Starting phenix.real_space_refine on Thu Feb 15 11:30:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9j_34569/02_2024/8h9j_34569.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9j_34569/02_2024/8h9j_34569.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9j_34569/02_2024/8h9j_34569.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9j_34569/02_2024/8h9j_34569.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9j_34569/02_2024/8h9j_34569.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9j_34569/02_2024/8h9j_34569.pdb" } resolution = 3.26 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= 0.014 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: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 7930 2.51 5 N 1932 2.21 5 O 2157 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "6 ASP 1": "OD1" <-> "OD2" Residue "6 ASP 3": "OD1" <-> "OD2" Residue "6 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 38": "NH1" <-> "NH2" Residue "6 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 1": "OD1" <-> "OD2" Residue "7 ASP 3": "OD1" <-> "OD2" Residue "7 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 38": "NH1" <-> "NH2" Residue "7 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 1": "OD1" <-> "OD2" Residue "8 ASP 3": "OD1" <-> "OD2" Residue "8 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 38": "NH1" <-> "NH2" Residue "8 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 1": "OD1" <-> "OD2" Residue "1 ASP 3": "OD1" <-> "OD2" Residue "1 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 38": "NH1" <-> "NH2" Residue "1 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 1": "OD1" <-> "OD2" Residue "2 ASP 3": "OD1" <-> "OD2" Residue "2 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 38": "NH1" <-> "NH2" Residue "2 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 1": "OD1" <-> "OD2" Residue "3 ASP 3": "OD1" <-> "OD2" Residue "3 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 38": "NH1" <-> "NH2" Residue "3 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 1": "OD1" <-> "OD2" Residue "4 ASP 3": "OD1" <-> "OD2" Residue "4 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 38": "NH1" <-> "NH2" Residue "4 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 1": "OD1" <-> "OD2" Residue "5 ASP 3": "OD1" <-> "OD2" Residue "5 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 38": "NH1" <-> "NH2" Residue "5 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 37": "OE1" <-> "OE2" Residue "G TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 53": "OE1" <-> "OE2" Residue "G ASP 56": "OD1" <-> "OD2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G ASP 62": "OD1" <-> "OD2" Residue "G GLU 102": "OE1" <-> "OE2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "G ASP 156": "OD1" <-> "OD2" Residue "G ASP 188": "OD1" <-> "OD2" Residue "G TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 194": "OD1" <-> "OD2" Residue "G ASP 195": "OD1" <-> "OD2" Residue "H PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "H ASP 124": "OD1" <-> "OD2" Residue "H GLU 125": "OE1" <-> "OE2" Residue "H GLU 130": "OE1" <-> "OE2" Residue "I PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 36": "OE1" <-> "OE2" Residue "K GLU 7": "OE1" <-> "OE2" Residue "K TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 20": "OE1" <-> "OE2" Residue "K GLU 49": "OE1" <-> "OE2" Residue "K TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 80": "OD1" <-> "OD2" Residue "K ASP 83": "OD1" <-> "OD2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "M PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 203": "OE1" <-> "OE2" Residue "P ASP 42": "OD1" <-> "OD2" Residue "R ARG 45": "NH1" <-> "NH2" Residue "R TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 87": "OE1" <-> "OE2" Residue "R TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 90": "OE1" <-> "OE2" Residue "S ASP 101": "OD1" <-> "OD2" Residue "T TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12082 Number of models: 1 Model: "" Number of chains: 19 Chain: "6" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "7" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "8" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "1" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "2" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "3" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "4" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "5" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "G" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1485 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 5, 'TRANS': 185} Chain: "H" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 975 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "I" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 354 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "K" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "M" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 311 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 30} Chain: "N" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1718 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 208} Chain: "P" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 344 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "R" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 621 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "T" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 346 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 39} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 307 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 5, 'TRANS': 32} Time building chain proxies: 7.59, per 1000 atoms: 0.63 Number of scatterers: 12082 At special positions: 0 Unit cell: (125.56, 87.6, 137.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 2157 8.00 N 1932 7.00 C 7930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.39 Conformation dependent library (CDL) restraints added in 2.7 seconds 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 4 sheets defined 77.8% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain '6' and resid 1 through 17 removed outlier: 4.121A pdb=" N GLY 6 17 " --> pdb=" O ALA 6 13 " (cutoff:3.500A) Processing helix chain '6' and resid 18 through 39 Processing helix chain '6' and resid 42 through 73 Processing helix chain '7' and resid 2 through 17 removed outlier: 4.122A pdb=" N GLY 7 17 " --> pdb=" O ALA 7 13 " (cutoff:3.500A) Processing helix chain '7' and resid 18 through 39 Processing helix chain '7' and resid 42 through 73 Processing helix chain '8' and resid 2 through 17 removed outlier: 4.121A pdb=" N GLY 8 17 " --> pdb=" O ALA 8 13 " (cutoff:3.500A) Processing helix chain '8' and resid 18 through 39 Processing helix chain '8' and resid 42 through 73 Processing helix chain '1' and resid 2 through 17 removed outlier: 4.122A pdb=" N GLY 1 17 " --> pdb=" O ALA 1 13 " (cutoff:3.500A) Processing helix chain '1' and resid 18 through 39 Processing helix chain '1' and resid 42 through 73 Processing helix chain '2' and resid 2 through 17 removed outlier: 4.122A pdb=" N GLY 2 17 " --> pdb=" O ALA 2 13 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 39 Processing helix chain '2' and resid 42 through 73 Processing helix chain '3' and resid 2 through 17 removed outlier: 4.121A pdb=" N GLY 3 17 " --> pdb=" O ALA 3 13 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 39 Processing helix chain '3' and resid 42 through 73 Processing helix chain '4' and resid 2 through 17 removed outlier: 4.122A pdb=" N GLY 4 17 " --> pdb=" O ALA 4 13 " (cutoff:3.500A) Processing helix chain '4' and resid 18 through 39 Processing helix chain '4' and resid 42 through 73 Processing helix chain '5' and resid 2 through 17 removed outlier: 4.122A pdb=" N GLY 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) Processing helix chain '5' and resid 18 through 39 Processing helix chain '5' and resid 42 through 73 Processing helix chain 'G' and resid 33 through 48 removed outlier: 4.097A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Proline residue: G 40 - end of helix Processing helix chain 'G' and resid 49 through 55 Processing helix chain 'G' and resid 80 through 99 Processing helix chain 'G' and resid 109 through 118 removed outlier: 4.339A pdb=" N ARG G 118 " --> pdb=" O GLY G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 removed outlier: 3.538A pdb=" N ALA G 141 " --> pdb=" O THR G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 187 Processing helix chain 'G' and resid 188 through 193 Processing helix chain 'G' and resid 197 through 221 Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'H' and resid 104 through 122 removed outlier: 3.966A pdb=" N ALA H 108 " --> pdb=" O ASP H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 146 Processing helix chain 'I' and resid 3 through 8 Processing helix chain 'I' and resid 11 through 26 Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.956A pdb=" N ALA I 33 " --> pdb=" O THR I 29 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ASN I 34 " --> pdb=" O GLU I 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 30 Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 31 through 48 removed outlier: 4.635A pdb=" N TYR K 35 " --> pdb=" O VAL