Starting phenix.real_space_refine on Tue Apr 16 05:30:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cai_16526/04_2024/8cai_16526_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cai_16526/04_2024/8cai_16526.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cai_16526/04_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_16526/04_2024/8cai_16526_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cai_16526/04_2024/8cai_16526_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cai_16526/04_2024/8cai_16526.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cai_16526/04_2024/8cai_16526.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cai_16526/04_2024/8cai_16526_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cai_16526/04_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 20.49, per 1000 atoms: 0.54 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: 23.01 Conformation dependent library (CDL) restraints added in 2.3 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: 22.44 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: 66.37 Time building geometry restraints manager: 23.63 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=" 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 angle pdb=" O3' C A 176 " pdb=" P G A 177 " pdb=" O5' G A 177 " ideal model delta sigma weight residual 104.00 93.72 10.28 1.50e+00 4.44e-01 4.70e+01 ... (remaining 58684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.20: 22002 29.20 - 58.39: 1952 58.39 - 87.59: 1225 87.59 - 116.79: 21 116.79 - 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: 11.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 29.140 Check model and map are aligned: 0.500 Set scattering table: 0.330 Process input model: 167.440 Find NCS groups from input model: 1.070 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:12.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 222.380 ------------------------------------------------------------------------------- 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 19.209 58689 Z= 0.940 Chirality : 0.129 4.893 7473 Planarity : 0.025 0.616 3267 Dihedral : 22.075 145.982 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 : 2.454 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: 2.2339 time to fit residues: 915.1458 Evaluate side-chains 289 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 284 time to evaluate : 2.450 ------------------------------------------------------------------------------- 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: 0.7857 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 39364 Z= 0.142 Angle : 0.626 22.618 58689 Z= 0.337 Chirality : 0.042 1.962 7473 Planarity : 0.006 0.124 3267 Dihedral : 22.729 143.921 19288 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.12 % Favored : 97.81 % Rotamer: Outliers : 1.80 % Allowed : 9.16 % Favored : 89.04 % 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: 0.22 (0.21), residues: 1509 helix: 1.04 (0.20), residues: 609 sheet: -0.39 (0.29), residues: 278 loop : -0.37 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 201 HIS 0.008 0.001 HIS F 11 PHE 0.016 0.002 PHE Q 28 TYR 0.015 0.002 TYR L 117 ARG 0.005 0.001 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 334 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 311 time to evaluate : 1.588 Fit side-chains REVERT: B 27 MET cc_start: 0.6638 (mmm) cc_final: 0.6375 (mmm) REVERT: B 35 ARG cc_start: 0.4404 (mtt90) cc_final: 0.3918 (tpp-160) REVERT: B 66 LYS cc_start: 0.3976 (mtmt) cc_final: 0.3454 (mttt) REVERT: B 105 LYS cc_start: 0.5170 (pttt) cc_final: 0.4827 (pptt) REVERT: B 108 ARG cc_start: 0.5429 (ptm160) cc_final: 0.4878 (ptm-80) REVERT: B 169 GLU cc_start: 0.5585 (mm-30) cc_final: 0.5358 (mm-30) REVERT: C 129 MET cc_start: 0.3522 (mmt) cc_final: 0.3243 (mtt) REVERT: C 166 GLU cc_start: 0.6430 (mt-10) cc_final: 0.6048 (tp30) REVERT: C 169 ARG cc_start: 0.7121 (ttp-170) cc_final: 0.6173 (ttp80) REVERT: C 170 GLU cc_start: 0.7192 (mp0) cc_final: 0.6936 (mp0) REVERT: D 35 GLU cc_start: 0.5564 (mt-10) cc_final: 0.5251 (pm20) REVERT: D 36 GLN cc_start: 0.6339 (tt0) cc_final: 0.5948 (tt0) REVERT: D 47 ARG cc_start: 0.5922 (ttm110) cc_final: 0.5436 (ttp-110) REVERT: D 50 ASP cc_start: 0.6875 (p0) cc_final: 0.6398 (m-30) REVERT: D 57 GLU cc_start: 0.7832 (tp30) cc_final: 0.7601 (tp30) REVERT: D 115 ARG cc_start: 0.6631 (ttt180) cc_final: 0.6402 (ttt180) REVERT: D 166 GLU cc_start: 0.6092 (tt0) cc_final: 0.5674 (tp30) REVERT: E 12 GLN cc_start: 0.6852 (mp10) cc_final: 0.6337 (tt0) REVERT: E 13 GLU cc_start: 0.7307 (mt-10) cc_final: 0.7057 (mt-10) REVERT: E 20 ARG cc_start: 0.7819 (ttp-170) cc_final: 0.7538 (ttp-110) REVERT: E 41 ASP cc_start: 0.7136 (p0) cc_final: 0.6607 (p0) REVERT: E 45 ARG cc_start: 0.6449 (ttt90) cc_final: 0.5793 (ttp80) REVERT: E 55 GLU cc_start: 0.6765 (mp0) cc_final: 0.6460 (mt-10) REVERT: E 61 GLN cc_start: 0.6482 (tt0) cc_final: 0.6180 (tp40) REVERT: E 64 MET cc_start: 0.6862 (mmt) cc_final: 0.6554 (mmt) REVERT: E 69 ARG cc_start: 0.6134 (ptp90) cc_final: 0.5333 (ptm160) REVERT: E 142 ASP cc_start: 0.6665 (t70) cc_final: 0.6374 (t70) REVERT: F 2 ARG cc_start: 0.7045 (mtt-85) cc_final: 0.6720 (mtp85) REVERT: F 44 ARG cc_start: 0.7069 (mtm-85) cc_final: 0.6589 (mtm-85) REVERT: F 55 HIS cc_start: 0.7493 (m90) cc_final: 0.7138 (m170) REVERT: F 90 MET cc_start: 0.7751 (mtm) cc_final: 0.7366 (mtm) REVERT: H 43 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7768 (mm-30) REVERT: H 50 LYS cc_start: 0.7137 (pttt) cc_final: 0.6839 (pttp) REVERT: H 58 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6540 (mp0) REVERT: H 60 GLU cc_start: 0.7356 (tt0) cc_final: 0.6796 (tp30) REVERT: H 88 ARG cc_start: 0.7739 (mtm180) cc_final: 0.7100 (mtp-110) REVERT: H 114 ARG cc_start: 0.6941 (ttm110) cc_final: 0.6128 (ttm-80) REVERT: K 37 ARG cc_start: 0.5920 (mtp-110) cc_final: 0.5619 (mmm160) REVERT: K 87 LYS cc_start: 0.7529 (ttmt) cc_final: 0.7181 (ttmm) REVERT: K 98 ARG cc_start: 0.6376 (mtp180) cc_final: 0.6166 (mtt90) REVERT: K 108 THR cc_start: 0.6380 (p) cc_final: 0.5820 (t) REVERT: L 10 LYS cc_start: 0.7390 (tttt) cc_final: 0.7096 (ttpm) REVERT: L 25 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6785 (mm-30) REVERT: L 36 ARG cc_start: 0.5816 (ttp80) cc_final: 0.5594 (ttm170) REVERT: L 64 THR cc_start: 0.7994 (m) cc_final: 0.7577 (p) REVERT: L 75 GLN cc_start: 0.5784 (mt0) cc_final: 0.5403 (pt0) REVERT: L 81 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7532 (tp) REVERT: L 108 LYS cc_start: 0.7019 (mmtt) cc_final: 0.6233 (mmtm) REVERT: L 121 ARG cc_start: 0.7068 (ttt-90) cc_final: 0.6653 (ttp80) REVERT: O 2 SER cc_start: 0.6564 (p) cc_final: 0.6314 (m) REVERT: O 10 LYS cc_start: 0.6477 (mptt) cc_final: 0.6122 (tttt) REVERT: O 57 LEU cc_start: 0.8234 (mt) cc_final: 0.7944 (mm) REVERT: O 58 ARG cc_start: 0.7808 (ttp-170) cc_final: 0.6752 (ttp-110) REVERT: O 62 GLN cc_start: 0.7892 (tt0) cc_final: 0.7531 (tt0) REVERT: O 68 ASP cc_start: 0.8064 (m-30) cc_final: 0.7740 (m-30) REVERT: O 84 ARG cc_start: 0.6602 (mtp180) cc_final: 0.6220 (mmm160) REVERT: P 53 ASP cc_start: 0.7396 (t0) cc_final: 0.7181 (t0) REVERT: P 76 LYS cc_start: 0.6339 (mtpp) cc_final: 0.5911 (mttp) REVERT: Q 6 ARG cc_start: 0.5934 (mtp180) cc_final: 0.5063 (ttt180) REVERT: Q 9 GLN cc_start: 0.8016 (tt0) cc_final: 0.7661 (tt0) REVERT: Q 11 ARG cc_start: 0.6472 (ttt90) cc_final: 0.6183 (mtp-110) REVERT: Q 17 MET cc_start: 0.6819 (mtm) cc_final: 0.6466 (mtm) REVERT: R 44 ILE cc_start: 0.7605 (mm) cc_final: 0.7399 (mm) REVERT: R 48 ARG cc_start: 0.6233 (mpt180) cc_final: 0.5958 (mmt90) REVERT: T 27 MET cc_start: 0.8054 (tmm) cc_final: 0.7645 (tmm) REVERT: U 21 ARG cc_start: 0.5170 (ttt90) cc_final: 0.4803 (ttt-90) REVERT: U 31 GLU cc_start: 0.5859 (OUTLIER) cc_final: 0.5491 (tp30) REVERT: U 44 GLU cc_start: 0.6933 (tt0) cc_final: 0.6462 (tm-30) outliers start: 23 outliers final: 6 residues processed: 322 average time/residue: 1.4972 time to fit residues: 556.7728 Evaluate side-chains 294 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 286 time to evaluate : 2.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU 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: 10.0000 chunk 72 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 159 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 234 optimal weight: 6.9990 chunk 253 optimal weight: 0.9980 chunk 209 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 188 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 HIS E 19 ASN E 73 ASN E 77 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 39364 Z= 0.344 Angle : 0.852 23.200 58689 Z= 0.431 Chirality : 0.050 1.995 7473 Planarity : 0.008 0.141 3267 Dihedral : 22.957 143.193 19277 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.98 % Allowed : 11.28 % Favored : 85.75 % 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: 0.06 (0.21), residues: 1509 helix: 0.66 (0.20), residues: 617 sheet: -0.11 (0.30), residues: 267 loop : -0.36 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP P 60 HIS 0.008 0.002 HIS D 198 PHE 0.030 0.003 PHE O 43 TYR 0.024 0.003 TYR L 117 ARG 0.008 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 312 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 274 time to evaluate : 2.363 Fit side-chains REVERT: B 35 ARG cc_start: 0.4561 (mtt90) cc_final: 0.4030 (tpp-160) REVERT: B 66 LYS cc_start: 0.4024 (mtmt) cc_final: 0.3522 (mttt) REVERT: B 78 GLU cc_start: 0.4481 (OUTLIER) cc_final: 0.3847 (tm-30) REVERT: B 105 LYS cc_start: 0.5256 (pttt) cc_final: 0.4906 (pptt) REVERT: B 108 ARG cc_start: 0.5534 (ptm160) cc_final: 0.4916 (ptm160) REVERT: B 112 LYS cc_start: 0.4454 (OUTLIER) cc_final: 0.3874 (mtpt) REVERT: B 169 GLU cc_start: 0.5676 (mm-30) cc_final: 0.5441 (mm-30) REVERT: C 164 ARG cc_start: 0.5101 (OUTLIER) cc_final: 0.4390 (ttt-90) REVERT: C 166 GLU cc_start: 0.6517 (mt-10) cc_final: 0.6280 (tp30) REVERT: C 169 ARG cc_start: 0.7059 (ttp-170) cc_final: 0.6026 (ttp80) REVERT: C 170 GLU cc_start: 0.7092 (mp0) cc_final: 0.6876 (mp0) REVERT: D 35 GLU cc_start: 0.5599 (mt-10) cc_final: 0.5326 (pm20) REVERT: D 36 GLN cc_start: 0.6351 (tt0) cc_final: 0.5914 (tt0) REVERT: D 47 ARG cc_start: 0.6011 (ttm110) cc_final: 0.5613 (ttp-170) REVERT: D 50 ASP cc_start: 0.6881 (p0) cc_final: 0.6484 (m-30) REVERT: D 57 GLU cc_start: 0.7912 (tp30) cc_final: 0.7655 (tp30) REVERT: D 166 GLU cc_start: 0.6282 (tt0) cc_final: 0.5848 (pm20) REVERT: E 12 GLN cc_start: 0.6725 (mp10) cc_final: 0.6186 (tt0) REVERT: E 20 ARG cc_start: 0.7818 (ttp-170) cc_final: 0.7531 (ttp-110) REVERT: E 45 ARG cc_start: 0.6358 (ttt90) cc_final: 0.5921 (ttp80) REVERT: E 55 GLU cc_start: 0.6719 (mp0) cc_final: 0.6480 (mt-10) REVERT: E 61 GLN cc_start: 0.6504 (tt0) cc_final: 0.6181 (tp40) REVERT: E 69 ARG cc_start: 0.6232 (ptp90) cc_final: 0.5473 (ptm160) REVERT: F 44 ARG cc_start: 0.6955 (mtm-85) cc_final: 0.6385 (mtm-85) REVERT: F 90 MET cc_start: 0.7896 (mtm) cc_final: 0.7317 (mtt) REVERT: H 43 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7842 (mm-30) REVERT: H 50 LYS cc_start: 0.7166 (pttt) cc_final: 0.6845 (pttp) REVERT: H 58 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6437 (mp0) REVERT: H 60 GLU cc_start: 0.7357 (tt0) cc_final: 0.7022 (tp30) REVERT: H 88 ARG cc_start: 0.7785 (mtm180) cc_final: 0.7084 (mtp-110) REVERT: H 114 ARG cc_start: 0.6996 (ttm110) cc_final: 0.6177 (ttm-80) REVERT: K 37 ARG cc_start: 0.5967 (mtp-110) cc_final: 0.5648 (mmm160) REVERT: K 98 ARG cc_start: 0.6406 (mtp180) cc_final: 0.6121 (mtt90) REVERT: K 108 THR cc_start: 0.6226 (p) cc_final: 0.5610 (t) REVERT: L 10 LYS cc_start: 0.7492 (tttt) cc_final: 0.7168 (ttpm) REVERT: L 75 GLN cc_start: 0.5510 (mt0) cc_final: 0.5174 (pt0) REVERT: L 81 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7625 (tp) REVERT: L 108 LYS cc_start: 0.7112 (mmtt) cc_final: 0.6342 (mmtm) REVERT: L 121 ARG cc_start: 0.6997 (ttt-90) cc_final: 0.6691 (ttt180) REVERT: O 2 SER cc_start: 0.6603 (p) cc_final: 0.6281 (t) REVERT: O 10 LYS cc_start: 0.6397 (mptt) cc_final: 0.6181 (ttpp) REVERT: O 17 ARG cc_start: 0.5192 (OUTLIER) cc_final: 0.4939 (mpt-90) REVERT: O 58 ARG cc_start: 0.7843 (ttp-170) cc_final: 0.6746 (ttp-110) REVERT: O 62 GLN cc_start: 0.7897 (tt0) cc_final: 0.7558 (tt0) REVERT: O 68 ASP cc_start: 0.7983 (m-30) cc_final: 0.7747 (m-30) REVERT: O 84 ARG cc_start: 0.6593 (mtp180) cc_final: 0.6214 (mmm160) REVERT: P 53 