 GLU cc_start: 0.4487 (OUTLIER) cc_final: 0.4050 (pm20) REVERT: B 105 LYS cc_start: 0.5371 (pttt) cc_final: 0.5070 (pttt) REVERT: B 106 THR cc_start: 0.5959 (OUTLIER) cc_final: 0.5520 (p) REVERT: B 108 ARG cc_start: 0.5578 (ptm160) cc_final: 0.4977 (ptm-80) REVERT: B 154 MET cc_start: 0.3773 (mtt) cc_final: 0.3436 (mtp) REVERT: B 169 GLU cc_start: 0.5641 (mm-30) cc_final: 0.5417 (mm-30) REVERT: C 129 MET cc_start: 0.3378 (mmt) cc_final: 0.3135 (mtt) REVERT: C 166 GLU cc_start: 0.6553 (mt-10) cc_final: 0.6174 (tp30) REVERT: C 169 ARG cc_start: 0.7047 (ttp-170) cc_final: 0.6009 (ttp80) REVERT: D 35 GLU cc_start: 0.5695 (mt-10) cc_final: 0.5427 (pm20) REVERT: D 36 GLN cc_start: 0.6333 (tt0) cc_final: 0.5833 (tt0) REVERT: D 47 ARG cc_start: 0.5955 (ttm110) cc_final: 0.5546 (ttp-170) REVERT: D 50 ASP cc_start: 0.6966 (p0) cc_final: 0.6511 (m-30) REVERT: D 156 LYS cc_start: 0.5904 (mtmm) cc_final: 0.5421 (tptm) REVERT: D 166 GLU cc_start: 0.6426 (tt0) cc_final: 0.5927 (pm20) REVERT: E 12 GLN cc_start: 0.6672 (mp10) cc_final: 0.6103 (tt0) REVERT: E 20 ARG cc_start: 0.7768 (ttp-170) cc_final: 0.7479 (ttp-110) REVERT: E 45 ARG cc_start: 0.6467 (ttt90) cc_final: 0.5970 (ttp80) REVERT: E 55 GLU cc_start: 0.6609 (mp0) cc_final: 0.6359 (mt-10) REVERT: E 61 GLN cc_start: 0.6442 (tt0) cc_final: 0.6146 (tp40) REVERT: E 69 ARG cc_start: 0.6362 (ptp90) cc_final: 0.5581 (ptm160) REVERT: F 2 ARG cc_start: 0.7134 (mtt-85) cc_final: 0.6733 (mtp85) REVERT: F 44 ARG cc_start: 0.6965 (mtm-85) cc_final: 0.6487 (mtm-85) REVERT: F 90 MET cc_start: 0.7630 (mtm) cc_final: 0.7273 (mtm) REVERT: F 93 LYS cc_start: 0.6542 (ttmt) cc_final: 0.6026 (mtpt) REVERT: H 50 LYS cc_start: 0.7207 (pttt) cc_final: 0.6871 (pttp) REVERT: H 58 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6436 (mp0) REVERT: H 60 GLU cc_start: 0.7305 (tt0) cc_final: 0.6850 (tp30) REVERT: H 88 ARG cc_start: 0.7765 (mtm180) cc_final: 0.7076 (mtp-110) REVERT: K 106 ARG cc_start: 0.5884 (ttt180) cc_final: 0.5568 (ttt180) REVERT: L 75 GLN cc_start: 0.5496 (mt0) cc_final: 0.5159 (pt0) REVERT: L 81 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7561 (tp) REVERT: L 108 LYS cc_start: 0.7032 (mmtt) cc_final: 0.6329 (mmtm) REVERT: O 2 SER cc_start: 0.6602 (p) cc_final: 0.6207 (t) REVERT: O 57 LEU cc_start: 0.8211 (mt) cc_final: 0.7943 (mm) REVERT: O 58 ARG cc_start: 0.7884 (ttp-170) cc_final: 0.6804 (ttp-110) REVERT: O 62 GLN cc_start: 0.7892 (tt0) cc_final: 0.7552 (tt0) REVERT: P 76 LYS cc_start: 0.6478 (mtpp) cc_final: 0.6252 (mttp) REVERT: Q 9 GLN cc_start: 0.7933 (tt0) cc_final: 0.7486 (mt0) REVERT: Q 11 ARG cc_start: 0.6637 (ttt90) cc_final: 0.6372 (ttp80) REVERT: Q 26 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6870 (mm-30) REVERT: Q 60 GLU cc_start: 0.7166 (tt0) cc_final: 0.6746 (tt0) REVERT: T 27 MET cc_start: 0.8130 (tmm) cc_final: 0.7787 (tmm) REVERT: U 21 ARG cc_start: 0.5119 (ttt90) cc_final: 0.4847 (mtp180) REVERT: U 31 GLU cc_start: 0.5852 (OUTLIER) cc_final: 0.5616 (tp30) REVERT: U 44 GLU cc_start: 0.6927 (tt0) cc_final: 0.6584 (tm-30) outliers start: 25 outliers final: 16 residues processed: 300 average time/residue: 2.2386 time to fit residues: 775.3445 Evaluate side-chains 303 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 282 time to evaluate : 2.