K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 96 removed outlier: 3.631A pdb=" N PHE K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Proline residue: K 76 - end of helix Processing helix chain 'M' and resid 131 through 139 Processing helix chain 'M' and resid 140 through 143 removed outlier: 3.540A pdb=" N LYS M 143 " --> pdb=" O PRO M 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 140 through 143' Processing helix chain 'N' and resid 5 through 10 removed outlier: 4.350A pdb=" N SER N 8 " --> pdb=" O LEU N 5 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE N 10 " --> pdb=" O ALA N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 26 Processing helix chain 'N' and resid 27 through 31 Processing helix chain 'N' and resid 40 through 59 removed outlier: 3.677A pdb=" N THR N 59 " --> pdb=" O LYS N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 67 Processing helix chain 'N' and resid 68 through 86 Processing helix chain 'N' and resid 93 through 96 Processing helix chain 'N' and resid 97 through 119 Proline residue: N 107 - end of helix removed outlier: 3.853A pdb=" N SER N 119 " --> pdb=" O MET N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 128 removed outlier: 4.015A pdb=" N PHE N 128 " --> pdb=" O ALA N 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 134 through 136 No H-bonds generated for 'chain 'N' and resid 134 through 136' Processing helix chain 'N' and resid 137 through 181 Proline residue: N 153 - end of helix removed outlier: 3.815A pdb=" N ASN N 163 " --> pdb=" O ARG N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 225 Processing helix chain 'P' and resid 4 through 9 removed outlier: 3.578A pdb=" N ASN P 8 " --> pdb=" O SER P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 20 removed outlier: 3.686A pdb=" N LYS P 19 " --> pdb=" O PRO P 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 41 Processing helix chain 'R' and resid 26 through 32 removed outlier: 3.531A pdb=" N LEU R 30 " --> pdb=" O PRO R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 55 Processing helix chain 'R' and resid 62 through 80 removed outlier: 4.372A pdb=" N VAL R 68 " --> pdb=" O GLY R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 85 Processing helix chain 'R' and resid 86 through 88 No H-bonds generated for 'chain 'R' and resid 86 through 88' Processing helix chain 'S' and resid 27 through 37 Processing helix chain 'S' and resid 44 through 62 Processing helix chain 'S' and resid 63 through 67 Processing helix chain 'S' and resid 68 through 95 removed outlier: 3.502A pdb=" N ARG S 95 " --> pdb=" O ILE S 91 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 43 Proline residue: T 35 - end of helix Processing helix chain 'T' and resid 44 through 45 No H-bonds generated for 'chain 'T' and resid 44 through 45' Processing helix chain 'Q' and resid 1 through 5 Processing helix chain 'Q' and resid 9 through 22 Proline residue: Q 15 - end of helix Processing helix chain 'Q' and resid 22 through 30 removed outlier: 3.579A pdb=" N ASN Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 171 through 179 removed outlier: 5.218A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N HIS G 66 " --> pdb=" O MET G 104 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL G 106 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU G 68 " --> pdb=" O VAL G 106 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ILE G 108 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLY G 70 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 9.714A pdb=" N VAL G 126 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU G 105 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N PHE G 128 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY G 107 " --> pdb=" O PHE G 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 43 through 47 removed outlier: 3.615A pdb=" N ALA H 31 " --> pdb=" O PHE H 18 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N SER H 17 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU H 92 " --> pdb=" O SER H 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 43 through 47 removed outlier: 7.113A pdb=" N LEU H 62 " --> pdb=" O PRO H 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 12 through 13 966 hydrogen bonds defined for protein. 2847 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.71 Time building geometry restraints manager: 5.