ASP cc_start: 0.7437 (t0) cc_final: 0.7236 (t0) REVERT: P 76 LYS cc_start: 0.6447 (mtpp) cc_final: 0.6179 (mttp) REVERT: Q 9 GLN cc_start: 0.8016 (tt0) cc_final: 0.7575 (mt0) REVERT: Q 11 ARG cc_start: 0.6621 (ttt90) cc_final: 0.6379 (ttp80) REVERT: R 48 ARG cc_start: 0.6403 (mpt180) cc_final: 0.6176 (mmt90) REVERT: T 27 MET cc_start: 0.8158 (tmm) cc_final: 0.7811 (tmm) REVERT: U 21 ARG cc_start: 0.5161 (ttt90) cc_final: 0.4800 (ttt-90) REVERT: U 31 GLU cc_start: 0.5899 (OUTLIER) cc_final: 0.5631 (tp30) REVERT: U 44 GLU cc_start: 0.6931 (tt0) cc_final: 0.6642 (tm-30) outliers start: 38 outliers final: 19 residues processed: 301 average time/residue: 2.2926 time to fit residues: 794.0755 Evaluate side-chains 287 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 262 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 VAL 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 B residue 112 LYS Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain D residue 160 GLU 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 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 17 ARG Chi-restraints excluded: chain O residue 75 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 231 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 235 optimal weight: 0.9980 chunk 249 optimal weight: 2.9990 chunk 123 optimal weight: 0.3980 chunk 223 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 ASN L 20 ASN O 40 GLN T 3 ASN T 52 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 39364 Z= 0.138 Angle : 0.602 23.088 58689 Z= 0.324 Chirality : 0.041 1.948 7473 Planarity : 0.006 0.126 3267 Dihedral : 22.741 143.856 19277 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.19 % Allowed : 12.92 % Favored : 84.89 % 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: 0.72 (0.21), residues: 1509 helix: 1.36 (0.21), residues: 607 sheet: 0.11 (0.31), residues: 245 loop : -0.09 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 201 HIS 0.004 0.001 HIS E 89 PHE 0.014 0.001 PHE F 8 TYR 0.013 0.002 TYR L 117 ARG 0.004 0.000 ARG E 54 *********************** 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 312 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 284 time to evaluate : 2.614 Fit side-chains REVERT: B 35 ARG cc_start: 0.4415 (mtt90) cc_final: 0.3880 (tpp-160) REVERT: B 59 LYS cc_start: 0.5417 (tttm) cc_final: 0.5159 (ttpp) REVERT: B 63 ARG cc_start: 0.4038 (ttp-110) cc_final: 0.3477 (ttp80) REVERT: B 66 LYS cc_start: 0.4009 (mtmt) cc_final: 0.3511 (mttt) REVERT: B 74 ARG cc_start: 0.3243 (OUTLIER) cc_final: 0.2939 (mtt90) REVERT: B 78 GLU cc_start: 0.4255 (OUTLIER) cc_final: 0.3679 (tm-30) REVERT: B 105 LYS cc_start: 0.5292 (pttt) cc_final: 0.4990 (pptt) REVERT: B 106 THR cc_start: 0.5856 (OUTLIER) cc_final: 0.5435 (p) REVERT: B 108 ARG cc_start: 0.5478 (ptm160) cc_final: 0.4619 (ptm-80) REVERT: B 112 LYS cc_start: 0.4510 (OUTLIER) cc_final: 0.4004 (mtpt) REVERT: B 169 GLU cc_start: 0.5627 (mm-30) cc_final: 0.5416 (mm-30) REVERT: C 166 GLU cc_start: 0.6424 (mt-10) cc_final: 0.6042 (tp30) REVERT: C 169 ARG cc_start: 0.7074 (ttp-170) cc_final: 0.6084 (ttp80) REVERT: C 170 GLU cc_start: 0.7094 (mp0) cc_final: 0.6881 (mp0) REVERT: D 35 GLU cc_start: 0.5620 (mt-10) cc_final: 0.5299 (pm20) REVERT: D 36 GLN cc_start: 0.6319 (tt0) cc_final: 0.5898 (tt0) REVERT: D 47 ARG cc_start: 0.6013 (ttm110) cc_final: 0.5604 (ttp-170) REVERT: D 50 ASP cc_start: 0.6890 (p0) cc_final: 0.6456 (m-30) REVERT: D 156 LYS cc_start: 0.6067 (mtmm) cc_final: 0.5441 (tptm) REVERT: D 166 GLU cc_start: 0.6360 (tt0) cc_final: 0.5900 (pm20) REVERT: E 12 GLN cc_start: 0.6720 (mp10) cc_final: 0.6226 (tt0) REVERT: E 20 ARG cc_start: 0.7758 (ttp-170) cc_final: 0.7487 (ttp-110) REVERT: E 45 ARG cc_start: 0.6528 (ttt90) cc_final: 0.6080 (ttp80) REVERT: E 55 GLU cc_start: 0.6566 (mp0) cc_final: 0.6362 (mp0) REVERT: E 61 GLN cc_start: 0.6401 (tt0) cc_final: 0.6109 (tp40) REVERT: E 69 ARG cc_start: 0.6416 (ptp90) cc_final: 0.5652 (ptm160) REVERT: F 2 ARG cc_start: 0.7072 (mtt-85) cc_final: 0.6743 (mtp85) REVERT: F 44 ARG cc_start: 0.6982 (mtm-85) cc_final: 0.6490 (mtm-85) REVERT: F 90 MET cc_start: 0.7822 (mtm) cc_final: 0.7046 (mtt) REVERT: F 93 LYS cc_start: 0.6649 (mtmt) cc_final: 0.6009 (mtpt) REVERT: H 50 LYS cc_start: 0.7157 (pttt) cc_final: 0.6814 (pttp) REVERT: H 58 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6454 (mp0) REVERT: H 60 GLU cc_start: 0.7367 (tt0) cc_final: 0.6803 (tp30) REVERT: H 88 ARG cc_start: 0.7708 (mtm180) cc_final: 0.7037 (mtp-110) REVERT: K 37 ARG cc_start: 0.5905 (mtp-110) cc_final: 0.5678 (mmm160) REVERT: K 98 ARG cc_start: 0.6347 (mtp180) cc_final: 0.6123 (mtt90) REVERT: K 108 THR cc_start: 0.6429 (p) cc_final: 0.5894 (t) REVERT: L 10 LYS cc_start: 0.7383 (tttt) cc_final: 0.7085 (ttpm) REVERT: L 75 GLN cc_start: 0.5710 (mt0) cc_final: 0.5370 (pt0) REVERT: L 81 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7516 (tp) REVERT: L 108 LYS cc_start: 0.6973 (mmtt) cc_final: 0.6205 (mmtm) REVERT: L 121 ARG cc_start: 0.6912 (ttt-90) cc_final: 0.6619 (ttt180) REVERT: O 2 SER cc_start: 0.6597 (p) cc_final: 0.6253 (t) REVERT: O 10 LYS cc_start: 0.6485 (mptt) cc_final: 0.6276 (ttpp) REVERT: O 57 LEU cc_start: 0.8181 (mt) cc_final: 0.7930 (mm) REVERT: O 58 ARG cc_start: 0.7843 (ttp-170) cc_final: 0.6777 (ttp-110) REVERT: O 62 GLN cc_start: 0.7880 (tt0) cc_final: 0.7495 (tt0) REVERT: O 84 ARG cc_start: 0.6612 (mtp180) cc_final: 0.6165 (mmm160) REVERT: P 53 ASP cc_start: 0.7461 (t0) cc_final: 0.7239 (t0) REVERT: P 76 LYS cc_start: 0.6423 (mtpp) cc_final: 0.6104 (mttp) REVERT: Q 6 ARG cc_start: 0.5730 (mtp180) cc_final: 0.5009 (ttt180) REVERT: Q 9 GLN cc_start: 0.7968 (tt0) cc_final: 0.7640 (tt0) REVERT: Q 11 ARG cc_start: 0.6574 (ttt90) cc_final: 0.6353 (ttp80) REVERT: R 35 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6619 (mm-30) REVERT: R 48 ARG cc_start: 0.6342 (mpt180) cc_final: 0.6128 (mmt90) REVERT: R 61 ARG cc_start: 0.7981 (mtt180) cc_final: 0.7343 (mtt90) REVERT: T 27 MET cc_start: 0.8135 (tmm) cc_final: 0.7711 (tmm) REVERT: U 21 ARG cc_start: 0.5230 (ttt90) cc_final: 0.4834 (ttt-90) REVERT: U 31 GLU cc_start: 0.5918 (OUTLIER) cc_final: 0.5610 (tp30) REVERT: U 44 GLU cc_start: 0.6882 (tt0) cc_final: 0.6524 (tm-30) outliers start: 28 outliers final: 12 residues processed: 303 average time/residue: 2.2721 time to fit residues: 793.9961 Evaluate side-chains 291 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 272 time to evaluate : 2.498 ------------------------------------------------------------------------------- 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 B residue 112 LYS 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 H residue 55 THR 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 R residue 35 GLU 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: 8.9990 chunk 3 optimal weight: 6.9990 chunk 185 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 212 optimal weight: 2.9990 chunk 172 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 223 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 ASN K 38 GLN L 20 ASN O 40 GLN T 52 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 39364 Z= 0.441 Angle : 0.964 22.863 58689 Z= 0.476 Chirality : 0.054 2.043 7473 Planarity : 0.009 0.145 3267 Dihedral : 22.993 142.363 19277 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.82 % Allowed : 13.00 % Favored : 84.18 % 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: -0.01 (0.21), residues: 1509 helix: 0.54 (0.20), residues: 612 sheet: -0.12 (0.31), residues: 275 loop : -0.35 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP P 60 HIS 0.010 0.003 HIS D 198 PHE 0.032 0.003 PHE O 43 TYR 0.022 0.004 TYR L 117 ARG 0.012 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 309 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 273 time to evaluate : 2.471 Fit side-chains revert: symmetry clash REVERT: B 35 ARG cc_start: 0.4534 (mtt90) cc_final: 0.3987 (tpp-160) REVERT: B 59 LYS cc_start: 0.5551 (tttm) cc_final: 0.5205 (ttpm) REVERT: B 66 LYS cc_start: 0.4021 (mtmt) cc_final: 0.3570 (mttt) REVERT: B 78 GLU cc_start: 0.4470 (OUTLIER) cc_final: 0.3994 (pm20) REVERT: B 105 LYS cc_start: 0.5392 (pttt) cc_final: 0.4977 (pptt) REVERT: B 108 ARG cc_start: 0.5550 (ptm160) cc_final: 0.5239 (ptm160) REVERT: B 169 GLU cc_start: 0.5635 (mm-30) cc_final: 0.5405 (mm-30) REVERT: C 166 GLU cc_start: 0.6520 (mt-10) cc_final: 0.6148 (tp30) REVERT: C 169 ARG cc_start: 0.7101 (ttp-170) cc_final: 0.6065 (ttp80) REVERT: D 35 GLU cc_start: 0.5683 (mt-10) cc_final: 0.5380 (pm20) REVERT: D 36 GLN cc_start: 0.6205 (tt0) cc_final: 0.5773 (tt0) REVERT: D 47 ARG cc_start: 0.5994 (ttm110) cc_final: 0.5593 (ttp-170) REVERT: D 50 ASP cc_start: 0.6821 (p0) cc_final: 0.6460 (m-30) REVERT: D 166 GLU cc_start: 0.6347 (tt0) cc_final: 0.5876 (pm20) REVERT: E 12 GLN cc_start: 0.6532 (mp10) cc_final: 0.5981 (tt0) REVERT: E 20 ARG cc_start: 0.7758 (ttp-170) cc_final: 0.7467 (ttp-110) REVERT: E 45 ARG cc_start: 0.6435 (ttt90) cc_final: 0.5929 (ttp80) REVERT: E 55 GLU cc_start: 0.6775 (mp0) cc_final: 0.6510 (mt-10) REVERT: E 61 GLN cc_start: 0.6575 (tt0) cc_final: 0.6252 (tp40) REVERT: E 69 ARG cc_start: 0.6360 (ptp90) cc_final: 0.5625 (ptm160) REVERT: F 2 ARG cc_start: 0.7180 (mtt-85) cc_final: 0.6859 (mtp85) REVERT: F 44 ARG cc_start: 0.6885 (mtm-85) cc_final: 0.6449 (mtm-85) REVERT: F 90 MET cc_start: 0.7903 (mtm) cc_final: 0.7416 (mtt) REVERT: F 93 LYS cc_start: 0.6650 (mtmt) cc_final: 0.6013 (mtpt) REVERT: H 50 LYS cc_start: 0.7191 (pttt) cc_final: 0.6847 (pttp) REVERT: H 58 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6500 (mp0) REVERT: H 60 GLU cc_start: 0.7349 (tt0) cc_final: 0.7016 (tp30) REVERT: H 88 ARG cc_start: 0.7809 (mtm180) cc_final: 0.7146 (mtp-110) REVERT: K 98 ARG cc_start: 0.6336 (mtp180) cc_final: 0.6044 (mtt90) REVERT: L 10 LYS cc_start: 0.7564 (tttt) cc_final: 0.7221 (ttpm) REVERT: L 75 GLN cc_start: 0.5452 (mt0) cc_final: 0.5124 (pt0) REVERT: L 81 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7669 (tp) REVERT: L 108 LYS cc_start: 0.7071 (mmtt) cc_final: 0.6323 (mmtm) REVERT: L 121 ARG cc_start: 0.7005 (ttt-90) cc_final: 0.6704 (ttt180) REVERT: O 2 SER cc_start: 0.6694 (p) cc_final: 0.6313 (t) REVERT: O 17 ARG cc_start: 0.5031 (OUTLIER) cc_final: 0.4748 (mpt-90) REVERT: O 58 ARG cc_start: 0.7882 (ttp-170) cc_final: 0.6772 (ttp-110) REVERT: O 62 GLN cc_start: 0.7920 (tt0) cc_final: 0.7592 (tt0) REVERT: O 68 ASP cc_start: 0.7946 (m-30) cc_final: 0.7731 (m-30) REVERT: O 84 ARG cc_start: 0.6658 (mtp180) cc_final: 0.6247 (mmm160) REVERT: P 76 LYS cc_start: 0.6473 (mtpp) cc_final: 0.6175 (mttp) REVERT: Q 9 GLN cc_start: 0.7989 (tt0) cc_final: 0.7626 (mt0) REVERT: Q 11 ARG cc_start: 0.6647 (ttt90) cc_final: 0.6376 (ttp80) REVERT: Q 60 GLU cc_start: 0.7172 (tt0) cc_final: 0.6799 (tt0) REVERT: Q 62 ARG cc_start: 0.7797 (ptt-90) cc_final: 0.7557 (ptm-80) REVERT: R 35 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6622 (mm-30) REVERT: R 48 ARG cc_start: 0.6425 (mpt180) cc_final: 0.6210 (mmt90) REVERT: T 27 MET cc_start: 0.8156 (tmm) cc_final: 0.7780 (tmm) REVERT: U 21 ARG cc_start: 0.5154 (ttt90) cc_final: 0.4755 (ttt-90) REVERT: U 31 GLU cc_start: 0.5987 (OUTLIER) cc_final: 0.5769 (tp30) REVERT: U 44 GLU cc_start: 0.6895 (tt0) cc_final: 0.6618 (tm-30) outliers start: 36 outliers final: 21 residues processed: 296 average time/residue: 2.3312 time to fit residues: 794.1820 Evaluate side-chains 297 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 271 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 VAL 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 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 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 17 ARG Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain R residue 35 GLU 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: 3.9990 chunk 224 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 146 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 249 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 39364 Z= 0.255 Angle : 0.733 23.207 58689 Z= 0.380 Chirality : 0.046 1.974 7473 Planarity : 0.007 0.135 3267 Dihedral : 22.893 143.644 19277 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.04 % Allowed : 14.64 % Favored : 83.32 % 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: 0.37 (0.21), residues: 1509 helix: 0.88 (0.21), residues: 608 sheet: 0.04 (0.31), residues: 257 loop : -0.15 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 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 0.007 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 309 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 283 time to evaluate : 2.592 Fit side-chains REVERT: B 35 ARG cc_start: 0.4411 (mtt90) cc_final: 0.3890 (tpp-160) REVERT: B 59 LYS cc_start: 0.5535 (tttm) cc_final: 0.5202 (ttpm) REVERT: B 63 ARG cc_start: 0.4074 (ttp-110) cc_final: 0.3455 (ttp80) REVERT: B 66 LYS cc_start: 0.4011 (mtmt) cc_final: 0.3584 (mttt) REVERT: B 78 GLU cc_start: 0.4424 (OUTLIER) cc_final: 0.3799 (tm-30) REVERT: B 105 LYS cc_start: 0.5462 (pttt) cc_final: 0.5048 (pptt) REVERT: B 108 ARG cc_start: 0.5567 (ptm160) cc_final: 0.5237 (ptm160) REVERT: B 169 GLU cc_start: 0.5732 (mm-30) cc_final: 0.5496 (mm-30) REVERT: C 166 GLU cc_start: 0.6527 (mt-10) cc_final: 0.6137 (tp30) REVERT: C 169 ARG cc_start: 0.7065 (ttp-170) cc_final: 0.6118 (ttp80) REVERT: D 35 GLU cc_start: 0.5651 (mt-10) cc_final: 0.5338 (pm20) REVERT: D 36 GLN cc_start: 0.6305 (tt0) cc_final: 0.5852 (tt0) REVERT: D 47 ARG cc_start: 0.5954 (ttm110) cc_final: 0.5552 (ttp-170) REVERT: D 50 ASP cc_start: 0.6942 (p0) cc_final: 0.6513 (m-30) REVERT: D 166 GLU cc_start: 0.6342 (tt0) cc_final: 0.5860 (pm20) REVERT: E 12 GLN cc_start: 0.6598 (mp10) cc_final: 0.6080 (tt0) REVERT: E 20 ARG cc_start: 0.7750 (ttp-170) cc_final: 0.7463 (ttp-110) REVERT: E 45 ARG cc_start: 0.6498 (ttt90) cc_final: 0.5992 (ttp80) REVERT: E 55 GLU cc_start: 0.6768 (mp0) cc_final: 0.6519 (mt-10) REVERT: E 61 GLN cc_start: 0.6456 (tt0) cc_final: 0.6136 (tp40) REVERT: E 69 ARG cc_start: 0.6378 (ptp90) cc_final: 0.5623 (ptm160) REVERT: F 2 ARG cc_start: 0.7166 (mtt-85) cc_final: 0.6803 (mtp85) REVERT: F 44 ARG cc_start: 0.6953 (mtm-85) cc_final: 0.6483 (mtm-85) REVERT: F 90 MET cc_start: 0.7757 (mtm) cc_final: 0.7329 (mtm) REVERT: H 50 LYS cc_start: 0.7195 (pttt) cc_final: 0.6858 (pttp) REVERT: H 58 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6486 (mp0) REVERT: H 60 GLU cc_start: 0.7334 (tt0) cc_final: 0.6871 (tp30) REVERT: H 88 ARG cc_start: 0.7781 (mtm180) cc_final: 0.7085 (mtp-110) REVERT: K 98 ARG cc_start: 0.6371 (mtp180) cc_final: 0.6170 (mtt90) REVERT: L 10 LYS cc_start: 0.7529 (tttt) cc_final: 0.7210 (ttpm) REVERT: L 75 GLN cc_start: 0.5466 (mt0) cc_final: 0.5103 (pt0) REVERT: L 81 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7598 (tp) REVERT: L 108 LYS cc_start: 0.7044 (mmtt) cc_final: 0.6304 (mmtm) REVERT: L 121 ARG cc_start: 0.6956 (ttt-90) cc_final: 0.6665 (ttt180) REVERT: O 2 SER cc_start: 0.6686 (p) cc_final: 0.6285 (t) REVERT: O 58 ARG cc_start: 0.7899 (ttp-170) cc_final: 0.6810 (ttp-110) REVERT: O 62 GLN cc_start: 0.7910 (tt0) cc_final: 0.7580 (tt0) REVERT: O 84 ARG cc_start: 0.6680 (mtp180) cc_final: 0.6261 (mmm160) REVERT: P 76 LYS cc_start: 0.6459 (mtpp) cc_final: 0.6094 (mttp) REVERT: Q 9 GLN cc_start: 0.7976 (tt0) cc_final: 0.7724 (tt0) REVERT: Q 11 ARG cc_start: 0.6620 (ttt90) cc_final: 0.6361 (ttp80) REVERT: Q 60 GLU cc_start: 0.7167 (tt0) cc_final: 0.6758 (tt0) REVERT: Q 62 ARG cc_start: 0.7827 (ptt-90) cc_final: 0.7580 (ptm-80) REVERT: R 35 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6617 (mm-30) REVERT: T 27 MET cc_start: 0.8127 (tmm) cc_final: 0.7786 (tmm) REVERT: U 21 ARG cc_start: 0.5096 (ttt90) cc_final: 0.4840 (mtp180) REVERT: U 31 GLU cc_start: 0.6028 (OUTLIER) cc_final: 0.5812 (tp30) REVERT: U 44 GLU cc_start: 0.6950 (tt0) cc_final: 0.6637 (tm-30) outliers start: 26 outliers final: 15 residues processed: 300 average time/residue: 2.3839 time to fit residues: 820.7719 Evaluate side-chains 295 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 276 time to evaluate : 2.556 ------------------------------------------------------------------------------- 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 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 75 VAL Chi-restraints excluded: chain R residue 35 GLU Chi-restraints excluded: chain U residue 31 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 240 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 182 optimal weight: 0.6980 chunk 141 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 248 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.1837 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= 0.290 Angle : 0.779 23.180 58689 Z= 0.399 Chirality : 0.047 1.982 7473 Planarity : 0.007 0.138 3267 Dihedral : 22.926 143.543 19277 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.96 % Allowed : 15.19 % Favored : 82.85 % 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: 0.85 (0.20), residues: 602 sheet: 0.09 (0.31), residues: 255 loop : -0.18 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 201 HIS 0.007 0.002 HIS E 89 PHE 0.022 0.002 PHE O 43 TYR 0.019 0.003 TYR L 117 ARG 0.008 0.001 ARG C 127 *********************** 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 302 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 277 time to evaluate : 2.382 Fit side-chains REVERT: B 35 ARG cc_start: 0.4420 (mtt90) cc_final: 0.3887 (tpp-160) REVERT: B 59 LYS cc_start: 0.5561 (tttm) cc_final: 0.5202 (ttpm) REVERT: B 63 ARG cc_start: 0.4089 (ttp-110) cc_final: 0.3861 (ptp90) REVERT: B 66 LYS cc_start: 0.3900 (mtmt) cc_final: 0.3549 (mttt) REVERT: B 78 GLU cc_start: 0.4507 (OUTLIER) cc_final: 0.3858 (tm-30) REVERT: B 105 LYS cc_start: 0.5356 (pttt) cc_final: 0.4987 (pttt) REVERT: B 108 ARG cc_start: 0.5557 (ptm160) cc_final: 0.5234 (ptm160) REVERT: B 169 GLU cc_start: 0.5639 (mm-30) cc_final: 0.5382 (mm-30) REVERT: C 166 GLU cc_start: 0.6564 (mt-10) cc_final: 0.6170 (tp30) REVERT: C 169 ARG cc_start: 0.7089 (ttp-170) cc_final: 0.6046 (ttp80) REVERT: D 35 GLU cc_start: 0.5657 (mt-10) cc_final: 0.5368 (pm20) REVERT: D 36 GLN cc_start: 0.6288 (tt0) cc_final: 0.5830 (tt0) REVERT: D 47 ARG cc_start: 0.5943 (ttm110) cc_final: 0.5547 (ttp-170) REVERT: D 50 ASP cc_start: 0.6968 (p0) cc_final: 0.6531 (m-30) REVERT: D 156 LYS cc_start: 0.5911 (mtmm) cc_final: 0.5443 (tptm) REVERT: D 166 GLU cc_start: 0.6329 (tt0) cc_final: 0.5853 (pm20) REVERT: E 12 GLN cc_start: 0.6612 (mp10) cc_final: 0.6073 (tt0) REVERT: E 20 ARG