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain K residue 126 LYS Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain O residue 4 SER Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain Q residue 26 GLU Chi-restraints excluded: chain U residue 31 GLU Chi-restraints excluded: chain U residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 245 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 257 optimal weight: 4.9990 chunk 236 optimal weight: 6.9990 chunk 204 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 158 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 162 optimal weight: 0.4980 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 HIS E 43 ASN L 20 ASN O 40 GLN P 63 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 39364 Z= 0.253 Angle : 0.732 23.220 58689 Z= 0.379 Chirality : 0.046 1.978 7473 Planarity : 0.007 0.134 3267 Dihedral : 22.865 143.733 19277 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.88 % Allowed : 15.66 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 (0.21), residues: 1509 helix: 0.97 (0.21), residues: 613 sheet: 0.12 (0.31), residues: 255 loop : -0.11 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 201 HIS 0.007 0.002 HIS E 89 PHE 0.020 0.002 PHE O 43 TYR 0.017 0.003 TYR L 117 ARG 0.009 0.001 ARG B 7 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 277 time to evaluate : 2.368 Fit side-chains revert: symmetry clash REVERT: B 35 ARG cc_start: 0.4332 (mtt90) cc_final: 0.3863 (tpp-160) REVERT: B 59 LYS cc_start: 0.5615 (tttm) cc_final: 0.5287 (ttpm) REVERT: B 63 ARG cc_start: 0.4151 (ttp-110) cc_final: 0.3854 (ptp90) REVERT: B 78 GLU cc_start: 0.4507 (OUTLIER) cc_final: 0.4066 (pm20) REVERT: B 105 LYS cc_start: 0.5343 (pttt) cc_final: 0.5021 (pttt) REVERT: B 106 THR cc_start: 0.5947 (OUTLIER) cc_final: 0.5475 (p) REVERT: B 108 ARG cc_start: 0.5566 (ptm160) cc_final: 0.5266 (ptm160) REVERT: B 154 MET cc_start: 0.3989 (mtt) cc_final: 0.3608 (mtp) REVERT: B 169 GLU cc_start: 0.5661 (mm-30) cc_final: 0.5438 (mm-30) REVERT: C 129 MET cc_start: 0.3393 (mmt) cc_final: 0.3149 (mtt) REVERT: C 166 GLU cc_start: 0.6570 (mt-10) cc_final: 0.6207 (tp30) REVERT: C 169 ARG cc_start: 0.7083 (ttp-170) cc_final: 0.6132 (ttp80) REVERT: D 35 GLU cc_start: 0.5631 (mt-10) cc_final: 0.5342 (pm20) REVERT: D 36 GLN cc_start: 0.6316 (tt0) cc_final: 0.5866 (tt0) REVERT: D 47 ARG cc_start: 0.5938 (ttm110) cc_final: 0.4777 (pmt-80) REVERT: D 50 ASP cc_start: 0.6995 (p0) cc_final: 0.6551 (m-30) REVERT: D 156 LYS cc_start: 0.5908 (mtmm) cc_final: 0.5432 (tptm) REVERT: D 166 GLU cc_start: 0.6388 (tt0) cc_final: 0.5904 (pm20) REVERT: E 12 GLN cc_start: 0.6620 (mp10) cc_final: 0.6068 (tt0) REVERT: E 20 ARG cc_start: 0.7757 (ttp-170) cc_final: 0.7468 (ttp-110) REVERT: E 45 ARG cc_start: 0.6452 (ttt90) cc_final: 0.5954 (ttp80) REVERT: E 55 GLU cc_start: 0.6630 (mp0) cc_final: 0.6384 (mt-10) REVERT: E 61 GLN cc_start: 0.6529 (tt0) cc_final: 0.6201 (tp40) REVERT: E 69 ARG cc_start: 0.6366 (ptp90) cc_final: 0.5601 (ptm160) REVERT: F 2 ARG cc_start: 0.7144 (mtt-85) cc_final: 0.6746 (mtp85) REVERT: F 44 ARG cc_start: 0.6948 (mtm-85) cc_final: 0.6618 (mtm-85) REVERT: F 90 MET cc_start: 0.7616 (mtm) cc_final: 0.7199 (mtm) REVERT: F 102 MET cc_start: 0.5667 (mmt) cc_final: 0.5132 (mpt) REVERT: H 50 LYS cc_start: 0.7205 (pttt) cc_final: 0.6866 (pttp) REVERT: H 58 GLU cc_start: 0.7125 (mm-30) cc_final: 0.6439 (mp0) REVERT: H 60 GLU cc_start: 0.7317 (tt0) cc_final: 0.6857 (tp30) REVERT: H 88 ARG cc_start: 0.7777 (mtm180) cc_final: 0.7078 (mtp-110) REVERT: L 75 GLN cc_start: 0.5454 (mt0) cc_final: 0.5110 (pt0) REVERT: L 81 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7610 (tp) REVERT: L 108 LYS cc_start: 0.7012 (mmtt) cc_final: 0.6296 (mmtm) REVERT: O 2 SER cc_start: 0.6613 (p) cc_final: 0.6209 (t) REVERT: O 58 ARG cc_start: 0.7892 (ttp-170) cc_final: 0.6804 (ttp-110) REVERT: O 62 GLN cc_start: 0.7908 (tt0) cc_final: 0.7569 (tt0) REVERT: P 76 LYS cc_start: 0.6467 (mtpp) cc_final: 0.6242 (mttp) REVERT: Q 9 GLN cc_start: 0.7947 (tt0) cc_final: 0.7511 (mt0) REVERT: Q 11 ARG cc_start: 0.6630 (ttt90) cc_final: 0.6377 (ttp80) REVERT: Q 26 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6886 (mm-30) REVERT: Q 60 GLU cc_start: 0.7152 (tt0) cc_final: 0.6737 (tt0) REVERT: Q 62 ARG cc_start: 0.7831 (ptt-90) cc_final: 0.7588 (ptm-80) REVERT: T 27 MET cc_start: 0.8138 (tmm) cc_final: 0.7792 (tmm) REVERT: U 21 ARG cc_start: 0.5072 (ttt90) cc_final: 0.4837 (mtp180) REVERT: U 31 GLU cc_start: 0.5852 (OUTLIER) cc_final: 0.5614 (tp30) REVERT: U 44 GLU cc_start: 0.6901 (tt0) cc_final: 0.6620 (tm-30) outliers start: 24 outliers final: 16 residues processed: 290 average time/residue: 2.2260 time to fit residues: 745.5296 Evaluate side-chains 296 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 275 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain K residue 126 LYS Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain O residue 4 SER Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain Q residue 26 GLU Chi-restraints excluded: chain U residue 31 GLU Chi-restraints excluded: chain U residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 218 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 188 optimal weight: 0.0980 chunk 30 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 205 optimal weight: 0.0670 chunk 85 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 179 optimal weight: 0.8980 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 ASN L 20 ASN O 40 GLN P 63 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.146408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.115692 restraints weight = 36515.188| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 0.56 r_work: 0.3260 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 39364 Z= 0.188 Angle : 0.663 23.501 58689 Z= 0.351 Chirality : 0.043 1.940 7473 Planarity : 0.006 0.131 3267 Dihedral : 22.874 143.755 19277 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.72 % Allowed : 16.05 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.55 (0.21), residues: 1509 helix: 1.09 (0.21), residues: 606 sheet: -0.01 (0.30), residues: 265 loop : -0.03 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 201 HIS 0.006 0.001 HIS P 9 PHE 0.014 0.002 PHE O 43 TYR 0.016 0.002 TYR D 51 ARG 0.007 0.001 ARG E 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13497.88 seconds wall clock time: 241 minutes 54.15 seconds (14514.15 seconds total)