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3673 1.34 - 1.46: 2307 1.46 - 1.57: 6228 1.57 - 1.69: 0 1.69 - 1.81: 115 Bond restraints: 12323 Sorted by residual: bond pdb=" N ARG 5 38 " pdb=" CA ARG 5 38 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.27e-02 6.20e+03 7.24e+00 bond pdb=" N ILE 3 2 " pdb=" CA ILE 3 2 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.30e-02 5.92e+03 6.99e+00 bond pdb=" N ILE 1 2 " pdb=" CA ILE 1 2 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.30e-02 5.92e+03 6.90e+00 bond pdb=" N ILE 8 2 " pdb=" CA ILE 8 2 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.30e-02 5.92e+03 6.82e+00 bond pdb=" N ILE 2 2 " pdb=" CA ILE 2 2 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.30e-02 5.92e+03 6.79e+00 ... (remaining 12318 not shown) Histogram of bond angle deviations from ideal: 98.19 - 105.37: 231 105.37 - 112.56: 6626 112.56 - 119.75: 4250 119.75 - 126.93: 5475 126.93 - 134.12: 105 Bond angle restraints: 16687 Sorted by residual: angle pdb=" N THR Q 7 " pdb=" CA THR Q 7 " pdb=" C THR Q 7 " ideal model delta sigma weight residual 114.56 106.01 8.55 1.27e+00 6.20e-01 4.53e+01 angle pdb=" C VAL T 5 " pdb=" N GLN T 6 " pdb=" CA GLN T 6 " ideal model delta sigma weight residual 121.31 127.06 -5.75 1.49e+00 4.50e-01 1.49e+01 angle pdb=" N GLN T 6 " pdb=" CA GLN T 6 " pdb=" C GLN T 6 " ideal model delta sigma weight residual 110.35 115.71 -5.36 1.40e+00 5.10e-01 1.47e+01 angle pdb=" C ILE P 9 " pdb=" N TRP P 10 " pdb=" CA TRP P 10 " ideal model delta sigma weight residual 122.79 116.51 6.28 1.78e+00 3.16e-01 1.24e+01 angle pdb=" N PHE N 26 " pdb=" CA PHE N 26 " pdb=" C PHE N 26 " ideal model delta sigma weight residual 109.81 116.94 -7.13 2.21e+00 2.05e-01 1.04e+01 ... (remaining 16682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.89: 6380 14.89 - 29.79: 642 29.79 - 44.68: 187 44.68 - 59.58: 31 59.58 - 74.47: 8 Dihedral angle restraints: 7248 sinusoidal: 2710 harmonic: 4538 Sorted by residual: dihedral pdb=" CA LYS N 120 " pdb=" C LYS N 120 " pdb=" N ILE N 121 " pdb=" CA ILE N 121 " ideal model delta harmonic sigma weight residual -180.00 -158.98 -21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ARG N 118 " pdb=" C ARG N 118 " pdb=" N SER N 119 " pdb=" CA SER N 119 " ideal model delta harmonic sigma weight residual 180.00 161.41 18.59 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA MET N 57 " pdb=" C MET N 57 " pdb=" N MET N 58 " pdb=" CA MET N 58 " ideal model delta harmonic sigma weight residual 180.00 -163.47 -16.53 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 7245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1030 0.035 - 0.070: 632 0.070 - 0.106: 215 0.106 - 0.141: 57 0.141 - 0.176: 37 Chirality restraints: 1971 Sorted by residual: chirality pdb=" CA LEU 8 70 " pdb=" N LEU 8 70 " pdb=" C LEU 8 70 " pdb=" CB LEU 8 70 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CA THR N 135 " pdb=" N THR N 135 " pdb=" C THR N 135 " pdb=" CB THR N 135 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" CA LEU 2 70 " pdb=" N LEU 2 70 " pdb=" C LEU 2 70 " pdb=" CB LEU 2 70 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.29e-01 ... (remaining 1968 not shown) Planarity restraints: 2065 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 133 " 0.273 9.50e-02 1.11e+02 1.23e-01 9.23e+00 pdb=" NE ARG G 133 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG G 133 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG G 133 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG G 133 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS T 12 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.20e+00 pdb=" C LYS T 12 " -0.035 2.00e-02 2.50e+03 pdb=" O LYS T 12 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU T 13 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 8 38 " 0.183 9.50e-02 1.11e+02 8.22e-02 4.14e+00 pdb=" NE ARG 8 38 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG 8 38 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG 8 38 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG 8 38 " 0.007 2.00e-02 2.50e+03 ... (remaining 2062 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2849 2.77 - 3.30: 13032 3.30 - 3.83: 20715 3.83 - 4.37: 24464 4.37 - 4.90: 41016 Nonbonded interactions: 102076 Sorted by model distance: nonbonded pdb=" OD1 ASN M 136 " pdb=" OG1 THR M 142 " model vdw 2.233 2.440 nonbonded pdb=" O MET N 181 " pdb=" OG1 THR N 189 " model vdw 2.235 2.440 nonbonded pdb=" OH TYR R 50 " pdb=" O GLY R 64 " model vdw 2.256 2.440 nonbonded pdb=" O SER H 88 " pdb=" OG SER H 88 " model vdw 2.265 2.440 nonbonded pdb=" ND2 ASN N 101 " pdb=" OG1 THR N 161 " model vdw 2.278 2.520 ... (remaining 102071 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' } 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: 26.570 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: 0.000 Extract box with map and model: 27.220 