cc_start: 0.7742 (ttp-170) cc_final: 0.7454 (ttp-110) REVERT: E 45 ARG cc_start: 0.6429 (ttt90) cc_final: 0.5946 (ttp80) REVERT: E 55 GLU cc_start: 0.6704 (mp0) cc_final: 0.6478 (mt-10) REVERT: E 61 GLN cc_start: 0.6463 (tt0) cc_final: 0.6115 (tp40) REVERT: E 69 ARG cc_start: 0.6376 (ptp90) cc_final: 0.5631 (ptm160) REVERT: F 2 ARG cc_start: 0.7146 (mtt-85) cc_final: 0.6780 (mtp85) REVERT: F 44 ARG cc_start: 0.6950 (mtm-85) cc_final: 0.6477 (mtm-85) REVERT: F 90 MET cc_start: 0.7725 (mtm) cc_final: 0.7227 (mtm) REVERT: H 50 LYS cc_start: 0.7193 (pttt) cc_final: 0.6859 (pttp) REVERT: H 58 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6484 (mp0) REVERT: H 60 GLU cc_start: 0.7339 (tt0) cc_final: 0.7008 (tp30) REVERT: H 88 ARG cc_start: 0.7806 (mtm180) cc_final: 0.7108 (mtp-110) REVERT: K 98 ARG cc_start: 0.6390 (mtp180) cc_final: 0.6184 (mtt90) REVERT: L 10 LYS cc_start: 0.7533 (tttt) cc_final: 0.7204 (ttpm) REVERT: L 75 GLN cc_start: 0.5453 (mt0) cc_final: 0.5092 (pt0) REVERT: L 81 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7625 (tp) REVERT: L 108 LYS cc_start: 0.7054 (mmtt) cc_final: 0.6315 (mmtm) REVERT: L 121 ARG cc_start: 0.6984 (ttt-90) cc_final: 0.6586 (ttp80) REVERT: O 2 SER cc_start: 0.6679 (p) cc_final: 0.6270 (t) REVERT: O 58 ARG cc_start: 0.7899 (ttp-170) cc_final: 0.6805 (ttp-110) REVERT: O 62 GLN cc_start: 0.7938 (tt0) cc_final: 0.7610 (tt0) REVERT: P 76 LYS cc_start: 0.6459 (mtpp) cc_final: 0.6086 (mttp) REVERT: Q 9 GLN cc_start: 0.7964 (tt0) cc_final: 0.7520 (mt0) REVERT: Q 11 ARG cc_start: 0.6621 (ttt90) cc_final: 0.6362 (ttp80) REVERT: Q 60 GLU cc_start: 0.7142 (tt0) cc_final: 0.6747 (tt0) REVERT: Q 62 ARG cc_start: 0.7823 (ptt-90) cc_final: 0.7578 (ptm-80) REVERT: R 35 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6601 (mm-30) REVERT: T 27 MET cc_start: 0.8134 (tmm) cc_final: 0.7797 (tmm) REVERT: U 21 ARG cc_start: 0.5076 (ttt90) cc_final: 0.4841 (mtp180) REVERT: U 31 GLU cc_start: 0.6017 (OUTLIER) cc_final: 0.5804 (tp30) REVERT: U 44 GLU cc_start: 0.6906 (tt0) cc_final: 0.6622 (tm-30) outliers start: 25 outliers final: 18 residues processed: 295 average time/residue: 2.3202 time to fit residues: 788.3495 Evaluate side-chains 296 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 274 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 46 THR 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 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 75 VAL Chi-restraints excluded: chain R residue 35 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: 3.9990 chunk 99 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 195 optimal weight: 5.9990 chunk 226 optimal weight: 0.0970 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 39364 Z= 0.306 Angle : 0.797 23.115 58689 Z= 0.406 Chirality : 0.048 1.990 7473 Planarity : 0.007 0.138 3267 Dihedral : 22.930 143.486 19277 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.19 % Allowed : 15.27 % 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: 0.29 (0.21), residues: 1509 helix: 0.80 (0.20), residues: 602 sheet: 0.05 (0.31), residues: 257 loop : -0.17 (0.24), residues: 650 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 0.024 0.003 PHE O 43 TYR 0.019 0.003 TYR L 117 ARG 0.008 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 307 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 279 time to evaluate : 2.658 Fit side-chains REVERT: B 14 VAL cc_start: 0.4226 (OUTLIER) cc_final: 0.3705 (m) REVERT: B 35 ARG cc_start: 0.4356 (mtt90) cc_final: 0.3824 (tpp-160) REVERT: B 59 LYS cc_start: 0.5563 (tttm) cc_final: 0.5199 (ttpm) REVERT: B 63 ARG cc_start: 0.4126 (ttp-110) cc_final: 0.3850 (ptp90) REVERT: B 66 LYS cc_start: 0.3871 (mtmt) cc_final: 0.3525 (mttt) REVERT: B 78 GLU cc_start: 0.4511 (OUTLIER) cc_final: 0.4070 (pm20) REVERT: B 105 LYS cc_start: 0.5370 (pttt) cc_final: 0.5020 (pttt) REVERT: B 108 ARG cc_start: 0.5557 (ptm160) cc_final: 0.5238 (ptm160) REVERT: B 154 MET cc_start: 0.4180 (mtt) cc_final: 0.3768 (mtp) REVERT: B 169 GLU cc_start: 0.5720 (mm-30) cc_final: 0.5510 (mm-30) REVERT: C 166 GLU cc_start: 0.6545 (mt-10) cc_final: 0.6155 (tp30) REVERT: C 169 ARG cc_start: 0.7065 (ttp-170) cc_final: 0.6075 (ttp80) REVERT: D 35 GLU cc_start: 0.5658 (mt-10) cc_final: 0.5368 (pm20) REVERT: D 36 GLN cc_start: 0.6231 (tt0) cc_final: 0.5768 (tt0) REVERT: D 47 ARG cc_start: 0.5914 (ttm110) cc_final: 0.5546 (ttp-170) REVERT: D 50 ASP cc_start: 0.6949 (p0) cc_final: 0.6516 (m-30) REVERT: D 156 LYS cc_start: 0.5906 (mtmm) cc_final: 0.5443 (tptm) REVERT: D 166 GLU cc_start: 0.6295 (tt0) cc_final: 0.5832 (pm20) REVERT: E 12 GLN cc_start: 0.6603 (mp10) cc_final: 0.6069 (tt0) REVERT: E 20 ARG cc_start: 0.7741 (ttp-170) cc_final: 0.7453 (ttp-110) REVERT: E 45 ARG cc_start: 0.6424 (ttt90) cc_final: 0.5938 (ttp80) REVERT: E 55 GLU cc_start: 0.6707 (mp0) cc_final: 0.6481 (mt-10) REVERT: E 61 GLN cc_start: 0.6469 (tt0) cc_final: 0.6120 (tp40) REVERT: E 69 ARG cc_start: 0.6382 (ptp90) cc_final: 0.5641 (ptm160) REVERT: F 2 ARG cc_start: 0.7178 (mtt-85) cc_final: 0.6808 (mtp85) REVERT: F 44 ARG cc_start: 0.6945 (mtm-85) cc_final: 0.6603 (mtm-85) REVERT: F 90 MET cc_start: 0.7695 (mtm) cc_final: 0.7200 (mtm) REVERT: H 50 LYS cc_start: 0.7185 (pttt) cc_final: 0.6843 (pttp) REVERT: H 58 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6485 (mp0) REVERT: H 60 GLU cc_start: 0.7351 (tt0) cc_final: 0.7014 (tp30) REVERT: H 88 ARG cc_start: 0.7804 (mtm180) cc_final: 0.7106 (mtp-110) REVERT: K 98 ARG cc_start: 0.6391 (mtp180) cc_final: 0.6095 (mtt90) REVERT: L 10 LYS cc_start: 0.7541 (tttt) cc_final: 0.7211 (ttpm) REVERT: L 75 GLN cc_start: 0.5449 (mt0) cc_final: 0.5100 (pt0) REVERT: L 81 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7626 (tp) REVERT: L 108 LYS cc_start: 0.7029 (mmtt) cc_final: 0.6309 (mmtm) REVERT: L 121 ARG cc_start: 0.6979 (ttt-90) cc_final: 0.6582 (ttp80) REVERT: O 2 SER cc_start: 0.6680 (p) cc_final: 0.6272 (t) REVERT: O 58 ARG cc_start: 0.7908 (ttp-170) cc_final: 0.6813 (ttp-110) REVERT: O 62 GLN cc_start: 0.7964 (tt0) cc_final: 0.7637 (tt0) REVERT: P 76 LYS cc_start: 0.6455 (mtpp) cc_final: 0.6081 (mttp) REVERT: Q 9 GLN cc_start: 0.7954 (tt0) cc_final: 0.7521 (mt0) REVERT: Q 11 ARG cc_start: 0.6623 (ttt90) cc_final: 0.6362 (ttp80) REVERT: Q 60 GLU cc_start: 0.7145 (tt0) cc_final: 0.6751 (tt0) REVERT: Q 62 ARG cc_start: 0.7822 (ptt-90) cc_final: 0.7577 (ptm-80) REVERT: R 35 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6600 (mm-30) REVERT: T 27 MET cc_start: 0.8131 (tmm) cc_final: 0.7793 (tmm) REVERT: U 21 ARG cc_start: 0.5060 (ttt90) cc_final: 0.4842 (mtp180) REVERT: U 31 GLU cc_start: 0.5994 (OUTLIER) cc_final: 0.5789 (tp30) REVERT: U 44 GLU cc_start: 0.6907 (tt0) cc_final: 0.6606 (tm-30) outliers start: 28 outliers final: 21 residues processed: 299 average time/residue: 2.3533 time to fit residues: 812.5726 Evaluate side-chains 303 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 277 time to evaluate : 2.402 ------------------------------------------------------------------------------- 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 46 THR 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 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 44 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 R residue 35 GLU 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: 0.9980 chunk 231 optimal weight: 0.8980 chunk 139 optimal weight: 0.1980 chunk 100 optimal weight: 7.9990 chunk 181 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 209 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 39364 Z= 0.164 Angle : 0.627 23.056 58689 Z= 0.334 Chirality : 0.042 1.954 7473 Planarity : 0.006 0.127 3267 Dihedral : 22.791 143.644 19277 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.80 % Allowed : 15.74 % 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: 0.71 (0.21), residues: 1509 helix: 1.23 (0.21), residues: 607 sheet: 0.14 (0.31), residues: 255 loop : 0.01 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 201 HIS 0.004 0.001 HIS E 89 PHE 0.014 0.002 PHE O 43 TYR 0.014 0.002 TYR L 117 ARG 0.005 0.000 ARG C 127 *********************** 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 301 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 278 time to evaluate : 2.334 Fit side-chains REVERT: B 35 ARG cc_start: 0.4234 (mtt90) cc_final: 0.3779 (tpp-160) REVERT: B 59 LYS cc_start: 0.5563 (tttm) cc_final: 0.5228 (ttpm) REVERT: B 63 ARG cc_start: 0.4025 (ttp-110) cc_final: 0.3346 (ttp80) REVERT: B 66 LYS cc_start: 0.3967 (mtmt) cc_final: 0.3527 (mttt) REVERT: B 78 GLU cc_start: 0.4417 (OUTLIER) cc_final: 0.4056 (pm20) REVERT: B 105 LYS cc_start: 0.5361 (pttt) cc_final: 0.5078 (pttt) REVERT: B 106 THR cc_start: 0.5904 (OUTLIER) cc_final: 0.5507 (p) REVERT: B 108 ARG cc_start: 0.5549 (ptm160) cc_final: 0.4934 (ptm-80) REVERT: B 154 MET cc_start: 0.4138 (mtt) cc_final: 0.3713 (mtp) REVERT: B 169 GLU cc_start: 0.5633 (mm-30) cc_final: 0.5400 (mm-30) REVERT: C 166 GLU cc_start: 0.6527 (mt-10) cc_final: 0.6145 (tp30) REVERT: C 169 ARG cc_start: 0.7059 (ttp-170) cc_final: 0.6105 (ttp80) REVERT: D 35 GLU cc_start: 0.5683 (mt-10) cc_final: 0.5418 (pm20) REVERT: D 36 GLN cc_start: 0.6334 (tt0) cc_final: 0.5868 (tt0) REVERT: D 47 ARG cc_start: 0.5938 (ttm110) cc_final: 0.5529 (ttp-170) REVERT: D 50 ASP cc_start: 0.6922 (p0) cc_final: 0.6451 (m-30) REVERT: D 156 LYS cc_start: 0.5953 (mtmm) cc_final: 0.5455 (tptm) REVERT: D 166 GLU cc_start: 0.6416 (tt0) cc_final: 0.5933 (pm20) REVERT: E 12 GLN cc_start: 0.6692 (mp10) cc_final: 0.6128 (tt0) REVERT: E 20 ARG cc_start: 0.7763 (ttp-170) cc_final: 0.7486 (ttp-110) REVERT: E 45 ARG cc_start: 0.6437 (ttt90) cc_final: 0.5930 (ttp80) REVERT: E 55 GLU cc_start: 0.6650 (mp0) cc_final: 0.6401 (mt-10) REVERT: E 61 GLN cc_start: 0.6367 (tt0) cc_final: 0.6038 (tp40) REVERT: E 69 ARG cc_start: 0.6356 (ptp90) cc_final: 0.5604 (ptm160) REVERT: F 1 MET cc_start: 0.5511 (mtp) cc_final: 0.5149 (mtm) REVERT: F 2 ARG cc_start: 0.7105 (mtt-85) cc_final: 0.6735 (mtp85) REVERT: F 44 ARG cc_start: 0.6989 (mtm-85) cc_final: 0.6450 (mtm-85) REVERT: F 90 MET cc_start: 0.7672 (mtm) cc_final: 0.7206 (mtm) REVERT: F 93 LYS cc_start: 0.6447 (mtmt) cc_final: 0.5950 (mtpt) REVERT: F 102 MET cc_start: 0.5565 (mmt) cc_final: 0.5122 (mpt) REVERT: H 50 LYS cc_start: 0.7238 (pttt) cc_final: 0.6905 (pttp) REVERT: H 58 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6488 (mp0) REVERT: H 60 GLU cc_start: 0.7305 (tt0) cc_final: 0.6873 (tp30) REVERT: H 88 ARG cc_start: 0.7740 (mtm180) cc_final: 0.7056 (mtp-110) REVERT: K 98 ARG cc_start: 0.6344 (mtp180) cc_final: 0.6131 (mtt90) REVERT: K 106 ARG cc_start: 0.5980 (ttt180) cc_final: 0.5668 (ttt180) REVERT: L 10 LYS cc_start: 0.7448 (tttt) cc_final: 0.7159 (ttpm) REVERT: L 75 GLN cc_start: 0.5474 (mt0) cc_final: 0.5126 (pt0) REVERT: L 81 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7545 (tp) REVERT: L 108 LYS cc_start: 0.7004 (mmtt) cc_final: 0.6287 (mmtm) REVERT: O 57 LEU cc_start: 0.8191 (mt) cc_final: 0.7936 (mm) REVERT: O 58 ARG cc_start: 0.7887 (ttp-170) cc_final: 0.6805 (ttp-110) REVERT: O 62 GLN cc_start: 0.7921 (tt0) cc_final: 0.7572 (tt0) REVERT: P 76 LYS cc_start: 0.6454 (mtpp) cc_final: 0.6232 (mttp) REVERT: Q 11 ARG cc_start: 0.6580 (ttt90) cc_final: 0.6147 (tmt90) REVERT: Q 60 GLU cc_start: 0.7171 (tt0) cc_final: 0.6732 (tt0) REVERT: R 35 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6629 (mm-30) REVERT: T 27 MET cc_start: 0.8126 (tmm) cc_final: 0.7752 (tmm) REVERT: U 21 ARG cc_start: 0.5072 (ttt90) cc_final: 0.4817 (mtp180) REVERT: U 31 GLU cc_start: 0.5962 (OUTLIER) cc_final: 0.5725 (tp30) REVERT: U 44 GLU cc_start: 0.6816 (tt0) cc_final: 0.6524 (tm-30) outliers start: 23 outliers final: 13 residues processed: 294 average time/residue: 2.3132 time to fit residues: 783.4412 Evaluate side-chains 291 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 273 time to evaluate : 2.295 ------------------------------------------------------------------------------- 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 H residue 55 THR 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 R residue 35 GLU Chi-restraints excluded: chain U residue 31 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 245 optimal weight: 0.7980 chunk 149 optimal weight: 0.0000 chunk 116 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 236 optimal weight: 6.9990 chunk 204 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 158 optimal weight: 0.0980 chunk 125 optimal weight: 7.9990 chunk 162 optimal weight: 0.