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 36.480 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.076 12323 Z= 0.671 Angle : 0.846 8.549 16687 Z= 0.497 Chirality : 0.052 0.176 1971 Planarity : 0.006 0.123 2065 Dihedral : 13.196 74.472 4352 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: -3.26 (0.18), residues: 1558 helix: -1.78 (0.13), residues: 1113 sheet: -1.57 (0.53), residues: 87 loop : -2.90 (0.29), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP P 10 HIS 0.007 0.002 HIS N 127 PHE 0.024 0.002 PHE H 45 TYR 0.024 0.002 TYR T 30 ARG 0.004 0.001 ARG 7 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 395 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 60 MET cc_start: 0.7499 (mmm) cc_final: 0.7072 (mpp) REVERT: G 77 LEU cc_start: 0.7792 (mp) cc_final: 0.7385 (tt) REVERT: I 13 ILE cc_start: 0.8979 (mm) cc_final: 0.8739 (mm) REVERT: T 36 ARG cc_start: 0.6748 (mpp80) cc_final: 0.6447 (mpp80) REVERT: Q 1 MET cc_start: 0.7790 (mmm) cc_final: 0.7018 (mmm) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.2586 time to fit residues: 140.9408 Evaluate side-chains 321 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 0.0770 chunk 114 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 137 optimal weight: 6.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 44 GLN G 120 HIS G 163 ASN H 66 HIS H 85 ASN H 111 ASN H 116 GLN I 42 ASN M 159 ASN N 4 ASN N 46 GLN N 47 GLN N 61 HIS N 123 ASN N 225 ASN P 8 ASN ** S 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 66 GLN Q 32 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12323 Z= 0.214 Angle : 0.608 9.648 16687 Z= 0.322 Chirality : 0.043 0.170 1971 Planarity : 0.004 0.044 2065 Dihedral : 4.640 59.966 1685 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.11 % Allowed : 15.24 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: -0.53 (0.20), residues: 1558 helix: 0.22 (0.15), residues: 1149 sheet: -1.40 (0.58), residues: 72 loop : -1.74 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP S 30 HIS 0.007 0.001 HIS N 127 PHE 0.028 0.002 PHE R 79 TYR 0.018 0.001 TYR K 74 ARG 0.008 0.001 ARG G 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 335 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 75 MET cc_start: 0.6460 (tpp) cc_final: 0.5906 (mtt) REVERT: 3 60 MET cc_start: 0.8136 (mmp) cc_final: 0.7923 (mmm) REVERT: G 77 LEU cc_start: 0.7823 (mp) cc_final: 0.7393 (tt) REVERT: H 79 SER cc_start: 0.8684 (t) cc_final: 0.8482 (p) REVERT: H 102 MET cc_start: 0.5781 (ttm) cc_final: 0.5534 (ttm) REVERT: R 29 ILE cc_start: 0.8387 (mp) cc_final: 0.7869 (tp) REVERT: T 36 ARG cc_start: 0.6547 (mpp80) cc_final: 0.6314 (mpp80) outliers start: 39 outliers final: 24 residues processed: 354 average time/residue: 0.2475 time to fit residues: 123.7446 Evaluate side-chains 322 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 298 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 3 ASP Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 60 GLN Chi-restraints excluded: chain T residue 5 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 137 optimal weight: 0.4980 chunk 148 optimal weight: 0.0050 chunk 122 optimal weight: 1.9990 chunk 136 optimal weight: 0.0970 chunk 46 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 45 GLN H 85 ASN M 159 ASN N 4 ASN ** N 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN R 83 HIS Q 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12323 Z= 0.185 Angle : 0.567 7.968 16687 Z= 0.298 Chirality : 0.042 0.187 1971 Planarity : 0.004 0.046 2065 Dihedral : 4.426 55.604 1685 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.27 % Allowed : 17.88 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.84 (0.21), residues: 1558 helix: 1.25 (0.15), residues: 1143 sheet: -1.22 (0.57), residues: 72 loop : -1.25 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.034 0.001 PHE 2 69 TYR 0.016 0.001 TYR T 30 ARG 0.004 0.000 ARG G 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 315 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8354 (mm) cc_final: 0.8123 (mm) REVERT: 5 7 LYS cc_start: 0.7998 (mmtp) cc_final: 0.7655 (mmtp) REVERT: G 77 LEU cc_start: 0.7854 (mp) cc_final: 0.7370 (tt) REVERT: H 102 MET cc_start: 0.5739 (ttm) cc_final: 0.5515 (ttm) REVERT: I 32 LYS cc_start: 0.7423 (tttp) cc_final: 0.7204 (tptt) REVERT: N 36 TYR cc_start: 0.7934 (m-10) cc_final: 0.7505 (m-10) REVERT: R 29 ILE cc_start: 0.8371 (mp) cc_final: 0.7960 (tp) REVERT: R 59 LYS cc_start: 0.8415 (mptt) cc_final: 0.8114 (mtpt) outliers start: 41 outliers final: 28 residues processed: 335 average time/residue: 0.2675 time to fit residues: 124.9280 Evaluate side-chains 319 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 291 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 3 ASP Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 71 ILE Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 60 GLN Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain Q residue 3 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 145 optimal weight: 9.9990 chunk 72 optimal weight: 0.0570 chunk 130 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 45 GLN 3 45 GLN N 4 ASN ** N 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN R 83 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12323 Z= 0.190 Angle : 0.556 7.283 16687 Z= 0.293 Chirality : 0.042 0.184 1971 Planarity : 0.004 0.045 2065 Dihedral : 4.389 53.914 1685 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.43 % Allowed : 19.31 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 1.34 (0.21), residues: 1558 helix: 1.61 (0.15), residues: 1143 sheet: -0.96 (0.57), residues: 72 loop : -1.08 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.026 0.001 PHE R 79 TYR 0.025 0.001 TYR T 30 ARG 0.012 0.000 ARG G 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 303 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8117 (mm) REVERT: 5 7 LYS cc_start: 0.8026 (mmtp) cc_final: 0.7727 (mmtp) REVERT: G 147 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7645 (tp30) REVERT: I 32 LYS cc_start: 0.7427 (tttp) cc_final: 0.7184 (tptt) REVERT: K 87 GLU cc_start: 0.7088 (mp0) cc_final: 0.6811 (mp0) REVERT: N 36 TYR cc_start: 0.7927 (m-10) cc_final: 0.7538 (m-10) REVERT: N 159 ARG cc_start: 0.8982 (ttm110) cc_final: 0.8725 (ttm170) REVERT: P 7 LYS cc_start: 0.7336 (mtmm) cc_final: 0.6944 (mtmm) REVERT: R 29 ILE cc_start: 0.8376 (mp) cc_final: 0.7994 (tp) REVERT: R 59 LYS cc_start: 0.8395 (mptt) cc_final: 0.8107 (mtpt) REVERT: T 13 LEU cc_start: 0.6841 (mm) cc_final: 0.6594 (mm) outliers start: 43 outliers final: 29 residues processed: 325 average time/residue: 0.2618 time to fit residues: 119.4970 Evaluate side-chains 319 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 289 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 45 GLN Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 3 ASP Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 19 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 108 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 131 optimal weight: 0.0470 chunk 36 optimal weight: 0.4980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 45 GLN I 42 ASN N 4 ASN ** N 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN R 83 HIS S 50 GLN S 57 ASN S 60 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12323 Z= 0.183 Angle : 0.553 7.314 16687 Z= 0.290 Chirality : 0.041 0.188 1971 Planarity : 0.004 0.041 2065 Dihedral : 4.321 50.503 1685 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.75 % Allowed : 20.59 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 1.53 (0.21), residues: 1558 helix: 1.74 (0.15), residues: 1147 sheet: -0.86 (0.59), residues: 68 loop : -1.03 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.025 0.001 PHE R 79 TYR 0.024 0.001 TYR T 30 ARG 0.004 0.000 ARG G 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 298 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8119 (mm) REVERT: 4 63 PHE cc_start: 0.8337 (m-10) cc_final: 0.8038 (m-10) REVERT: 5 7 LYS cc_start: 0.7993 (mmtp) cc_final: 0.7703 (mmtp) REVERT: G 147 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7627 (tp30) REVERT: N 4 ASN cc_start: 0.6159 (OUTLIER) cc_final: 0.5584 (t0) REVERT: N 36 TYR cc_start: 0.7931 (m-10) cc_final: 0.7584 (m-10) REVERT: R 29 ILE cc_start: 0.8338 (mp) cc_final: 0.8002 (tp) REVERT: R 59 LYS cc_start: 0.8382 (mptt) cc_final: 0.8105 (mtpt) outliers start: 47 outliers final: 34 residues processed: 319 average time/residue: 0.2824 time to fit residues: 128.7157 Evaluate side-chains 321 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 285 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 54 PHE Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 3 ASP Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain P residue 2 LEU Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 11 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 0.9980 chunk 131 optimal weight: 0.0570 chunk 28 optimal weight: 0.0470 chunk 85 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 121 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 39 ASN 3 45 GLN I 42 ASN N 4 ASN ** N 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12323 Z= 0.182 Angle : 0.558 7.246 16687 Z= 0.291 Chirality : 0.041 0.193 1971 Planarity : 0.004 0.041 2065 