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS E 43 ASN E 146 ASN L 20 ASN O 40 GLN P 63 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 39364 Z= 0.146 Angle : 0.613 23.276 58689 Z= 0.328 Chirality : 0.041 1.942 7473 Planarity : 0.006 0.126 3267 Dihedral : 22.794 143.651 19277 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.57 % Allowed : 16.21 % 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: 0.82 (0.22), residues: 1509 helix: 1.32 (0.21), residues: 607 sheet: 0.17 (0.31), residues: 255 loop : 0.08 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 201 HIS 0.004 0.001 HIS E 89 PHE 0.014 0.001 PHE F 8 TYR 0.013 0.002 TYR D 51 ARG 0.008 0.000 ARG E 54 ********************** 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 292 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 272 time to evaluate : 2.526 Fit side-chains REVERT: B 35 ARG cc_start: 0.4144 (mtt90) cc_final: 0.3732 (tpp-160) REVERT: B 59 LYS cc_start: 0.5565 (tttm) cc_final: 0.5232 (ttpm) REVERT: B 63 ARG cc_start: 0.4038 (ttp-110) cc_final: 0.3357 (ttp80) REVERT: B 66 LYS cc_start: 0.3971 (mtmt) cc_final: 0.3528 (mttt) REVERT: B 78 GLU cc_start: 0.4414 (OUTLIER) cc_final: 0.4050 (pm20) REVERT: B 105 LYS cc_start: 0.5358 (pttt) cc_final: 0.5075 (pttt) REVERT: B 106 THR cc_start: 0.5886 (OUTLIER) cc_final: 0.5500 (p) REVERT: B 108 ARG cc_start: 0.5547 (ptm160) cc_final: 0.4668 (ptm-80) REVERT: B 154 MET cc_start: 0.4132 (mtt) cc_final: 0.3786 (mtt) REVERT: B 169 GLU cc_start: 0.5617 (mm-30) cc_final: 0.5386 (mm-30) REVERT: C 166 GLU cc_start: 0.6544 (mt-10) cc_final: 0.6154 (tp30) REVERT: D 35 GLU cc_start: 0.5688 (mt-10) cc_final: 0.5436 (pm20) REVERT: D 36 GLN cc_start: 0.6346 (tt0) cc_final: 0.5872 (tt0) REVERT: D 47 ARG cc_start: 0.5882 (ttm110) cc_final: 0.5537 (ttp-170) REVERT: D 50 ASP cc_start: 0.6916 (p0) cc_final: 0.6447 (m-30) REVERT: D 156 LYS cc_start: 0.5942 (mtmm) cc_final: 0.5474 (tptm) REVERT: D 166 GLU cc_start: 0.6402 (tt0) cc_final: 0.5925 (pm20) REVERT: D 177 LYS cc_start: 0.4994 (mtmm) cc_final: 0.4712 (mtpp) REVERT: E 12 GLN cc_start: 0.6686 (mp10) cc_final: 0.6128 (tt0) REVERT: E 20 ARG cc_start: 0.7754 (ttp-170) cc_final: 0.7478 (ttp-110) REVERT: E 45 ARG cc_start: 0.6423 (ttt90) cc_final: 0.6019 (mtm180) REVERT: E 55 GLU cc_start: 0.6656 (mp0) cc_final: 0.6392 (mt-10) REVERT: E 61 GLN cc_start: 0.6377 (tt0) cc_final: 0.6041 (tp40) REVERT: E 69 ARG cc_start: 0.6391 (ptp90) cc_final: 0.5644 (ptm160) REVERT: F 1 MET cc_start: 0.5473 (mtp) cc_final: 0.5115 (mtm) REVERT: F 2 ARG cc_start: 0.7098 (mtt-85) cc_final: 0.6722 (mtp85) REVERT: F 44 ARG cc_start: 0.6975 (mtm-85) cc_final: 0.6435 (mtm-85) REVERT: F 90 MET cc_start: 0.7683 (mtm) cc_final: 0.7256 (mtm) REVERT: F 93 LYS cc_start: 0.6448 (mtmt) cc_final: 0.5952 (mtpt) REVERT: F 102 MET cc_start: 0.5495 (mmt) cc_final: 0.5077 (mpt) REVERT: H 50 LYS cc_start: 0.7237 (pttt) cc_final: 0.6903 (pttp) REVERT: H 58 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6499 (mp0) REVERT: H 60 GLU cc_start: 0.7303 (tt0) cc_final: 0.6874 (tp30) REVERT: H 88 ARG cc_start: 0.7739 (mtm180) cc_final: 0.7055 (mtp-110) REVERT: K 98 ARG cc_start: 0.6342 (mtp180) cc_final: 0.6126 (mtt90) REVERT: K 106 ARG cc_start: 0.5976 (ttt180) cc_final: 0.5670 (ttt180) REVERT: L 10 LYS cc_start: 0.7435 (tttt) cc_final: 0.7150 (ttpm) REVERT: L 75 GLN cc_start: 0.5482 (mt0) cc_final: 0.5134 (pt0) REVERT: L 81 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7525 (tp) REVERT: L 108 LYS cc_start: 0.6999 (mmtt) cc_final: 0.6284 (mmtm) REVERT: O 57 LEU cc_start: 0.8189 (mt) cc_final: 0.7940 (mm) REVERT: O 58 ARG cc_start: 0.7877 (ttp-170) cc_final: 0.6797 (ttp-110) REVERT: O 62 GLN cc_start: 0.7919 (tt0) cc_final: 0.7569 (tt0) REVERT: P 76 LYS cc_start: 0.6454 (mtpp) cc_final: 0.6226 (mttp) REVERT: Q 60 GLU cc_start: 0.7164 (tt0) cc_final: 0.6722 (tt0) REVERT: R 35 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6632 (mm-30) REVERT: T 27 MET cc_start: 0.8121 (tmm) cc_final: 0.7743 (tmm) REVERT: U 21 ARG cc_start: 0.5070 (ttt90) cc_final: 0.4769 (mmm160) REVERT: U 31 GLU cc_start: 0.5966 (OUTLIER) cc_final: 0.5729 (tp30) REVERT: U 44 GLU cc_start: 0.6838 (tt0) cc_final: 0.6566 (tm-30) outliers start: 20 outliers final: 12 residues processed: 286 average time/residue: 2.3389 time to fit residues: 770.8571 Evaluate side-chains 289 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 272 time to evaluate : 2.576 ------------------------------------------------------------------------------- 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 H residue 55 THR 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 R residue 35 GLU Chi-restraints excluded: chain U residue 31 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 218 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 205 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 210 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 179 optimal weight: 0.6980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 ASN E 146 ASN L 20 ASN O 40 GLN P 63 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.145836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.115892 restraints weight = 36487.894| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 0.53 r_work: 0.3245 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 2.16 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 39364 Z= 0.220 Angle : 0.694 23.188 58689 Z= 0.362 Chirality : 0.044 1.972 7473 Planarity : 0.006 0.132 3267 Dihedral : 22.852 143.659 19277 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.64 % Allowed : 16.29 % Favored : 82.07 % 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: 0.69 (0.21), residues: 1509 helix: 1.16 (0.21), residues: 608 sheet: 0.15 (0.31), residues: 255 loop : 0.05 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 201 HIS 0.006 0.001 HIS E 89 PHE 0.017 0.002 PHE O 43 TYR 0.016 0.002 TYR L 117 ARG 0.006 0.001 ARG E 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13499.15 seconds wall clock time: 257 minutes 23.07 seconds (15443.07 seconds total)