Dihedral : 4.278 47.453 1685 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.99 % Allowed : 21.39 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 1.76 (0.21), residues: 1558 helix: 1.89 (0.15), residues: 1142 sheet: -0.67 (0.59), residues: 70 loop : -0.85 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.024 0.001 PHE R 79 TYR 0.032 0.001 TYR T 30 ARG 0.006 0.000 ARG G 118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 295 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8123 (mm) REVERT: 5 7 LYS cc_start: 0.8040 (mmtp) cc_final: 0.7719 (mmtp) REVERT: G 111 LYS cc_start: 0.7533 (mmmt) cc_final: 0.7294 (mmtm) REVERT: G 147 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7662 (tp30) REVERT: N 4 ASN cc_start: 0.5704 (OUTLIER) cc_final: 0.5479 (t0) REVERT: N 36 TYR cc_start: 0.7930 (m-10) cc_final: 0.7564 (m-10) REVERT: N 159 ARG cc_start: 0.8939 (ttm110) cc_final: 0.8679 (ttm170) REVERT: R 29 ILE cc_start: 0.8292 (mp) cc_final: 0.7930 (tp) REVERT: R 59 LYS cc_start: 0.8333 (mptt) cc_final: 0.8066 (mtpt) REVERT: R 82 LYS cc_start: 0.8823 (mtmm) cc_final: 0.8153 (mptt) outliers start: 50 outliers final: 35 residues processed: 320 average time/residue: 0.2561 time to fit residues: 114.4025 Evaluate side-chains 323 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 286 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 54 PHE Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 3 ASP Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain Q residue 11 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 83 optimal weight: 0.0770 chunk 106 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 45 GLN 8 45 GLN 3 45 GLN 4 45 GLN 5 45 GLN I 42 ASN N 4 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12323 Z= 0.309 Angle : 0.631 10.543 16687 Z= 0.327 Chirality : 0.044 0.212 1971 Planarity : 0.004 0.043 2065 Dihedral : 4.436 54.829 1685 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.47 % Allowed : 21.31 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 1.62 (0.21), residues: 1558 helix: 1.79 (0.15), residues: 1142 sheet: -0.95 (0.53), residues: 85 loop : -0.82 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.026 0.002 PHE R 79 TYR 0.040 0.002 TYR T 30 ARG 0.009 0.000 ARG I 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 293 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8122 (mm) REVERT: 4 63 PHE cc_start: 0.8465 (m-10) cc_final: 0.8179 (m-10) REVERT: 5 7 LYS cc_start: 0.8074 (mmtp) cc_final: 0.7794 (mmtp) REVERT: G 77 LEU cc_start: 0.7732 (mp) cc_final: 0.7195 (tt) REVERT: G 147 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7670 (tp30) REVERT: N 36 TYR cc_start: 0.7998 (m-10) cc_final: 0.7632 (m-10) REVERT: N 159 ARG cc_start: 0.9033 (ttm110) cc_final: 0.8750 (ttm170) outliers start: 56 outliers final: 40 residues processed: 322 average time/residue: 0.2561 time to fit residues: 115.1169 Evaluate side-chains 326 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 285 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 65 LEU Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 45 GLN Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 11 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 0.9980 chunk 58 optimal weight: 0.0070 chunk 86 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 114 optimal weight: 0.0970 chunk 132 optimal weight: 0.8980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 45 GLN G 208 ASN K 23 GLN P 8 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12323 Z= 0.189 Angle : 0.587 9.727 16687 Z= 0.299 Chirality : 0.041 0.216 1971 Planarity : 0.004 0.041 2065 Dihedral : 4.310 50.380 1685 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.83 % Allowed : 22.27 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 1.90 (0.21), residues: 1558 helix: 1.97 (0.15), residues: 1141 sheet: -0.67 (0.56), residues: 78 loop : -0.66 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.025 0.001 PHE R 79 TYR 0.033 0.001 TYR T 30 ARG 0.011 0.000 ARG G 118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 287 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8126 (mm) REVERT: 4 63 PHE cc_start: 0.8381 (m-10) cc_final: 0.8138 (m-10) REVERT: 5 7 LYS cc_start: 0.7958 (mmtp) cc_final: 0.7708 (mmtp) REVERT: G 147 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7656 (tp30) REVERT: N 36 TYR cc_start: 0.7959 (m-10) cc_final: 0.7560 (m-10) REVERT: N 159 ARG cc_start: 0.8995 (ttm110) cc_final: 0.8745 (ttm170) REVERT: R 29 ILE cc_start: 0.8360 (mp) cc_final: 0.7974 (tp) REVERT: R 82 LYS cc_start: 0.8810 (mtmm) cc_final: 0.8152 (mptt) outliers start: 48 outliers final: 38 residues processed: 314 average time/residue: 0.2519 time to fit residues: 110.6274 Evaluate side-chains 315 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 276 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 28 VAL Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 45 GLN Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 7 LYS Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 11 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 106 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 128 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 143 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 39 ASN 3 45 GLN I 7 GLN I 42 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12323 Z= 0.220 Angle : 0.600 9.656 16687 Z= 0.307 Chirality : 0.042 0.234 1971 Planarity : 0.004 0.042 2065 Dihedral : 4.316 50.727 1685 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.51 % Allowed : 23.06 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 1.92 (0.21), residues: 1558 helix: 1.98 (0.15), residues: 1140 sheet: -1.01 (0.54), residues: 85 loop : -0.52 (0.36), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.025 0.001 PHE R 79 TYR 0.035 0.001 TYR T 30 ARG 0.008 0.000 ARG I 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 281 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8128 (mm) REVERT: 4 63 PHE cc_start: 0.8406 (m-10) cc_final: 0.8151 (m-10) REVERT: 5 7 LYS cc_start: 0.7963 (mmtp) cc_final: 0.7730 (mmtp) REVERT: N 36 TYR cc_start: 0.7978 (m-10) cc_final: 0.7569 (m-10) REVERT: R 29 ILE cc_start: 0.8359 (mp) cc_final: 0.7993 (tp) REVERT: T 13 LEU cc_start: 0.6655 (mm) cc_final: 0.6317 (mm) outliers start: 44 outliers final: 39 residues processed: 302 average time/residue: 0.2554 time to fit residues: 108.2923 Evaluate side-chains 315 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 275 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 28 VAL Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 39 ASN Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 11 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 119 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 45 GLN ** 5 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12323 Z= 0.211 Angle : 0.610 9.631 16687 Z= 0.310 Chirality : 0.042 0.241 1971 Planarity : 0.004 0.049 2065 Dihedral : 4.313 49.744 1685 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.75 % Allowed : 23.30 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 1.96 (0.22), residues: 1558 helix: 2.00 (0.15), residues: 1140 sheet: -1.04 (0.53), residues: 85 loop : -0.47 (0.36), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.025 0.001 PHE R 79 TYR 0.033 0.001 TYR T 30 ARG 0.009 0.001 ARG I 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 274 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8178 (mm) REVERT: 4 63 PHE cc_start: 0.8385 (m-10) cc_final: 0.8174 (m-10) REVERT: 5 7 LYS cc_start: 0.7925 (mmtp) cc_final: 0.7696 (mmtp) REVERT: K 26 TYR cc_start: 0.8496 (t80) cc_final: 0.8265 (t80) REVERT: N 36 TYR cc_start: 0.7977 (m-10) cc_final: 0.7565 (m-10) REVERT: R 29 ILE cc_start: 0.8364 (mp) cc_final: 0.7987 (tp) REVERT: R 82 LYS cc_start: 0.8804 (mtmm) cc_final: 0.8156 (mptt) REVERT: T 13 LEU cc_start: 0.6705 (mm) cc_final: 0.6354 (mm) outliers start: 47 outliers final: 40 residues processed: 299 average time/residue: 0.2582 time to fit residues: 107.6751 Evaluate side-chains 310 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 269 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 28 VAL Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 11 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 105 optimal weight: 0.0980 chunk 6 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 39 ASN 3 45 GLN ** 5 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.161197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.126548 restraints weight = 17483.103| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.38 r_work: 0.3443 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12323 Z= 0.202 Angle : 0.611 9.393 16687 Z= 0.309 Chirality : 0.042 0.246 1971 Planarity : 0.004 0.041 2065 Dihedral : 4.272 47.149 1685 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.59 % Allowed : 23.22 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.21), residues: 1558 helix: 2.04 (0.15), residues: 1140 sheet: -0.74 (0.55), residues: 78 loop : -0.52 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.025 0.001 PHE R 79 TYR 0.033 0.001 TYR T 30 ARG 0.008 0.000 ARG I 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3489.12 seconds wall clock time: 64 minutes 18.82 seconds (3858.82 seconds total)